From dde3e1ba8672455fd7893239fb0f3db239264b5f Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Mon, 22 Apr 2024 11:50:58 +0200 Subject: [PATCH 001/264] Increment version number to 3.5.1 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0cec3a66ca..aa36b34895 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: ggplot2 -Version: 3.5.0.9000 +Version: 3.5.1 Title: Create Elegant Data Visualisations Using the Grammar of Graphics Authors@R: c( person("Hadley", "Wickham", , "hadley@posit.co", role = "aut", diff --git a/NEWS.md b/NEWS.md index a6ee8c266e..9d31feec74 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# ggplot2 3.5.1 + # ggplot2 (development version) From 7d4166fafa05297d5e49cea14a9f14892802f697 Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Mon, 22 Apr 2024 11:52:56 +0200 Subject: [PATCH 002/264] update cran comments --- cran-comments.md | 222 +---------------------------------------------- 1 file changed, 2 insertions(+), 220 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 63d8a4bc4c..df78ca7e28 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,220 +1,2 @@ -This is a large minor release with both a lot of new features and a complete -rewrite of part of the internals. As a result, this release does break a range -of reverse dependencies. All of them has been informed very well in advance (4 -weeks) and have been provided with patches to fix their issues. The remaining -problematic reverse dependencies were further notified 2 weeks ago to remind -them to submit a fix, so we believe we have been very lenient towards them. - -## revdepcheck results - -We checked 4935 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 56 new problems - * We failed to check 13 packages - -Issues with CRAN packages are summarised below. - -### New problems -(This reports the first line of each new failure) - -* AcademicThemes - checking tests ... ERROR - -* afex - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - -* archeoViz - checking tests ... ERROR - -* assignPOP - checking tests ... ERROR - -* bioassays - checking tests ... ERROR - -* BOSO - checking re-building of vignette outputs ... ERROR - -* breakDown - checking tests ... ERROR - -* canadianmaps - checking tests ... ERROR - -* CAST - checking installed package size ... NOTE - -* CEDA - checking re-building of vignette outputs ... ERROR - -* cobalt - checking examples ... ERROR - checking re-building of vignette outputs ... ERROR - -* constructive - checking tests ... ERROR - -* docxtools - checking tests ... ERROR - -* dynamAedes - checking re-building of vignette outputs ... ERROR - -* EcoDiet - checking re-building of vignette outputs ... ERROR - -* epos - checking tests ... ERROR - -* feasts - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - -* fitODBODRshiny - checking examples ... ERROR - -* fmeffects - checking examples ... ERROR - checking re-building of vignette outputs ... ERROR - -* genekitr - checking examples ... ERROR - -* geomtextpath - checking tests ... ERROR - -* ggedit - checking examples ... ERROR - -* gghdr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - -* ggiraph - checking examples ... ERROR - checking tests ... ERROR - -* ggiraphExtra - checking examples ... ERROR - -* ggparallel - checking tests ... ERROR - -* ggprism - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - -* ggraph - checking examples ... ERROR - checking re-building of vignette outputs ... ERROR - -* ggside - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - -* ggstance - checking tests ... ERROR - -* ggstatsplot - checking examples ... ERROR - checking tests ... ERROR - -* ghibli - checking tests ... ERROR - -* glancedata - checking tests ... ERROR - -* grafify - checking tests ... ERROR - -* inTextSummaryTable - checking tests ... ERROR - -* LMoFit - checking re-building of vignette outputs ... ERROR - -* manydata - checking tests ... ERROR - -* MiscMetabar - checking examples ... ERROR - checking re-building of vignette outputs ... ERROR - -* miWQS - checking re-building of vignette outputs ... ERROR - -* NAIR - checking tests ... ERROR - -* OpenLand - checking tests ... ERROR - -* platetools - checking tests ... ERROR - -* plot3logit - checking re-building of vignette outputs ... ERROR - -* PTXQC - checking examples ... ERROR - checking tests ... ERROR - -* rabhit - checking re-building of vignette outputs ... ERROR - -* santaR - checking tests ... ERROR - -* saros - checking examples ... ERROR - checking tests ... ERROR - -* scCustomize - checking examples ... ERROR - -* scdhlm - checking tests ... ERROR - -* see - checking examples ... ERROR - -* spqdep - checking re-building of vignette outputs ... ERROR - -* TCIU - checking re-building of vignette outputs ... ERROR - -* tmt - checking tests ... ERROR - -* tvthemes - checking tests ... ERROR - -* ufs - checking examples ... ERROR - -* visR - checking examples ... ERROR - checking tests ... ERROR - -### Failed to check - -* bayesdfa (NA) -* ctsem (NA) -* geostan (NA) -* ggtern (NA) -* grandR (NA) -* rmsb (NA) -* rstanarm (NA) -* Seurat (NA) -* streamDAG (NA) -* treestats (NA) -* TriDimRegression (NA) -* triptych (NA) -* valse (NA) +This is a small patch release fixing regressions from the last release. No +issues with reverse dependencies detected. From c67d961fd53f18463903f1caa7acc475e7167742 Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Mon, 22 Apr 2024 12:38:36 +0200 Subject: [PATCH 003/264] fix wrong automatic version bump --- NEWS.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 9d31feec74..24cd6a5e80 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,5 @@ # ggplot2 3.5.1 - -# ggplot2 (development version) - This is a small release focusing on fixing regressions from 3.5.0 and documentation updates. From e1be8b4b3597db1d792b43ec0c031b11803fefd3 Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Tue, 23 Apr 2024 12:21:56 +0200 Subject: [PATCH 004/264] Increment version number to 3.5.1.9000 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index aa36b34895..f3b9ee7208 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: ggplot2 -Version: 3.5.1 +Version: 3.5.1.9000 Title: Create Elegant Data Visualisations Using the Grammar of Graphics Authors@R: c( person("Hadley", "Wickham", , "hadley@posit.co", role = "aut", diff --git a/NEWS.md b/NEWS.md index 24cd6a5e80..cd39c0b8ad 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# ggplot2 (development version) + # ggplot2 3.5.1 This is a small release focusing on fixing regressions from 3.5.0 and From 9af10fa8646f1b239870794dc9594b17f92d5a58 Mon Sep 17 00:00:00 2001 From: Hadley Wickham Date: Wed, 24 Apr 2024 08:24:43 -0500 Subject: [PATCH 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fkU6XKy#s;lTb2KnXOC8kFs*2pDzu?3edzoDO09LE From e24cbba78576c1a1d1910fde834c0139262c57d7 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 09:50:49 +0200 Subject: [PATCH 006/264] Be clearer on what shapes the fill aesthetic applies (#5868) --- R/geom-point.R | 2 +- man/geom_point.Rd | 2 ++ vignettes/ggplot2-specs.Rmd | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/R/geom-point.R b/R/geom-point.R index 20a7f46b58..32291466bb 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -27,7 +27,7 @@ #' `geom_point(alpha = 0.05)`) or very small (e.g. #' `geom_point(shape = ".")`). #' -#' @eval rd_aesthetics("geom", "point") +#' @eval rd_aesthetics("geom", "point", "The `fill` aesthetic only applies to shapes 21-25.") #' @inheritParams layer #' @param na.rm If `FALSE`, the default, missing values are removed with #' a warning. If `TRUE`, missing values are silently removed. diff --git a/man/geom_point.Rd b/man/geom_point.Rd index 88e06e22aa..b7e6a0d5d2 100644 --- a/man/geom_point.Rd +++ b/man/geom_point.Rd @@ -148,6 +148,8 @@ Another technique is to make the points transparent (e.g. \item \code{\link[=aes_linetype_size_shape]{size}} \item \code{stroke} } +The \code{fill} aesthetic only applies to shapes 21-25. + Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } diff --git a/vignettes/ggplot2-specs.Rmd b/vignettes/ggplot2-specs.Rmd index bc7761763c..d66cb5951b 100644 --- a/vignettes/ggplot2-specs.Rmd +++ b/vignettes/ggplot2-specs.Rmd @@ -230,7 +230,7 @@ Shapes take five types of values: ### Colour and fill -Note that shapes 21-24 have both stroke `colour` and a `fill`. The size of the filled part is controlled by `size`, the size of the stroke is controlled by `stroke`. Each is measured in mm, and the total size of the point is the sum of the two. Note that the size is constant along the diagonal in the following figure. +While `colour` applies to all shapes, `fill` only applies to shapes 21-25, as can be seen above. The size of the filled part is controlled by `size`, the size of the stroke is controlled by `stroke`. Each is measured in mm, and the total size of the point is the sum of the two. Note that the size is constant along the diagonal in the following figure. ```{r} #| fig.alt = "A plot showing a 4-by-4 grid of red points, the top 12 points with From 6c2e102065fca4f600768d48eae736a8f6fd23b5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:34:23 +0200 Subject: [PATCH 007/264] Interpreter/wrapper for `gpar()` (#5867) * write wrapper * use wrapper * add news bullet * remove defunct `len0_null()` --- NAMESPACE | 1 + NEWS.md | 3 +++ R/annotation-logticks.R | 8 +++--- R/annotation-map.R | 4 +-- R/coord-radial.R | 4 +-- R/coord-sf.R | 4 +-- R/geom-curve.R | 4 +-- R/geom-dotplot.R | 4 +-- R/geom-hex.R | 4 +-- R/geom-label.R | 10 ++++---- R/geom-map.R | 4 +-- R/geom-path.R | 8 +++--- R/geom-point.R | 9 +++---- R/geom-polygon.R | 8 +++--- R/geom-rect.R | 4 +-- R/geom-ribbon.R | 8 +++--- R/geom-rug.R | 4 +-- R/geom-segment.R | 4 +-- R/geom-text.R | 2 +- R/guide-colorbar.R | 4 +-- R/guide-colorsteps.R | 2 +- R/legend-draw.R | 55 +++++++++++++++++++---------------------- R/margins.R | 10 ++++---- R/theme-elements.R | 24 ++++++------------ R/utilities-grid.R | 32 ++++++++++++++++++++++++ man/ggpar.Rd | 23 +++++++++++++++++ 26 files changed, 146 insertions(+), 101 deletions(-) create mode 100644 man/ggpar.Rd diff --git a/NAMESPACE b/NAMESPACE index 67c7a4941a..3dbc9d5ca6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -422,6 +422,7 @@ export(get_alt_text) export(get_element_tree) export(get_guide_data) export(gg_dep) +export(ggpar) export(ggplot) export(ggplotGrob) export(ggplot_add) diff --git a/NEWS.md b/NEWS.md index cd39c0b8ad..dcd22bdd8d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* New helper function `ggpar()` to translate ggplot2's interpretation of + graphical parameters to {grid}'s interpretation (@teunbrand, #5866). + # ggplot2 3.5.1 This is a small release focusing on fixing regressions from 3.5.0 and diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R index 8f3e8a63c2..1d25332a91 100644 --- a/R/annotation-logticks.R +++ b/R/annotation-logticks.R @@ -175,14 +175,14 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, ticks$x_b <- with(data, segmentsGrob( x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"), y0 = unit(xticks$start, "cm"), y1 = unit(xticks$end, "cm"), - gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt) + gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } if (grepl("t", sides) && nrow(xticks) > 0) { ticks$x_t <- with(data, segmentsGrob( x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"), y0 = unit(1, "npc") - unit(xticks$start, "cm"), y1 = unit(1, "npc") - unit(xticks$end, "cm"), - gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt) + gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } } @@ -213,14 +213,14 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, ticks$y_l <- with(data, segmentsGrob( y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"), x0 = unit(yticks$start, "cm"), x1 = unit(yticks$end, "cm"), - gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt) + gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } if (grepl("r", sides) && nrow(yticks) > 0) { ticks$y_r <- with(data, segmentsGrob( y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"), x0 = unit(1, "npc") - unit(yticks$start, "cm"), x1 = unit(1, "npc") - unit(yticks$end, "cm"), - gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth * .pt) + gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } } diff --git a/R/annotation-map.R b/R/annotation-map.R index 86fd0e0952..2e53b3b9c2 100644 --- a/R/annotation-map.R +++ b/R/annotation-map.R @@ -95,9 +95,9 @@ GeomAnnotationMap <- ggproto("GeomAnnotationMap", GeomMap, polygonGrob(coords$x, coords$y, default.units = "native", id = grob_id, - gp = gpar( + gp = ggpar( col = data$colour, fill = alpha(data$fill, data$alpha), - lwd = data$linewidth * .pt) + lwd = data$linewidth) ) }, diff --git a/R/coord-radial.R b/R/coord-radial.R index 62b3bff136..89c84dd5dc 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -326,8 +326,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, y = c(Inf, -Inf, -Inf, Inf) ) background <- coord_munch(self, background, panel_params, is_closed = TRUE) - bg_gp <- gpar( - lwd = len0_null(bg_element$linewidth * .pt), + bg_gp <- ggpar( + lwd = bg_element$linewidth, col = bg_element$colour, fill = bg_element$fill, lty = bg_element$linetype ) diff --git a/R/coord-sf.R b/R/coord-sf.R index 331ca4f1f0..12f7371003 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -326,9 +326,9 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, if (inherits(el, "element_blank")) { grobs <- list(element_render(theme, "panel.background")) } else { - line_gp <- gpar( + line_gp <- ggpar( col = el$colour, - lwd = len0_null(el$linewidth * .pt), + lwd = el$linewidth, lty = el$linetype ) grobs <- c( diff --git a/R/geom-curve.R b/R/geom-curve.R index a2597a8d72..7ef935caeb 100644 --- a/R/geom-curve.R +++ b/R/geom-curve.R @@ -57,10 +57,10 @@ GeomCurve <- ggproto("GeomCurve", GeomSegment, default.units = "native", curvature = curvature, angle = angle, ncp = ncp, square = FALSE, squareShape = 1, inflect = FALSE, open = TRUE, - gp = gpar( + gp = ggpar( col = alpha(trans$colour, trans$alpha), fill = alpha(arrow.fill, trans$alpha), - lwd = trans$linewidth * .pt, + lwd = trans$linewidth, lty = trans$linetype, lineend = lineend), arrow = arrow diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index d79e6a823e..cdbc137fe7 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -293,9 +293,9 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y, dotdia = dotdianpc, stackposition = tdata$stackpos, stackdir = stackdir, stackratio = stackratio, default.units = "npc", - gp = gpar(col = alpha(tdata$colour, tdata$alpha), + gp = ggpar(col = alpha(tdata$colour, tdata$alpha), fill = fill_alpha(tdata$fill, tdata$alpha), - lwd = tdata$stroke, lty = tdata$linetype, + lwd = tdata$stroke / .pt, lty = tdata$linetype, lineend = lineend)) ) }, diff --git a/R/geom-hex.R b/R/geom-hex.R index a220e12140..19076138dc 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -89,10 +89,10 @@ GeomHex <- ggproto("GeomHex", Geom, ggname("geom_hex", polygonGrob( coords$x, coords$y, - gp = gpar( + gp = ggpar( col = data$colour, fill = fill_alpha(data$fill, data$alpha), - lwd = data$linewidth * .pt, + lwd = data$linewidth, lty = data$linetype, lineend = lineend, linejoin = linejoin, diff --git a/R/geom-label.R b/R/geom-label.R index c292fa1a66..30ee6aa388 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -90,17 +90,17 @@ GeomLabel <- ggproto("GeomLabel", Geom, padding = label.padding, r = label.r, angle = row$angle, - text.gp = gpar( + text.gp = ggpar( col = row$colour, fontsize = row$size * size.unit, fontfamily = row$family, fontface = row$fontface, lineheight = row$lineheight ), - rect.gp = gpar( + rect.gp = ggpar( col = if (isTRUE(all.equal(label.size, 0))) NA else row$colour, fill = fill_alpha(row$fill, row$alpha), - lwd = label.size * .pt + lwd = label.size ) ) }) @@ -115,7 +115,7 @@ GeomLabel <- ggproto("GeomLabel", Geom, labelGrob <- function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "center", padding = unit(0.25, "lines"), r = unit(0.1, "snpc"), angle = NULL, default.units = "npc", name = NULL, - text.gp = gpar(), rect.gp = gpar(fill = "white"), vp = NULL) { + text.gp = gpar(), rect.gp = ggpar(fill = "white"), vp = NULL) { if (length(label) != 1) { cli::cli_abort("{.arg label} must be of length 1.") @@ -130,7 +130,7 @@ labelGrob <- function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), vp <- viewport( angle = angle, x = x, y = y, width = unit(0, "cm"), height = unit(0, "cm"), - gp = gpar(fontsize = text.gp$fontsize) + gp = ggpar(fontsize = text.gp$fontsize) ) x <- unit(rep(0.5, length(x)), "npc") y <- unit(rep(0.5, length(y)), "npc") diff --git a/R/geom-map.R b/R/geom-map.R index 01024ebeff..8086db6209 100644 --- a/R/geom-map.R +++ b/R/geom-map.R @@ -144,10 +144,10 @@ GeomMap <- ggproto("GeomMap", GeomPolygon, data <- data[data_rows, , drop = FALSE] polygonGrob(coords$x, coords$y, default.units = "native", id = grob_id, - gp = gpar( + gp = ggpar( col = data$colour, fill = fill_alpha(data$fill, data$alpha), - lwd = data$linewidth * .pt, + lwd = data$linewidth, lineend = lineend, linejoin = linejoin, linemitre = linemitre diff --git a/R/geom-path.R b/R/geom-path.R index ad7589a028..b705162b9f 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -200,10 +200,10 @@ GeomPath <- ggproto("GeomPath", Geom, segmentsGrob( munched$x[!end], munched$y[!end], munched$x[!start], munched$y[!start], default.units = "native", arrow = arrow, - gp = gpar( + gp = ggpar( col = alpha(munched$colour, munched$alpha)[!end], fill = alpha(munched$colour, munched$alpha)[!end], - lwd = munched$linewidth[!end] * .pt, + lwd = munched$linewidth[!end], lty = munched$linetype[!end], lineend = lineend, linejoin = linejoin, @@ -215,10 +215,10 @@ GeomPath <- ggproto("GeomPath", Geom, polylineGrob( munched$x, munched$y, id = id, default.units = "native", arrow = arrow, - gp = gpar( + gp = ggpar( col = alpha(munched$colour, munched$alpha)[start], fill = alpha(munched$colour, munched$alpha)[start], - lwd = munched$linewidth[start] * .pt, + lwd = munched$linewidth[start], lty = munched$linetype[start], lineend = lineend, linejoin = linejoin, diff --git a/R/geom-point.R b/R/geom-point.R index 32291466bb..990b2778c3 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -145,18 +145,15 @@ GeomPoint <- ggproto("GeomPoint", Geom, } coords <- coord$transform(data, panel_params) - stroke_size <- coords$stroke - stroke_size[is.na(stroke_size)] <- 0 ggname("geom_point", pointsGrob( coords$x, coords$y, pch = coords$shape, - gp = gpar( + gp = ggpar( col = alpha(coords$colour, coords$alpha), fill = fill_alpha(coords$fill, coords$alpha), - # Stroke is added around the outside of the point - fontsize = coords$size * .pt + stroke_size * .stroke / 2, - lwd = coords$stroke * .stroke / 2 + pointsize = coords$size, + stroke = coords$stroke ) ) ) diff --git a/R/geom-polygon.R b/R/geom-polygon.R index c644d9daad..3cdce9b53e 100644 --- a/R/geom-polygon.R +++ b/R/geom-polygon.R @@ -130,10 +130,10 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, polygonGrob( munched$x, munched$y, default.units = "native", id = munched$group, - gp = gpar( + gp = ggpar( col = first_rows$colour, fill = fill_alpha(first_rows$fill, first_rows$alpha), - lwd = first_rows$linewidth * .pt, + lwd = first_rows$linewidth, lty = first_rows$linetype, lineend = lineend, linejoin = linejoin, @@ -161,10 +161,10 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, munched$x, munched$y, default.units = "native", id = id, pathId = munched$group, rule = rule, - gp = gpar( + gp = ggpar( col = first_rows$colour, fill = fill_alpha(first_rows$fill, first_rows$alpha), - lwd = first_rows$linewidth * .pt, + lwd = first_rows$linewidth, lty = first_rows$linetype, lineend = lineend, linejoin = linejoin, diff --git a/R/geom-rect.R b/R/geom-rect.R index d39978897a..cfd39dab4a 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -57,10 +57,10 @@ GeomRect <- ggproto("GeomRect", Geom, height = coords$ymax - coords$ymin, default.units = "native", just = c("left", "top"), - gp = gpar( + gp = ggpar( col = coords$colour, fill = fill_alpha(coords$fill, coords$alpha), - lwd = coords$linewidth * .pt, + lwd = coords$linewidth, lty = coords$linetype, linejoin = linejoin, lineend = lineend diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index d93df77850..11774c97f5 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -182,10 +182,10 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, g_poly <- polygonGrob( munched_poly$x, munched_poly$y, id = munched_poly$id, default.units = "native", - gp = gpar( + gp = ggpar( fill = fill_alpha(aes$fill, aes$alpha), col = if (is_full_outline) aes$colour else NA, - lwd = if (is_full_outline) aes$linewidth * .pt else 0, + lwd = if (is_full_outline) aes$linewidth else 0, lty = if (is_full_outline) aes$linetype else 1, lineend = lineend, linejoin = linejoin, @@ -213,9 +213,9 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, g_lines <- polylineGrob( munched_lines$x, munched_lines$y, id = munched_lines$id, default.units = "native", - gp = gpar( + gp = ggpar( col = aes$colour, - lwd = aes$linewidth * .pt, + lwd = aes$linewidth, lty = aes$linetype, lineend = lineend, linejoin = linejoin, diff --git a/R/geom-rug.R b/R/geom-rug.R index 0fe393bb95..cda6a01bc4 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -108,10 +108,10 @@ GeomRug <- ggproto("GeomRug", Geom, list(min = -1 * length, max = unit(1, "npc") + length) } - gp <- gpar( + gp <- ggpar( col = alpha(data$colour, data$alpha), lty = data$linetype, - lwd = data$linewidth * .pt, + lwd = data$linewidth, lineend = lineend ) if (!is.null(data$x)) { diff --git a/R/geom-segment.R b/R/geom-segment.R index f32b61f876..9a4de4dbb3 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -122,10 +122,10 @@ GeomSegment <- ggproto("GeomSegment", Geom, arrow.fill <- arrow.fill %||% coord$colour return(segmentsGrob(coord$x, coord$y, coord$xend, coord$yend, default.units = "native", - gp = gpar( + gp = ggpar( col = alpha(coord$colour, coord$alpha), fill = alpha(arrow.fill, coord$alpha), - lwd = coord$linewidth * .pt, + lwd = coord$linewidth, lty = coord$linetype, lineend = lineend, linejoin = linejoin diff --git a/R/geom-text.R b/R/geom-text.R index acfbb0337a..ea996cb040 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -239,7 +239,7 @@ GeomText <- ggproto("GeomText", Geom, data$x, data$y, default.units = "native", hjust = data$hjust, vjust = data$vjust, rot = data$angle, - gp = gpar( + gp = ggpar( col = alpha(data$colour, data$alpha), fontsize = data$size * size.unit, fontfamily = data$family, diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index b8e62f82c9..6d90f13a82 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -379,7 +379,7 @@ GuideColourbar <- ggproto( vjust = 0, hjust = 0, width = width, height = height, default.units = "npc", - gp = gpar(col = NA, fill = decor$colour) + gp = ggpar(col = NA, fill = decor$colour) ) } else if (params$display == "gradient") { check_device("gradients", call = expr(guide_colourbar())) @@ -394,7 +394,7 @@ GuideColourbar <- ggproto( vertical = list(x1 = unit(0.5, "npc"), x2 = unit(0.5, "npc")) ) gradient <- inject(linearGradient(decor$colour, value, !!!position)) - grob <- rectGrob(gp = gpar(fill = gradient, col = NA)) + grob <- rectGrob(gp = ggpar(fill = gradient, col = NA)) } frame <- element_grob(elements$frame, fill = NA) diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index d85421bbc9..cd21dce6a4 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -204,7 +204,7 @@ GuideColoursteps <- ggproto( size <- abs(decor$max - decor$min) just <- as.numeric(decor$min > decor$max) - gp <- gpar(col = NA, fill = decor$colour) + gp <- ggpar(col = NA, fill = decor$colour) if (params$direction == "vertical") { grob <- rectGrob( x = 0, y = decor$min, diff --git a/R/legend-draw.R b/R/legend-draw.R index f1de0b80e5..ce16f7a6ab 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -31,16 +31,13 @@ draw_key_point <- function(data, params, size) { } # NULL means the default stroke size, and NA means no stroke. - stroke_size <- data$stroke %||% 0.5 - stroke_size[is.na(stroke_size)] <- 0 - pointsGrob(0.5, 0.5, pch = data$shape, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% "black", data$alpha), fill = fill_alpha(data$fill %||% "black", data$alpha), - fontsize = (data$size %||% 1.5) * .pt + stroke_size * .stroke / 2, - lwd = stroke_size * .stroke / 2 + pointsize = data$size %||% 1.5, + stroke = data$stroke %||% 0.5 ) ) } @@ -49,9 +46,9 @@ draw_key_point <- function(data, params, size) { #' @rdname draw_key draw_key_abline <- function(data, params, size) { segmentsGrob(0, 0, 1, 1, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt" ) @@ -61,7 +58,7 @@ draw_key_abline <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_rect <- function(data, params, size) { - rectGrob(gp = gpar( + rectGrob(gp = ggpar( col = NA, fill = fill_alpha(data$fill %||% data$colour %||% "grey20", data$alpha), lty = data$linetype %||% 1 @@ -79,11 +76,11 @@ draw_key_polygon <- function(data, params, size) { rectGrob( width = unit(1, "npc") - unit(lwd, "mm"), height = unit(1, "npc") - unit(lwd, "mm"), - gp = gpar( + gp = ggpar( col = data$colour %||% NA, fill = fill_alpha(data$fill %||% "grey20", data$alpha), lty = data$linetype %||% 1, - lwd = lwd * .pt, + lwd = lwd, linejoin = params$linejoin %||% "mitre", lineend = params$lineend %||% "butt" )) @@ -98,10 +95,10 @@ draw_key_blank <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_boxplot <- function(data, params, size) { - gp <- gpar( + gp <- ggpar( col = data$colour %||% "grey20", fill = fill_alpha(data$fill %||% "white", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt", linejoin = params$linejoin %||% "mitre" @@ -129,10 +126,10 @@ draw_key_boxplot <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_crossbar <- function(data, params, size) { - gp <- gpar( + gp <- ggpar( col = data$colour %||% "grey20", fill = fill_alpha(data$fill %||% "white", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt", linejoin = params$linejoin %||% "mitre" @@ -161,11 +158,11 @@ draw_key_path <- function(data, params, size) { data$linetype[is.na(data$linetype)] <- 0 } grob <- segmentsGrob(0.1, 0.5, 0.9, 0.5, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), fill = alpha(params$arrow.fill %||% data$colour %||% data$fill %||% "black", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt" ), @@ -184,9 +181,9 @@ draw_key_path <- function(data, params, size) { #' @rdname draw_key draw_key_vpath <- function(data, params, size) { grob <- segmentsGrob(0.5, 0.1, 0.5, 0.9, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt" ), @@ -206,7 +203,7 @@ draw_key_vpath <- function(data, params, size) { draw_key_dotplot <- function(data, params, size) { pointsGrob(0.5, 0.5, size = unit(.5, "npc"), pch = 21, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% "black", data$alpha), fill = fill_alpha(data$fill %||% "black", data$alpha), lty = data$linetype %||% 1, @@ -247,7 +244,7 @@ draw_key_smooth <- function(data, params, size) { path <- draw_key_path(data, params, size) grob <- grobTree( - if (isTRUE(params$se)) rectGrob(gp = gpar(col = NA, fill = data$fill)), + if (isTRUE(params$se)) rectGrob(gp = ggpar(col = NA, fill = data$fill)), path ) attr(grob, "width") <- attr(path, "width") @@ -268,7 +265,7 @@ draw_key_text <- function(data, params, size) { angle = data$angle, hjust = hjust, vjust = vjust, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), fontfamily = data$family %||% "", fontface = data$fontface %||% 1, @@ -304,16 +301,16 @@ draw_key_label <- function(data, params, size) { just = c(hjust, vjust), padding = padding, r = params$label.r %||% unit(0.15, "lines"), - text.gp = gpar( + text.gp = ggpar( col = data$colour %||% "black", fontfamily = data$family %||% "", fontface = data$fontface %||% 1, fontsize = (data$size %||% 3.88) * .pt ), - rect.gp = gpar( + rect.gp = ggpar( col = if (isTRUE(all.equal(params$label.size, 0))) NA else data$colour, fill = alpha(data$fill %||% "white", data$alpha), - lwd = params$label.size * .pt + lwd = params$label.size ) ) angle <- deg2rad(data$angle %||% 0) @@ -331,9 +328,9 @@ draw_key_label <- function(data, params, size) { #' @rdname draw_key draw_key_vline <- function(data, params, size) { segmentsGrob(0.5, 0, 0.5, 1, - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt" ) @@ -352,9 +349,9 @@ draw_key_timeseries <- function(data, params, size) { grid::linesGrob( x = c(0, 0.4, 0.6, 1), y = c(0.1, 0.6, 0.4, 0.9), - gp = gpar( + gp = ggpar( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), - lwd = (data$linewidth %||% 0.5) * .pt, + lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, lineend = params$lineend %||% "butt", linejoin = params$linejoin %||% "round" diff --git a/R/margins.R b/R/margins.R index b563331002..c1ad607a21 100644 --- a/R/margins.R +++ b/R/margins.R @@ -124,9 +124,9 @@ titleGrob <- function(label, x, y, hjust, vjust, angle = 0, gp = gpar(), rectGrob( x = x, y = y, width = width, height = height, hjust = just$hjust, vjust = just$vjust, - gp = gpar(fill = "cornsilk", col = NA) + gp = ggpar(fill = "cornsilk", col = NA) ), - pointsGrob(x, y, pch = 20, gp = gpar(col = "gold")), + pointsGrob(x, y, pch = 20, gp = ggpar(col = "gold")), grob ) } else { @@ -193,7 +193,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, if (isTRUE(debug)) { children <- gList( - rectGrob(gp = gpar(fill = "lightcyan", col = NA)), + rectGrob(gp = ggpar(fill = "lightcyan", col = NA)), grobs ) } @@ -219,7 +219,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, #cat("E - hjust, vjust:", c(hjust, vjust), "\n") grobTree( result_grob, - pointsGrob(x, y, pch = 20, gp = gpar(col = "mediumturquoise")) + pointsGrob(x, y, pch = 20, gp = ggpar(col = "mediumturquoise")) ) } else { result_grob @@ -307,7 +307,7 @@ font_descent <- function(family = "", face = "plain", size = 12, cex = 1) { if (is.null(descent)) { descent <- convertHeight(grobDescent(textGrob( label = "gjpqyQ", - gp = gpar( + gp = ggpar( fontsize = size, cex = cex, fontfamily = family, diff --git a/R/theme-elements.R b/R/theme-elements.R index b8e83c75e4..41b989df7e 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -187,14 +187,6 @@ element_render <- function(theme, element, ..., name = NULL) { ggname(paste(element, name, sep = "."), grob) } - -# Returns NULL if x is length 0 -len0_null <- function(x) { - if (length(x) == 0) NULL - else x -} - - #' Generate grid grob from theme element #' #' @param element Theme element, i.e. `element_rect` or similar. @@ -220,8 +212,8 @@ element_grob.element_rect <- function(element, x = 0.5, y = 0.5, } # The gp settings can override element_gp - gp <- gpar(lwd = len0_null(linewidth * .pt), col = colour, fill = fill, lty = linetype) - element_gp <- gpar(lwd = len0_null(element$linewidth * .pt), col = element$colour, + gp <- ggpar(lwd = linewidth, col = colour, fill = fill, lty = linetype) + element_gp <- ggpar(lwd = element$linewidth, col = element$colour, fill = element$fill, lty = element$linetype) rectGrob(x, y, width, height, gp = modify_list(element_gp, gp), ...) @@ -244,10 +236,10 @@ element_grob.element_text <- function(element, label = "", x = NULL, y = NULL, angle <- angle %||% element$angle %||% 0 # The gp settings can override element_gp - gp <- gpar(fontsize = size, col = colour, + gp <- ggpar(fontsize = size, col = colour, fontfamily = family, fontface = face, lineheight = lineheight) - element_gp <- gpar(fontsize = element$size, col = element$colour, + element_gp <- ggpar(fontsize = element$size, col = element$colour, fontfamily = element$family, fontface = element$face, lineheight = element$lineheight) @@ -269,13 +261,13 @@ element_grob.element_line <- function(element, x = 0:1, y = 0:1, } # The gp settings can override element_gp - gp <- gpar( + gp <- ggpar( col = colour, fill = colour, - lwd = len0_null(linewidth * .pt), lty = linetype, lineend = lineend + lwd = linewidth, lty = linetype, lineend = lineend ) - element_gp <- gpar( + element_gp <- ggpar( col = element$colour, fill = element$colour, - lwd = len0_null(element$linewidth * .pt), lty = element$linetype, + lwd = element$linewidth, lty = element$linetype, lineend = element$lineend ) arrow <- if (is.logical(element$arrow) && !element$arrow) { diff --git a/R/utilities-grid.R b/R/utilities-grid.R index 389dad3eea..8efdee4d02 100644 --- a/R/utilities-grid.R +++ b/R/utilities-grid.R @@ -13,6 +13,38 @@ ggname <- function(prefix, grob) { grob } +#' Interpreter for graphical parameters +#' +#' This is a wrapper for [`grid::gpar()`] that applies ggplot2's interpretation +#' of graphical parameters. +#' +#' @param ... Named arguments passed on to `gpar()`. +#' @param stroke Linewidth for points. Populates the `lwd` grid parameter. +#' @param pointsize Size for points. Populates the `fontsize` grid parameter. +#' +#' @return An object of class 'gpar'. +#' @keywords internal +#' @export +ggpar <- function(..., stroke = NULL, pointsize = NULL) { + args <- list2(...) + args <- args[lengths(args) > 0] + + if (!is.null(args$lwd)) { + args$lwd <- args$lwd * .pt + } + if (!is.null(stroke)) { + args$lwd <- stroke * .stroke / 2 + } + if (!is.null(pointsize)) { + # Stroke is added around the outside of the point + stroke <- stroke %||% 0 + stroke[is.na(stroke)] <- 0 + args$fontsize <- pointsize * .pt + stroke * .stroke / 2 + } + + inject(gpar(!!!args)) +} + width_cm <- function(x) { if (is.grob(x)) { convertWidth(grobWidth(x), "cm", TRUE) diff --git a/man/ggpar.Rd b/man/ggpar.Rd new file mode 100644 index 0000000000..3186597d02 --- /dev/null +++ b/man/ggpar.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utilities-grid.R +\name{ggpar} +\alias{ggpar} +\title{Interpreter for graphical parameters} +\usage{ +ggpar(..., stroke = NULL, pointsize = NULL) +} +\arguments{ +\item{...}{Named arguments passed on to \code{gpar()}.} + +\item{stroke}{Linewidth for points. Populates the \code{lwd} grid parameter.} + +\item{pointsize}{Size for points. Populates the \code{fontsize} grid parameter.} +} +\value{ +An object of class 'gpar'. +} +\description{ +This is a wrapper for \code{\link[grid:gpar]{grid::gpar()}} that applies ggplot2's interpretation +of graphical parameters. +} +\keyword{internal} From 4eb6587e32b4af6d5ec688c78b08577ac45a630a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:35:21 +0200 Subject: [PATCH 008/264] Fix missing margin error in `guide_custom()` (#5858) * fallback to empty margin * add tests * add news bullet --- NEWS.md | 4 +- R/guide-custom.R | 2 +- .../guides/guide-custom-with-void-theme.svg | 34 +++++++++++++++++ .../_snaps/guides/stylised-guide-custom.svg | 37 +++++++++++++++++++ tests/testthat/test-guides.R | 20 ++++++++++ 5 files changed, 95 insertions(+), 2 deletions(-) create mode 100644 tests/testthat/_snaps/guides/guide-custom-with-void-theme.svg create mode 100644 tests/testthat/_snaps/guides/stylised-guide-custom.svg diff --git a/NEWS.md b/NEWS.md index dcd22bdd8d..c1ad8337ad 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug in `guide_custom()` that would throw error with `theme_void()` + (@teunbrand, #5856). * New helper function `ggpar()` to translate ggplot2's interpretation of graphical parameters to {grid}'s interpretation (@teunbrand, #5866). @@ -23,7 +25,7 @@ documentation updates. (@teunbrand, #5757). ## Improvements - + * When facets coerce the faceting variables to factors, the 'ordered' class is dropped (@teunbrand, #5666). * `coord_map()` and `coord_polar()` throw informative warnings when used diff --git a/R/guide-custom.R b/R/guide-custom.R index 16a737d3fd..990712b36b 100644 --- a/R/guide-custom.R +++ b/R/guide-custom.R @@ -117,7 +117,7 @@ GuideCustom <- ggproto( ) # Add padding and background - gt <- gtable_add_padding(gt, elems$margin) + gt <- gtable_add_padding(gt, elems$margin %||% margin()) gt <- gtable_add_grob( gt, element_grob(elems$background), diff --git a/tests/testthat/_snaps/guides/guide-custom-with-void-theme.svg b/tests/testthat/_snaps/guides/guide-custom-with-void-theme.svg new file mode 100644 index 0000000000..ac52f62280 --- /dev/null +++ b/tests/testthat/_snaps/guides/guide-custom-with-void-theme.svg @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + +custom guide + +guide_custom with void theme + + diff --git a/tests/testthat/_snaps/guides/stylised-guide-custom.svg b/tests/testthat/_snaps/guides/stylised-guide-custom.svg new file mode 100644 index 0000000000..85d3aa01f9 --- /dev/null +++ b/tests/testthat/_snaps/guides/stylised-guide-custom.svg @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + +custom guide + +stylised guide_custom + + diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index bc359938ae..4930188025 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -1273,3 +1273,23 @@ test_that("old S3 guides can be implemented", { ) ) }) + +test_that("guide_custom can be drawn and styled", { + + p <- ggplot() + guides(custom = guide_custom( + circleGrob(r = unit(1, "cm")), + title = "custom guide" + )) + + expect_doppelganger( + "stylised guide_custom", + p + theme(legend.background = element_rect(fill = "grey50"), + legend.title.position = "left", + legend.title = element_text(angle = 90, hjust = 0.5)) + ) + + expect_doppelganger( + "guide_custom with void theme", + p + theme_void() + ) +}) From da60e8fe8710063816cc5e84ecb442c35f493007 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:36:44 +0200 Subject: [PATCH 009/264] Prevent mismapping when limits contain `NA` in non-last position (#5848) * protect against early NAs * add test * add news bullet * fix typos * simplify by discarding `NA` limits --- NEWS.md | 2 ++ R/scale-.R | 3 ++- tests/testthat/test-scales.R | 25 +++++++++++++++++++++++++ 3 files changed, 29 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index c1ad8337ad..b6321b90bb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug where `na.value` was incorrectly mapped to non-`NA` values + (@teunbrand, #5756). * Fixed bug in `guide_custom()` that would throw error with `theme_void()` (@teunbrand, #5856). * New helper function `ggpar()` to translate ggplot2's interpretation of diff --git a/R/scale-.R b/R/scale-.R index 0b374d72ef..6233caf54f 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -947,7 +947,8 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, transform = identity, map = function(self, x, limits = self$get_limits()) { - n <- sum(!is.na(limits)) + limits <- limits[!is.na(limits)] + n <- length(limits) if (n < 1) { return(rep(self$na.value, length(x))) } diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 691f0920aa..79bd27af22 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -730,3 +730,28 @@ test_that("Discrete scales with only NAs return `na.value`", { sc$train(x) expect_equal(sc$map(x), c(NA_real_, NA_real_)) }) + +test_that("discrete scales work with NAs in arbitrary positions", { + # Prevents intermediate caching of palettes + map <- function(x, limits) { + sc <- scale_colour_manual( + values = c("red", "green", "blue"), + na.value = "gray" + ) + sc$map(x, limits) + } + + # All inputs should yield output regardless of where NA is + input <- c("A", "B", "C", NA) + output <- c("red", "green", "blue", "gray") + + test <- map(input, limits = c("A", "B", "C", NA)) + expect_equal(test, output) + + test <- map(input, limits = c("A", NA, "B", "C")) + expect_equal(test, output) + + test <- map(input, limits = c(NA, "A", "B", "C")) + expect_equal(test, output) + +}) From b0a4a400bb9532e15936ef90a32d2e3f6efe9baa Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:38:00 +0200 Subject: [PATCH 010/264] Dodge points vertically (#5845) * allow custom default in `has_flipped_aes()` * Use fallback orientation * add test * add news bullet --- NEWS.md | 2 ++ R/position-dodge.R | 11 ++++++++--- R/utilities.R | 7 ++++--- man/bidirection.Rd | 6 +++++- man/position_dodge.Rd | 6 +++++- tests/testthat/test-position_dodge.R | 14 ++++++++++++++ 6 files changed, 38 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index b6321b90bb..749a360908 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_point()` can be dodged vertically by using + `position_dodge(..., orientation = "y")` (@teunbrand, #5809). * Fixed bug where `na.value` was incorrectly mapped to non-`NA` values (@teunbrand, #5756). * Fixed bug in `guide_custom()` that would throw error with `theme_void()` diff --git a/R/position-dodge.R b/R/position-dodge.R index ef24531207..17bd607324 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -13,6 +13,9 @@ #' geoms. See the examples. #' @param preserve Should dodging preserve the `"total"` width of all elements #' at a position, or the width of a `"single"` element? +#' @param orientation Fallback orientation when the layer or the data does not +#' indicate an explicit orientation, like `geom_point()`. Can be `"x"` +#' (default) or `"y"`. #' @family position adjustments #' @export #' @examples @@ -79,10 +82,11 @@ #' #' ggplot(mtcars, aes(factor(cyl), fill = factor(vs))) + #' geom_bar(position = position_dodge2(preserve = "total")) -position_dodge <- function(width = NULL, preserve = "total") { +position_dodge <- function(width = NULL, preserve = "total", orientation = "x") { ggproto(NULL, PositionDodge, width = width, - preserve = arg_match0(preserve, c("total", "single")) + preserve = arg_match0(preserve, c("total", "single")), + orientation = arg_match0(orientation, c("x", "y")) ) } @@ -93,8 +97,9 @@ position_dodge <- function(width = NULL, preserve = "total") { PositionDodge <- ggproto("PositionDodge", Position, width = NULL, preserve = "total", + orientation = "x", setup_params = function(self, data) { - flipped_aes <- has_flipped_aes(data) + flipped_aes <- has_flipped_aes(data, default = self$orientation == "y") data <- flip_data(data, flipped_aes) if (is.null(data$xmin) && is.null(data$xmax) && is.null(self$width)) { cli::cli_warn(c( diff --git a/R/utilities.R b/R/utilities.R index 9f9133a0b5..1a9181be69 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -476,6 +476,8 @@ switch_orientation <- function(aesthetics) { #' @param main_is_optional Is the main axis aesthetic optional and, if not #' given, set to `0` #' @param flip Logical. Is the layer flipped. +#' @param default The logical value to return if no orientation can be discerned +#' from the data. #' #' @return `has_flipped_aes()` returns `TRUE` if it detects a layer in the other #' orientation and `FALSE` otherwise. `flip_data()` will return the input @@ -492,7 +494,7 @@ switch_orientation <- function(aesthetics) { has_flipped_aes <- function(data, params = list(), main_is_orthogonal = NA, range_is_orthogonal = NA, group_has_equal = FALSE, ambiguous = FALSE, main_is_continuous = FALSE, - main_is_optional = FALSE) { + main_is_optional = FALSE, default = FALSE) { # Is orientation already encoded in data? if (!is.null(data$flipped_aes)) { not_na <- which(!is.na(data$flipped_aes)) @@ -561,8 +563,7 @@ has_flipped_aes <- function(data, params = list(), main_is_orthogonal = NA, } } - # default to no - FALSE + isTRUE(default) } #' @rdname bidirection #' @export diff --git a/man/bidirection.Rd b/man/bidirection.Rd index f58460091c..be6ffec336 100644 --- a/man/bidirection.Rd +++ b/man/bidirection.Rd @@ -15,7 +15,8 @@ has_flipped_aes( group_has_equal = FALSE, ambiguous = FALSE, main_is_continuous = FALSE, - main_is_optional = FALSE + main_is_optional = FALSE, + default = FALSE ) flip_data(data, flip = NULL) @@ -48,6 +49,9 @@ the continuous one correspond to the main orientation?} \item{main_is_optional}{Is the main axis aesthetic optional and, if not given, set to \code{0}} +\item{default}{The logical value to return if no orientation can be discerned +from the data.} + \item{flip}{Logical. Is the layer flipped.} } \value{ diff --git a/man/position_dodge.Rd b/man/position_dodge.Rd index b42353b35e..3efb462168 100644 --- a/man/position_dodge.Rd +++ b/man/position_dodge.Rd @@ -5,7 +5,7 @@ \alias{position_dodge2} \title{Dodge overlapping objects side-to-side} \usage{ -position_dodge(width = NULL, preserve = "total") +position_dodge(width = NULL, preserve = "total", orientation = "x") position_dodge2( width = NULL, @@ -22,6 +22,10 @@ geoms. See the examples.} \item{preserve}{Should dodging preserve the \code{"total"} width of all elements at a position, or the width of a \code{"single"} element?} +\item{orientation}{Fallback orientation when the layer or the data does not +indicate an explicit orientation, like \code{geom_point()}. Can be \code{"x"} +(default) or \code{"y"}.} + \item{padding}{Padding between elements at the same position. Elements are shrunk by this proportion to allow space between them. Defaults to 0.1.} diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index 4d540176ad..aa036c7abe 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -9,3 +9,17 @@ test_that("can control whether to preserve total or individual width", { expect_equal(layer_data(p_total)$x, new_mapped_discrete(c(1, 1.75, 2.25))) expect_equal(layer_data(p_single)$x, new_mapped_discrete(c(0.75, 1.75, 2.25))) }) + +test_that("position_dodge() can dodge points vertically", { + + df <- data.frame(x = c(1, 2, 3, 4), y = c("a", "a", "b", "b")) + + horizontal <- ggplot(df, aes(y, x, group = seq_along(x))) + + geom_point(position = position_dodge(width = 1, orientation = "x")) + vertical <- ggplot(df, aes(x, y, group = seq_along(x))) + + geom_point(position = position_dodge(width = 1, orientation = "y")) + + expect_equal(layer_data(horizontal)$x, c(0.75, 1.25, 1.75, 2.25), ignore_attr = "class") + expect_equal(layer_data(vertical)$y, c(0.75, 1.25, 1.75, 2.25), ignore_attr = "class") + +}) From 5dd26335540737ee46dddccdf303c7259f98d296 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:38:22 +0200 Subject: [PATCH 011/264] clarify when `dpi` applies (#5842) --- R/save.R | 3 ++- man/ggsave.Rd | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/R/save.R b/R/save.R index 2be88a3459..dc71365c25 100644 --- a/R/save.R +++ b/R/save.R @@ -37,7 +37,8 @@ #' @param units One of the following units in which the `width` and `height` #' arguments are expressed: `"in"`, `"cm"`, `"mm"` or `"px"`. #' @param dpi Plot resolution. Also accepts a string input: "retina" (320), -#' "print" (300), or "screen" (72). Applies only to raster output types. +#' "print" (300), or "screen" (72). Only applies when converting pixel units, +#' as is typical for raster output types. #' @param limitsize When `TRUE` (the default), `ggsave()` will not #' save images larger than 50x50 inches, to prevent the common error of #' specifying dimensions in pixels. diff --git a/man/ggsave.Rd b/man/ggsave.Rd index 97b50458cc..6c6f97d16d 100644 --- a/man/ggsave.Rd +++ b/man/ggsave.Rd @@ -43,7 +43,8 @@ If not supplied, uses the size of the current graphics device.} arguments are expressed: \code{"in"}, \code{"cm"}, \code{"mm"} or \code{"px"}.} \item{dpi}{Plot resolution. Also accepts a string input: "retina" (320), -"print" (300), or "screen" (72). Applies only to raster output types.} +"print" (300), or "screen" (72). Only applies when converting pixel units, +as is typical for raster output types.} \item{limitsize}{When \code{TRUE} (the default), \code{ggsave()} will not save images larger than 50x50 inches, to prevent the common error of From 073958df38a479dc0551e9e3a68f737c6664d665 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:39:11 +0200 Subject: [PATCH 012/264] Restore axis line when `breaks = NULL`. (#5838) * preserve empty keys * Don't skip decor transformation when key is empty * add news bullet * deal with 0-length breaks in `guide_axis_theta()` * capping deals with empty keys --- NEWS.md | 2 ++ R/guide-axis-theta.R | 23 ++++++++++++++++------ R/guide-axis.R | 46 +++++++++++++++++++++++++++----------------- 3 files changed, 47 insertions(+), 24 deletions(-) diff --git a/NEWS.md b/NEWS.md index 749a360908..0163d4d9cf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed regression in axes where `breaks = NULL` caused the axes to disappear + instead of just rendering the axis line (@teunbrand, #5816). * `geom_point()` can be dodged vertically by using `position_dodge(..., orientation = "y")` (@teunbrand, #5809). * Fixed bug where `na.value` was incorrectly mapped to non-`NA` values diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index 567cf08020..2e4f7a6cef 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -74,17 +74,22 @@ GuideAxisTheta <- ggproto( transform = function(params, coord, panel_params) { - opposite <- setdiff(c("x", "y"), params$aesthetic) - params$key[[opposite]] <- switch(params$position, - theta.sec = -Inf, - top = -Inf, - right = -Inf, - Inf) + if (nrow(params$key) > 0) { + opposite <- setdiff(c("x", "y"), params$aesthetic) + params$key[[opposite]] <- switch(params$position, + theta.sec = -Inf, + top = -Inf, + right = -Inf, + Inf) + } params <- GuideAxis$transform(params, coord, panel_params) key <- params$key n <- nrow(key) + if (n < 1) { + return(params) + } if (!("theta" %in% names(key))) { # We likely have a linear coord, so we match the text angles to @@ -242,6 +247,12 @@ GuideAxisTheta <- ggproto( grobTree(major, minor, name = "ticks") }, + draw_early_exit = function(self, params, elements) { + line <- self$build_decor(decor = params$decor, elements = elements, + params = params) + gTree(children = gList(line), offset = unit(0, "cm")) + }, + measure_grobs = function(grobs, params, elements) { # As this guide is expected to be placed in the interior of coord_radial, # we don't need to measure grob sizes nor arrange the layout. diff --git a/R/guide-axis.R b/R/guide-axis.R index 22cda82454..8eafccf114 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -115,6 +115,9 @@ GuideAxis <- ggproto( extract_key = function(scale, aesthetic, minor.ticks = FALSE, ...) { major <- Guide$extract_key(scale, aesthetic, ...) + if (is.null(major) && is.null(scale$scale$get_breaks())) { + major <- data_frame0() + } if (!minor.ticks) { return(major) } @@ -147,10 +150,11 @@ GuideAxis <- ggproto( extract_decor = function(scale, aesthetic, position, key, cap = "none", ...) { value <- c(-Inf, Inf) - if (cap %in% c("both", "upper")) { + has_key <- !(is.null(key) || nrow(key) < 1) + if (cap %in% c("both", "upper") && has_key) { value[2] <- max(key[[aesthetic]]) } - if (cap %in% c("both", "lower")) { + if (cap %in% c("both", "lower") && has_key) { value[1] <- min(key[[aesthetic]]) } @@ -166,26 +170,32 @@ GuideAxis <- ggproto( transform = function(self, params, coord, panel_params) { key <- params$key position <- params$position - - if (is.null(position) || nrow(key) == 0) { - return(params) + check <- FALSE + + if (!(is.null(position) || nrow(key) == 0)) { + check <- TRUE + aesthetics <- names(key)[!grepl("^\\.", names(key))] + if (!all(c("x", "y") %in% aesthetics)) { + other_aesthetic <- setdiff(c("x", "y"), aesthetics) + override_value <- if (position %in% c("bottom", "left")) -Inf else Inf + key[[other_aesthetic]] <- override_value + } + key <- coord$transform(key, panel_params) + params$key <- key } - aesthetics <- names(key)[!grepl("^\\.", names(key))] - if (!all(c("x", "y") %in% aesthetics)) { - other_aesthetic <- setdiff(c("x", "y"), aesthetics) - override_value <- if (position %in% c("bottom", "left")) -Inf else Inf - key[[other_aesthetic]] <- override_value - } - key <- coord$transform(key, panel_params) - params$key <- key + if (!is.null(params$decor)) { + params$decor <- coord_munch(coord, params$decor, panel_params) - params$decor <- coord_munch(coord, params$decor, panel_params) + if (!coord$is_linear()) { + # For non-linear coords, we hardcode the opposite position + params$decor$x <- switch(position, left = 1, right = 0, params$decor$x) + params$decor$y <- switch(position, top = 0, bottom = 1, params$decor$y) + } + } - if (!coord$is_linear()) { - # For non-linear coords, we hardcode the opposite position - params$decor$x <- switch(position, left = 1, right = 0, params$decor$x) - params$decor$y <- switch(position, top = 0, bottom = 1, params$decor$y) + if (!check) { + return(params) } # Ported over from `warn_for_position_guide` From a4202647cf71f2b26e13c1e6ad553e929256cf1c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:44:22 +0200 Subject: [PATCH 013/264] Update to `update_*_defaults()` (reviving #5781) (#5846) * Update to `update_*_defaults()` (#5781) * unify updating mechanism * add tests * redocument * add news bullet * add review suggestion * move news bullet --- NEWS.md | 2 ++ R/geom-defaults.R | 54 +++++++++++++++++++++++++------------ man/update_defaults.Rd | 10 ++++--- tests/testthat/test-geom-.R | 20 +++++++++++--- 4 files changed, 63 insertions(+), 23 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0163d4d9cf..12ad2c0612 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `update_geom_defaults()` and `update_stat_defaults()` have a reset mechanism + when using `new = NULL` and invisible return the previous defaults (#4993). * Fixed regression in axes where `breaks = NULL` caused the axes to disappear instead of just rendering the axis line (@teunbrand, #5816). * `geom_point()` can be dodged vertically by using diff --git a/R/geom-defaults.R b/R/geom-defaults.R index afd2e598d4..8b81eeef94 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -3,7 +3,9 @@ #' @param stat,geom Name of geom/stat to modify (like `"point"` or #' `"bin"`), or a Geom/Stat object (like `GeomPoint` or #' `StatBin`). -#' @param new Named list of aesthetics. +#' @param new One of the following: +#' * A named list of aesthetics to serve as new defaults. +#' * `NULL` to reset the defaults. #' @keywords internal #' @export #' @examples @@ -16,7 +18,7 @@ #' ggplot(mtcars, aes(mpg, wt)) + geom_point() #' #' # reset default -#' update_geom_defaults("point", aes(color = "black")) +#' update_geom_defaults("point", NULL) #' #' #' # updating a stat's default aesthetic settings @@ -29,27 +31,45 @@ #' geom_function(fun = dnorm, color = "red") #' #' # reset default -#' update_stat_defaults("bin", aes(y = after_stat(count))) +#' update_stat_defaults("bin", NULL) #' #' @rdname update_defaults update_geom_defaults <- function(geom, new) { - g <- check_subclass(geom, "Geom", env = parent.frame()) - old <- g$default_aes - new <- rename_aes(new) - new_names_order <- unique(c(names(old), names(new))) - new <- defaults(new, old)[new_names_order] - g$default_aes[names(new)] <- new - invisible() + update_defaults(geom, "Geom", new, env = parent.frame()) } #' @rdname update_defaults #' @export update_stat_defaults <- function(stat, new) { - g <- check_subclass(stat, "Stat", env = parent.frame()) - old <- g$default_aes - new <- rename_aes(new) - new_names_order <- unique(c(names(old), names(new))) - new <- defaults(new, old)[new_names_order] - g$default_aes[names(new)] <- new - invisible() + update_defaults(stat, "Stat", new, env = parent.frame()) +} + +cache_defaults <- new_environment() + +update_defaults <- function(name, subclass, new, env = parent.frame()) { + obj <- check_subclass(name, subclass, env = env) + index <- snake_class(obj) + + if (is.null(new)) { # Reset from cache + + old <- cache_defaults[[index]] + if (!is.null(old)) { + new <- update_defaults(name, subclass, new = old, env = env) + } + invisible(new) + + } else { # Update default aesthetics + + old <- obj$default_aes + # Only update cache the first time defaults are changed + if (!exists(index, envir = cache_defaults)) { + cache_defaults[[index]] <- old + } + new <- rename_aes(new) + name_order <- unique(c(names(old), names(new))) + new <- defaults(new, old)[name_order] + obj$default_aes[names(new)] <- new + invisible(old) + + } } diff --git a/man/update_defaults.Rd b/man/update_defaults.Rd index e009b99d32..8006bf8246 100644 --- a/man/update_defaults.Rd +++ b/man/update_defaults.Rd @@ -10,7 +10,11 @@ update_geom_defaults(geom, new) update_stat_defaults(stat, new) } \arguments{ -\item{new}{Named list of aesthetics.} +\item{new}{One of the following: +\itemize{ +\item A named list of aesthetics to serve as new defaults. +\item \code{NULL} to reset the defaults. +}} \item{stat, geom}{Name of geom/stat to modify (like \code{"point"} or \code{"bin"}), or a Geom/Stat object (like \code{GeomPoint} or @@ -29,7 +33,7 @@ GeomPoint$default_aes ggplot(mtcars, aes(mpg, wt)) + geom_point() # reset default -update_geom_defaults("point", aes(color = "black")) +update_geom_defaults("point", NULL) # updating a stat's default aesthetic settings @@ -42,7 +46,7 @@ ggplot(data.frame(x = rnorm(1e3)), aes(x)) + geom_function(fun = dnorm, color = "red") # reset default -update_stat_defaults("bin", aes(y = after_stat(count))) +update_stat_defaults("bin", NULL) } \keyword{internal} diff --git a/tests/testthat/test-geom-.R b/tests/testthat/test-geom-.R index 409aa19b8f..61063d5d95 100644 --- a/tests/testthat/test-geom-.R +++ b/tests/testthat/test-geom-.R @@ -6,7 +6,21 @@ test_that("aesthetic checking in geom throws correct errors", { expect_snapshot_error(check_aesthetics(aes, 4)) }) - +test_that("geom defaults can be set and reset", { + l <- geom_point() + test <- l$geom$use_defaults(data_frame0()) + expect_equal(test$colour, "black") + + inv <- update_geom_defaults("point", list(colour = "red")) + test <- l$geom$use_defaults(data_frame0()) + expect_equal(test$colour, "red") + expect_equal(inv$colour, "black") + + inv <- update_geom_defaults("point", NULL) + test <- l$geom$use_defaults(data_frame0()) + expect_equal(test$colour, "black") + expect_equal(inv$colour, "red") +}) test_that("updating geom aesthetic defaults preserves class and order", { @@ -23,7 +37,7 @@ test_that("updating geom aesthetic defaults preserves class and order", { expect_equal(updated_defaults, intended_defaults) - update_geom_defaults("point", original_defaults) + update_geom_defaults("point", NULL) }) @@ -46,6 +60,6 @@ test_that("updating stat aesthetic defaults preserves class and order", { expect_equal(updated_defaults, intended_defaults) - update_stat_defaults("bin", original_defaults) + update_stat_defaults("bin", NULL) }) From 09bcda61e29f0cabbf58bf757fb54246e5745fe0 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:57:25 +0200 Subject: [PATCH 014/264] `geom_curve()` removes missing data (#5832) * apply remove_missing() * add news bullet --- NEWS.md | 2 ++ R/geom-curve.R | 5 +++++ 2 files changed, 7 insertions(+) diff --git a/NEWS.md b/NEWS.md index 12ad2c0612..f3275ccf7c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_curve()` now appropriately removes missing data instead of throwing + errors (@teunbrand, #5831). * `update_geom_defaults()` and `update_stat_defaults()` have a reset mechanism when using `new = NULL` and invisible return the previous defaults (#4993). * Fixed regression in axes where `breaks = NULL` caused the axes to disappear diff --git a/R/geom-curve.R b/R/geom-curve.R index 7ef935caeb..079bf636df 100644 --- a/R/geom-curve.R +++ b/R/geom-curve.R @@ -47,6 +47,11 @@ GeomCurve <- ggproto("GeomCurve", GeomSegment, if (!coord$is_linear()) { cli::cli_warn("{.fn geom_curve} is not implemented for non-linear coordinates") } + data <- remove_missing( + data, na.rm = na.rm, + c("x", "y", "xend", "yend", "linetype", "linewidth"), + name = "geom_curve" + ) trans <- coord$transform(data, panel_params) From c5a9c680370a16514a0c513fccaecca4d368099a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 11:04:45 +0200 Subject: [PATCH 015/264] `facet_wrap(drop = TRUE)` can handle character variables with `NA`s (#5847) * `ulevels()` only drops character NAs on request * add test * add news bullet --- NEWS.md | 4 ++++ R/facet-grid-.R | 4 ++-- R/stat-summary-2d.R | 2 +- tests/testthat/test-facet-layout.R | 8 +++++++- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index f3275ccf7c..bfeaffcbae 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* Prevented `facet_wrap(..., drop = FALSE)` from throwing spurious errors when + a character facetting variable contained `NA`s (@teunbrand, #5485). +* When facets coerce the faceting variables to factors, the 'ordered' class + is dropped (@teunbrand, #5666). * `geom_curve()` now appropriately removes missing data instead of throwing errors (@teunbrand, #5831). * `update_geom_defaults()` and `update_stat_defaults()` have a reset mechanism diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 43897e4c9c..54c4b8f971 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -511,11 +511,11 @@ FacetGrid <- ggproto("FacetGrid", Facet, # Helpers ----------------------------------------------------------------- -ulevels <- function(x) { +ulevels <- function(x, na.last = TRUE) { if (is.factor(x)) { x <- addNA(x, TRUE) factor(levels(x), levels(x), exclude = NULL) } else { - sort(unique0(x)) + sort(unique0(x), na.last = na.last) } } diff --git a/R/stat-summary-2d.R b/R/stat-summary-2d.R index 30b61e6f58..60e5e49813 100644 --- a/R/stat-summary-2d.R +++ b/R/stat-summary-2d.R @@ -126,7 +126,7 @@ StatSummary2d <- ggproto("StatSummary2d", Stat, # Adaptation of tapply that returns a data frame instead of a matrix tapply_df <- function(x, index, fun, ..., drop = TRUE) { - labels <- lapply(index, ulevels) + labels <- lapply(index, ulevels, na.last = NA) # drop NA out <- expand.grid(labels, KEEP.OUT.ATTRS = FALSE, stringsAsFactors = FALSE) grps <- split(x, index) diff --git a/tests/testthat/test-facet-layout.R b/tests/testthat/test-facet-layout.R index 9ab6e80eeb..c22d1c36ca 100644 --- a/tests/testthat/test-facet-layout.R +++ b/tests/testthat/test-facet-layout.R @@ -100,7 +100,8 @@ test_that("grid: as.table reverses rows", { a2 <- data_frame( a = factor(1:3, levels = 1:4), - b = factor(1:3, levels = 4:1) + b = factor(1:3, levels = 4:1), + c = as.character(c(1:2, NA)) ) test_that("wrap: drop = FALSE preserves unused levels", { @@ -111,6 +112,11 @@ test_that("wrap: drop = FALSE preserves unused levels", { wrap_b <- panel_layout(facet_wrap(~b, drop = FALSE), list(a2)) expect_equal(nrow(wrap_b), 4) expect_equal(as.character(wrap_b$b), as.character(4:1)) + + # NA character should not be dropped or throw errors #5485 + wrap_c <- panel_layout(facet_wrap(~c, drop = FALSE), list(a2)) + expect_equal(nrow(wrap_c), 3) + expect_equal(wrap_c$c, a2$c) }) test_that("grid: drop = FALSE preserves unused levels", { From 8fa0fb4e06a9bccd9fbc88cba42d2a96a44fb848 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 11:05:29 +0200 Subject: [PATCH 016/264] More sorting options for `facet_wrap()` (#5855) * resolve `dir`/`as.table` * new wrap layouts * add tests * add news bullet * skip `as.table` option in vignette * add example --- NEWS.md | 2 + R/facet-wrap.R | 70 ++++++++++++++++++++++-------- man/facet_wrap.Rd | 15 ++++++- tests/testthat/test-facet-layout.R | 38 ++++++++++++++++ vignettes/extending-ggplot2.Rmd | 6 +-- 5 files changed, 107 insertions(+), 24 deletions(-) diff --git a/NEWS.md b/NEWS.md index bfeaffcbae..e4361c5556 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `facet_wrap()` has new options for the `dir` argument to more precisely + control panel directions (@teunbrand, #5212) * Prevented `facet_wrap(..., drop = FALSE)` from throwing spurious errors when a character facetting variable contained `NA`s (@teunbrand, #5485). * When facets coerce the faceting variables to factors, the 'ordered' class diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 3fcd05eacd..f69cdd8f95 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -23,7 +23,12 @@ NULL #' either of the four sides by setting \code{strip.position = c("top", #' "bottom", "left", "right")} #' @param dir Direction: either `"h"` for horizontal, the default, or `"v"`, -#' for vertical. +#' for vertical. When `"h"` or `"v"` will be combined with `as.table` to +#' set final layout. Alternatively, a combination of `"t"` (top) or +#' `"b"` (bottom) with `"l"` (left) or `"r"` (right) to set a layout directly. +#' These two letters give the starting position and the first letter gives +#' the growing direction. For example `"rt"` will place the first panel in +#' the top-right and starts filling in panels right-to-left. #' @param axes Determines which axes will be drawn in case of fixed scales. #' When `"margins"` (default), axes will be drawn at the exterior margins. #' `"all_x"` and `"all_y"` will draw the respective axes at the interior @@ -95,13 +100,29 @@ NULL #' facet_wrap(vars(variable), scales = "free_y", nrow = 2, strip.position = "top") + #' theme(strip.background = element_blank(), strip.placement = "outside") #' } +#' +#' # The two letters determine the starting position, so 'tr' starts +#' # in the top-right. +#' # The first letter determines direction, so 'tr' fills top-to-bottom. +#' # `dir = "tr"` is equivalent to `dir = "v", as.table = FALSE` +#' ggplot(mpg, aes(displ, hwy)) + +#' geom_point() + +#' facet_wrap(vars(class), dir = "tr") facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", shrink = TRUE, labeller = "label_value", as.table = TRUE, switch = deprecated(), drop = TRUE, dir = "h", strip.position = 'top', axes = "margins", axis.labels = "all") { scales <- arg_match0(scales %||% "fixed", c("fixed", "free_x", "free_y", "free")) - dir <- arg_match0(dir, c("h", "v")) + dir <- arg_match0(dir, c("h", "v", "lt", "tl", "lb", "bl", "rt", "tr", "rb", "br")) + if (nchar(dir) == 1) { + dir <- base::switch( + dir, + h = if (as.table) "lt" else "lb", + v = if (as.table) "tl" else "tr" + ) + } + free <- list( x = any(scales %in% c("free_x", "free")), y = any(scales %in% c("free_y", "free")) @@ -149,7 +170,6 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", params = list( facets = facets, free = free, - as.table = as.table, strip.position = strip.position, drop = drop, ncol = ncol, @@ -189,21 +209,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, n <- attr(id, "n") dims <- wrap_dims(n, params$nrow, params$ncol) - layout <- data_frame0( - PANEL = factor(id, levels = seq_len(n)), - ROW = if (params$as.table) { - as.integer((id - 1L) %/% dims[2] + 1L) - } else { - as.integer(dims[1] - (id - 1L) %/% dims[2]) - }, - COL = as.integer((id - 1L) %% dims[2] + 1L), - .size = length(id) - ) - - # For vertical direction, flip row and col - if (identical(params$dir, "v")) { - layout[c("ROW", "COL")] <- layout[c("COL", "ROW")] - } + layout <- wrap_layout(id, dims, params$dir) panels <- vec_cbind(layout, base) panels <- panels[order(panels$PANEL), , drop = FALSE] @@ -576,3 +582,31 @@ measure_axes <- function(empty_idx, axis, margin = 1L, shift = 0) { cm[set_zero] <- 0 unit(apply(cm, margin, max), "cm") } + +wrap_layout <- function(id, dims, dir) { + as.table <- TRUE + n <- attr(id, "n") + + ROW <- switch( + dir, + lt = , rt = (id - 1L) %/% dims[2] + 1L, + tl = , tr = (id - 1L) %% dims[1] + 1L, + lb = , rb = dims[1] - (id - 1L) %/% dims[2], + bl = , br = dims[1] - (id - 1L) %% dims[1] + ) + + COL <- switch( + dir, + lt = , lb = (id - 1L) %% dims[2] + 1L, + tl = , bl = (id - 1L) %/% dims[1] + 1L, + rt = , rb = dims[2] - (id - 1L) %% dims[2], + tr = , br = dims[2] - (id - 1L) %/% dims[1] + ) + + data_frame0( + PANEL = factor(id, levels = seq_len(n)), + ROW = as.integer(ROW), + COL = as.integer(COL), + .size = length(id) + ) +} diff --git a/man/facet_wrap.Rd b/man/facet_wrap.Rd index b765efe1dd..d431f0098a 100644 --- a/man/facet_wrap.Rd +++ b/man/facet_wrap.Rd @@ -65,7 +65,12 @@ data will automatically be dropped. If \code{FALSE}, all factor levels will be shown, regardless of whether or not they appear in the data.} \item{dir}{Direction: either \code{"h"} for horizontal, the default, or \code{"v"}, -for vertical.} +for vertical. When \code{"h"} or \code{"v"} will be combined with \code{as.table} to +set final layout. Alternatively, a combination of \code{"t"} (top) or +\code{"b"} (bottom) with \code{"l"} (left) or \code{"r"} (right) to set a layout directly. +These two letters give the starting position and the first letter gives +the growing direction. For example \code{"rt"} will place the first panel in +the top-right and starts filling in panels right-to-left.} \item{strip.position}{By default, the labels are displayed on the top of the plot. Using \code{strip.position} it is possible to place the labels on @@ -146,6 +151,14 @@ ggplot(economics_long, aes(date, value)) + facet_wrap(vars(variable), scales = "free_y", nrow = 2, strip.position = "top") + theme(strip.background = element_blank(), strip.placement = "outside") } + +# The two letters determine the starting position, so 'tr' starts +# in the top-right. +# The first letter determines direction, so 'tr' fills top-to-bottom. +# `dir = "tr"` is equivalent to `dir = "v", as.table = FALSE` +ggplot(mpg, aes(displ, hwy)) + + geom_point() + + facet_wrap(vars(class), dir = "tr") } \seealso{ The \href{https://ggplot2-book.org/facet#sec-facet-wrap}{facet wrap section} of the online ggplot2 book. diff --git a/tests/testthat/test-facet-layout.R b/tests/testthat/test-facet-layout.R index c22d1c36ca..70a4ed30e8 100644 --- a/tests/testthat/test-facet-layout.R +++ b/tests/testthat/test-facet-layout.R @@ -32,6 +32,44 @@ test_that("grid: includes all combinations", { expect_equal(nrow(all), 4) }) +test_that("wrap: layout sorting is correct", { + + dummy <- list(data_frame0(x = 1:5)) + + test <- panel_layout(facet_wrap(~x, dir = "lt"), dummy) + expect_equal(test$ROW, rep(c(1,2), c(3, 2))) + expect_equal(test$COL, c(1:3, 1:2)) + + test <- panel_layout(facet_wrap(~x, dir = "tl"), dummy) + expect_equal(test$ROW, c(1, 2, 1, 2, 1)) + expect_equal(test$COL, c(1, 1, 2, 2, 3)) + + test <- panel_layout(facet_wrap(~x, dir = "lb"), dummy) + expect_equal(test$ROW, c(2, 2, 2, 1, 1)) + expect_equal(test$COL, c(1, 2, 3, 1, 2)) + + test <- panel_layout(facet_wrap(~x, dir = "bl"), dummy) + expect_equal(test$ROW, c(2, 1, 2, 1, 2)) + expect_equal(test$COL, c(1, 1, 2, 2, 3)) + + test <- panel_layout(facet_wrap(~x, dir = "rt"), dummy) + expect_equal(test$ROW, c(1, 1, 1, 2, 2)) + expect_equal(test$COL, c(3, 2, 1, 3, 2)) + + test <- panel_layout(facet_wrap(~x, dir = "tr"), dummy) + expect_equal(test$ROW, c(1, 2, 1, 2, 1)) + expect_equal(test$COL, c(3, 3, 2, 2, 1)) + + test <- panel_layout(facet_wrap(~x, dir = "rb"), dummy) + expect_equal(test$ROW, c(2, 2, 2, 1, 1)) + expect_equal(test$COL, c(3, 2, 1, 3, 2)) + + test <- panel_layout(facet_wrap(~x, dir = "br"), dummy) + expect_equal(test$ROW, c(2, 1, 2, 1, 2)) + expect_equal(test$COL, c(3, 3, 2, 2, 1)) + +}) + test_that("wrap and grid are equivalent for 1d data", { rowg <- panel_layout(facet_grid(a~.), list(a)) roww <- panel_layout(facet_wrap(~a, ncol = 1), list(a)) diff --git a/vignettes/extending-ggplot2.Rmd b/vignettes/extending-ggplot2.Rmd index e658092339..01383378bc 100644 --- a/vignettes/extending-ggplot2.Rmd +++ b/vignettes/extending-ggplot2.Rmd @@ -1054,11 +1054,7 @@ FacetBootstrap <- ggproto("FacetBootstrap", FacetWrap, dims <- wrap_dims(params$n, params$nrow, params$ncol) layout <- data.frame(PANEL = factor(id)) - if (params$as.table) { - layout$ROW <- as.integer((id - 1L) %/% dims[2] + 1L) - } else { - layout$ROW <- as.integer(dims[1] - (id - 1L) %/% dims[2]) - } + layout$ROW <- as.integer((id - 1L) %/% dims[2] + 1L) layout$COL <- as.integer((id - 1L) %% dims[2] + 1L) layout <- layout[order(layout$PANEL), , drop = FALSE] From 8e63882c3c36259785baac0eed5d51525bc40f70 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 29 Apr 2024 11:12:38 +0200 Subject: [PATCH 017/264] Refactor applying defaults in `geom_sf()` (#5834) * add test for mixed geometry types * allow custom defaults in `Geom$use_defaults()` * Implement `GeomSf$use_defaults()` * trim default setting in `sf_grob()` * use `defer()` in case test fails * add news bullet --- NEWS.md | 2 + R/geom-.R | 4 +- R/geom-sf.R | 91 ++++++++++++++----- .../_snaps/geom-sf/mixed-geometry-types.svg | 85 +++++++++++++++++ tests/testthat/test-geom-sf.R | 37 ++++++++ 5 files changed, 194 insertions(+), 25 deletions(-) create mode 100644 tests/testthat/_snaps/geom-sf/mixed-geometry-types.svg diff --git a/NEWS.md b/NEWS.md index e4361c5556..070c74dd40 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* (Internal) Applying defaults in `geom_sf()` has moved from the internal + `sf_grob()` to `GeomSf$use_defaults()` (@teunbrand). * `facet_wrap()` has new options for the `dir` argument to more precisely control panel directions (@teunbrand, #5212) * Prevented `facet_wrap(..., drop = FALSE)` from throwing spurious errors when diff --git a/R/geom-.R b/R/geom-.R index c1967a89c1..ab4e1ed1b7 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -114,8 +114,8 @@ Geom <- ggproto("Geom", setup_data = function(data, params) data, # Combine data with defaults and set aesthetics from parameters - use_defaults = function(self, data, params = list(), modifiers = aes()) { - default_aes <- self$default_aes + use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL) { + default_aes <- default_aes %||% self$default_aes # Inherit size as linewidth if no linewidth aesthetic and param exist if (self$rename_size && is.null(data$linewidth) && is.null(params$linewidth)) { diff --git a/R/geom-sf.R b/R/geom-sf.R index a8f70d7f4e..cdcadb1140 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -131,6 +131,63 @@ GeomSf <- ggproto("GeomSf", Geom, stroke = 0.5 ), + use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL) { + data <- ggproto_parent(Geom, self)$use_defaults(data, params, modifiers, default_aes) + # Early exit for e.g. legend data that don't have geometry columns + if (!"geometry" %in% names(data)) { + return(data) + } + + # Devise splitting index for geometry types + type <- sf_types[sf::st_geometry_type(data$geometry)] + type <- factor(type, c("point", "line", "other", "collection")) + index <- split(seq_len(nrow(data)), type) + + # Initialise parts of the data + points <- lines <- others <- collections <- NULL + + # Go through every part, applying different defaults + if (length(index$point) > 0) { + points <- GeomPoint$use_defaults( + vec_slice(data, index$point), + params, modifiers + ) + } + if (length(index$line) > 0) { + lines <- GeomLine$use_defaults( + vec_slice(data, index$line), + params, modifiers + ) + } + other_default <- modify_list( + GeomPolygon$default_aes, + list(fill = "grey90", colour = "grey35", linewidth = 0.2) + ) + if (length(index$other) > 0) { + others <- GeomPolygon$use_defaults( + vec_slice(data, index$other), + params, modifiers, + default_aes = other_default + ) + } + if (length(index$collection) > 0) { + modified <- rename( + GeomPoint$default_aes, + c(fill = "point_fill") + ) + modified <- modify_list(other_default, modified) + collections <- Geom$use_defaults( + vec_slice(data, index$collection), + params, modifiers, + default_aes = modified + ) + } + + # Recombine data in original order + data <- vec_c(points, lines, others, collections) + vec_slice(data, order(unlist(index))) + }, + draw_panel = function(self, data, panel_params, coord, legend = NULL, lineend = "butt", linejoin = "round", linemitre = 10, arrow = NULL, na.rm = TRUE) { @@ -189,36 +246,24 @@ sf_grob <- function(x, lineend = "butt", linejoin = "round", linemitre = 10, type_ind <- type_ind[!remove] is_collection <- is_collection[!remove] } - defaults <- list( - GeomPoint$default_aes, - GeomLine$default_aes, - modify_list(GeomPolygon$default_aes, list(fill = "grey90", colour = "grey35", linewidth = 0.2)) - ) - defaults[[4]] <- modify_list( - defaults[[3]], - rename(GeomPoint$default_aes, c(size = "point_size", fill = "point_fill")) - ) - default_names <- unique0(unlist(lapply(defaults, names))) - defaults <- lapply(setNames(default_names, default_names), function(n) { - unlist(lapply(defaults, function(def) def[[n]] %||% NA)) - }) - alpha <- x$alpha %||% defaults$alpha[type_ind] - col <- x$colour %||% defaults$colour[type_ind] + + alpha <- x$alpha %||% NA + fill <- fill_alpha(x$fill %||% NA, alpha) + col <- x$colour %||% NA col[is_point | is_line] <- alpha(col[is_point | is_line], alpha[is_point | is_line]) - fill <- x$fill %||% defaults$fill[type_ind] - fill <- fill_alpha(fill, alpha) - size <- x$size %||% defaults$size[type_ind] - linewidth <- x$linewidth %||% defaults$linewidth[type_ind] + + size <- x$size %||% 0.5 + linewidth <- x$linewidth %||% 0.5 point_size <- ifelse( is_collection, - x$size %||% defaults$point_size[type_ind], + x$size, ifelse(is_point, size, linewidth) ) - stroke <- (x$stroke %||% defaults$stroke[1]) * .stroke / 2 + stroke <- (x$stroke %||% 0) * .stroke / 2 fontsize <- point_size * .pt + stroke lwd <- ifelse(is_point, stroke, linewidth * .pt) - pch <- x$shape %||% defaults$shape[type_ind] - lty <- x$linetype %||% defaults$linetype[type_ind] + pch <- x$shape + lty <- x$linetype gp <- gpar( col = col, fill = fill, fontsize = fontsize, lwd = lwd, lty = lty, lineend = lineend, linejoin = linejoin, linemitre = linemitre diff --git a/tests/testthat/_snaps/geom-sf/mixed-geometry-types.svg b/tests/testthat/_snaps/geom-sf/mixed-geometry-types.svg new file mode 100644 index 0000000000..c8dc5b6922 --- /dev/null +++ b/tests/testthat/_snaps/geom-sf/mixed-geometry-types.svg @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1 + 0 + 1 + 2 + 3 + 4 + 5 + 6 + + + + + + + + + + + + + + + + +-1 + 0 + 1 + 2 + 3 + 4 + 5 + 6 +mixed geometry types + + diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index af5d6bdb9d..1db38a1fff 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -196,6 +196,43 @@ test_that("geom_sf draws correctly", { ) }) +test_that("geom_sf uses combinations of geometry correctly", { + skip_if_not_installed("sf") + + t <- seq(0, 2 *pi, length.out = 10) + data <- sf::st_sf(sf::st_sfc( + sf::st_multipoint(cbind(1:2, 3:4)), + sf::st_multilinestring(list( + cbind(c(1, 1.8), c(3.8, 3)), + cbind(c(1.2, 2), c(4, 3.2)) + )), + sf::st_polygon(list( + cbind(cos(t), zapsmall(sin(t))), + cbind(cos(t), zapsmall(sin(t))) + 5 + )), + sf::st_geometrycollection(x = list( + sf::st_point(x = c(3, 2)), + sf::st_linestring(cbind(c(2, 4, 4), c(1, 1, 3))) + )), + sf::st_linestring(x = cbind(c(2, 6), c(-1, 3))), + sf::st_point(c(5, 0)) + )) + + update_geom_defaults("point", list(colour = "blue")) + update_geom_defaults("line", list(colour = "red")) + # Note: polygon defaults are mostly ignored or overridden + + withr::defer({ + update_geom_defaults("point", NULL) + update_geom_defaults("line", NULL) + }) + + expect_doppelganger( + "mixed geometry types", + ggplot(data) + geom_sf() + ) +}) + test_that("geom_sf_text() and geom_sf_label() draws correctly", { skip_if_not_installed("sf") if (packageVersion("sf") < "0.5.3") skip("Need sf 0.5.3") From 4bbb15e613e33518f537ef28ccca947ff18900cc Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Sun, 12 May 2024 07:36:49 +0900 Subject: [PATCH 018/264] Ignore installation error of quantreg on R <4.3 (#5889) --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 37117d0a2f..985fef4cf8 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -64,7 +64,7 @@ jobs: extra-packages: > any::rcmdcheck, Hmisc=?ignore-before-r=4.1.0, - quantreg=?ignore-before-r=3.6.0, + quantreg=?ignore-before-r=4.3.0, needs: check - uses: r-lib/actions/check-r-package@v2 From 54cbb98612a006dab65b67fb69a1632907042e2e Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Sun, 12 May 2024 07:37:11 +0900 Subject: [PATCH 019/264] Stop CI on R 3.6 (#5888) --- .github/workflows/R-CMD-check.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 985fef4cf8..cfdefdb714 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -25,8 +25,6 @@ jobs: - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - # Use 3.6 to trigger usage of RTools35 - - {os: windows-latest, r: '3.6'} # use 4.1 to check with rtools40's older compiler - {os: windows-latest, r: '4.1'} From 9af5d810164c05b7f7abaea357a664433470b48d Mon Sep 17 00:00:00 2001 From: Randy Zwitch Date: Wed, 15 May 2024 03:33:26 -0400 Subject: [PATCH 020/264] Update forum URL (#5876) --- R/zzz.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/zzz.R b/R/zzz.R index 4d6755b53b..398cb7d7b6 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -9,7 +9,7 @@ random_tip <- function() { tips <- c( - "RStudio Community is a great place to get help: https://community.rstudio.com/c/tidyverse", + "RStudio Community is a great place to get help: https://forum.posit.co/c/tidyverse", "Learn more about the underlying theory at https://ggplot2-book.org/", "Keep up to date with changes at https://tidyverse.org/blog/", "Use suppressPackageStartupMessages() to eliminate package startup messages", From 7f6ca679e8aff8b1ff39e42602b8005d177318d3 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 09:34:29 +0200 Subject: [PATCH 021/264] Discrete secondary axes (#5620) * set secondary axes * add missing `sec_name` method * only allow identity transforms * map discrete breaks * breaks plumbing * default to identity transform * document `sec.axis` argument * only test when non-waiver * Don't derive discrete breaks from transformation * add test * add news bullet --- NEWS.md | 3 +++ R/axis-secondary.R | 31 ++++++++++++++++++++++++------- R/scale-discrete-.R | 19 +++++++++++++++---- man/scale_discrete.Rd | 8 ++++++-- man/sec_axis.Rd | 2 +- tests/testthat/test-sec-axis.R | 20 ++++++++++++++++++++ 6 files changed, 69 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 070c74dd40..462cc692f3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -22,6 +22,9 @@ (@teunbrand, #5856). * New helper function `ggpar()` to translate ggplot2's interpretation of graphical parameters to {grid}'s interpretation (@teunbrand, #5866). +* `scale_{x/y}_discrete()` can now accept a `sec.axis`. It is recommended to + only use `dup_axis()` to set custom breaks or labels, as discrete variables + cannot be transformed (@teunbrand, #3171). # ggplot2 3.5.1 diff --git a/R/axis-secondary.R b/R/axis-secondary.R index 088df64713..e535b1a95a 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -119,7 +119,7 @@ sec_axis <- function(transform = NULL, #' @rdname sec_axis #' #' @export -dup_axis <- function(transform = ~., name = derive(), breaks = derive(), +dup_axis <- function(transform = identity, name = derive(), breaks = derive(), labels = derive(), guide = derive(), trans = deprecated()) { sec_axis(transform, trans = trans, name, breaks, labels, guide) } @@ -130,6 +130,11 @@ is.sec_axis <- function(x) { set_sec_axis <- function(sec.axis, scale) { if (!is.waive(sec.axis)) { + if (scale$is_discrete()) { + if (!identical(.subset2(sec.axis, "trans"), identity)) { + cli::cli_abort("Discrete secondary axes must have the {.fn identity} transformation.") + } + } if (is.formula(sec.axis)) sec.axis <- sec_axis(sec.axis) if (!is.sec_axis(sec.axis)) { cli::cli_abort("Secondary axes must be specified using {.fn sec_axis}.") @@ -179,7 +184,13 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, } if (is.derived(self$name) && !is.waive(scale$name)) self$name <- scale$name if (is.derived(self$breaks)) self$breaks <- scale$breaks - if (is.waive(self$breaks)) self$breaks <- scale$get_transformation()$breaks + if (is.waive(self$breaks)) { + if (scale$is_discrete()) { + self$breaks <- scale$get_breaks() + } else { + self$breaks <- scale$get_transformation()$breaks + } + } if (is.derived(self$labels)) self$labels <- scale$labels if (is.derived(self$guide)) self$guide <- scale$guide }, @@ -214,10 +225,15 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, if (self$empty()) return() # Test for monotonicity on unexpanded range - self$mono_test(scale) + if (!scale$is_discrete()) { + self$mono_test(scale) + breaks <- self$breaks + } else { + breaks <- scale$map(self$breaks) + } # Get scale's original range before transformation - transformation <- scale$get_transformation() + transformation <- scale$get_transformation() %||% transform_identity() along_range <- seq(range[1], range[2], length.out = self$detail) old_range <- transformation$inverse(along_range) @@ -245,7 +261,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, old_val_trans <- rescale(range_info$major, from = c(0, 1), to = range) old_val_minor_trans <- rescale(range_info$minor, from = c(0, 1), to = range) } else { - temp_scale <- self$create_scale(new_range) + temp_scale <- self$create_scale(new_range, breaks = breaks) range_info <- temp_scale$break_info() # Map the break values back to their correct position on the primary scale @@ -294,10 +310,11 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, }, # Temporary scale for the purpose of calling break_info() - create_scale = function(self, range, transformation = transform_identity()) { + create_scale = function(self, range, transformation = transform_identity(), + breaks = self$breaks) { scale <- ggproto(NULL, ScaleContinuousPosition, name = self$name, - breaks = self$breaks, + breaks = breaks, labels = self$labels, limits = range, expand = c(0, 0), diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index 268448f844..60bcc3f8b7 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -12,6 +12,7 @@ #' #' @inheritDotParams discrete_scale -scale_name #' @inheritParams discrete_scale +#' @param sec.axis [dup_axis()] is used to specify a secondary axis. #' @rdname scale_discrete #' @family position scales #' @seealso @@ -64,7 +65,8 @@ #' scale_x_discrete(labels = abbreviate) #' } scale_x_discrete <- function(name = waiver(), ..., expand = waiver(), - guide = waiver(), position = "bottom") { + guide = waiver(), position = "bottom", + sec.axis = waiver()) { sc <- discrete_scale( aesthetics = c("x", "xmin", "xmax", "xend"), name = name, palette = identity, ..., @@ -73,12 +75,13 @@ scale_x_discrete <- function(name = waiver(), ..., expand = waiver(), ) sc$range_c <- ContinuousRange$new() - sc + set_sec_axis(sec.axis, sc) } #' @rdname scale_discrete #' @export scale_y_discrete <- function(name = waiver(), ..., expand = waiver(), - guide = waiver(), position = "left") { + guide = waiver(), position = "left", + sec.axis = waiver()) { sc <- discrete_scale( aesthetics = c("y", "ymin", "ymax", "yend"), name = name, palette = identity, ..., @@ -87,7 +90,7 @@ scale_y_discrete <- function(name = waiver(), ..., expand = waiver(), ) sc$range_c <- ContinuousRange$new() - sc + set_sec_axis(sec.axis, sc) } # The discrete position scale maintains two separate ranges - one for @@ -147,6 +150,14 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, expand_limits_scale(self, expand, limits) }, + sec_name = function(self) { + if (is.waive(self$secondary.axis)) { + waiver() + } else { + self$secondary.axis$name + } + }, + clone = function(self) { new <- ggproto(NULL, self) new$range <- DiscreteRange$new() diff --git a/man/scale_discrete.Rd b/man/scale_discrete.Rd index 1b4c19710f..e92179a921 100644 --- a/man/scale_discrete.Rd +++ b/man/scale_discrete.Rd @@ -10,7 +10,8 @@ scale_x_discrete( ..., expand = waiver(), guide = waiver(), - position = "bottom" + position = "bottom", + sec.axis = waiver() ) scale_y_discrete( @@ -18,7 +19,8 @@ scale_y_discrete( ..., expand = waiver(), guide = waiver(), - position = "left" + position = "left", + sec.axis = waiver() ) } \arguments{ @@ -89,6 +91,8 @@ expand the scale by 5\% on each side for continuous variables, and by \item{position}{For position scales, The position of the axis. \code{left} or \code{right} for y axes, \code{top} or \code{bottom} for x axes.} + +\item{sec.axis}{\code{\link[=dup_axis]{dup_axis()}} is used to specify a secondary axis.} } \description{ \code{scale_x_discrete()} and \code{scale_y_discrete()} are used to set the values for diff --git a/man/sec_axis.Rd b/man/sec_axis.Rd index c3e273f7f3..e54bbf502c 100644 --- a/man/sec_axis.Rd +++ b/man/sec_axis.Rd @@ -16,7 +16,7 @@ sec_axis( ) dup_axis( - transform = ~., + transform = identity, name = derive(), breaks = derive(), labels = derive(), diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index bcef0ae7aa..cd02fe5459 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -380,3 +380,23 @@ test_that("sec_axis() works for power transformations (monotonicity test doesn't breaks <- scale$break_info() expect_equal(breaks$major, breaks$sec.major, tolerance = .001) }) + +test_that("discrete scales can have secondary axes", { + + data <- data.frame(x = c("A", "B", "C"), y = c("D", "E", "F")) + p <- ggplot(data, aes(x, y)) + + geom_point() + + scale_x_discrete(sec.axis = dup_axis(labels = c("foo", "bar", "baz"))) + + scale_y_discrete(sec.axis = dup_axis( + breaks = c(1.5, 2.5), labels = c("grault", "garply") + )) + b <- ggplot_build(p) + + x <- get_guide_data(b, "x.sec") + expect_equal(x$.value, 1:3, ignore_attr = TRUE) + expect_equal(x$.label, c("foo", "bar", "baz")) + + y <- get_guide_data(b, "y.sec") + expect_equal(y$.value, c(1.5, 2.5), ignore_attr = TRUE) + expect_equal(y$.label, c("grault", "garply")) +}) From b74570c063c455da7c08be0f0713071a2365f541 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 09:43:54 +0200 Subject: [PATCH 022/264] `coord_sf()` scale function breaks (#5442) * Helper function for breaks * Use new breaks * NULL breaks discard gridlines * Fix typo * Add tests * fallback for problematic crs * Add news bullet * Fix `breaks = NULL` case * replace removed `len0_null()` * remove duplicated news entry --- NEWS.md | 3 + R/coord-sf.R | 60 +++++++++++++++++++- tests/testthat/_snaps/coord_sf/no-breaks.svg | 48 ++++++++++++++++ tests/testthat/test-coord_sf.R | 39 +++++++++++++ 4 files changed, 148 insertions(+), 2 deletions(-) create mode 100644 tests/testthat/_snaps/coord_sf/no-breaks.svg diff --git a/NEWS.md b/NEWS.md index 462cc692f3..2b32681c31 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* Position scales combined with `coord_sf()` can now use functions in the + `breaks` argument. In addition, `n.breaks` works as intended and + `breaks = NULL` removes grid lines and axes (@teunbrand, #4622). * (Internal) Applying defaults in `geom_sf()` has moved from the internal `sf_grob()` to `GeomSf$use_defaults()` (@teunbrand). * `facet_wrap()` has new options for the `dir` argument to more precisely diff --git a/R/coord-sf.R b/R/coord-sf.R index 12f7371003..bb408b4126 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -222,16 +222,25 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, x_range[2], y_range[2] ) + breaks <- sf_breaks(scale_x, scale_y, bbox, params$crs) + # Generate graticule and rescale to plot coords graticule <- sf::st_graticule( bbox, crs = params$crs, - lat = scale_y$breaks %|W|% NULL, - lon = scale_x$breaks %|W|% NULL, + lat = breaks$y %|W|% NULL, + lon = breaks$x %|W|% NULL, datum = self$datum, ndiscr = self$ndiscr ) + if (is.null(breaks$x)) { + graticule <- vec_slice(graticule, graticule$type != "E") + } + if (is.null(breaks$y)) { + graticule <- vec_slice(graticule, graticule$type != "N") + } + # override graticule labels provided by sf::st_graticule() if necessary graticule <- self$fixup_graticule_labels(graticule, scale_x, scale_y, params) @@ -580,6 +589,53 @@ parse_axes_labeling <- function(x) { list(top = labs[1], right = labs[2], bottom = labs[3], left = labs[4]) } +# This function does two things differently from standard breaks: +# 1. It does not resolve `waiver()`, unless `n.breaks` is given. In the case +# that breaks are `waiver()`, we use the default graticule breaks. +# 2. It discards non-finite breaks because they are invalid input to the +# graticule. This may cause atomic `labels` to be out-of-sync. +sf_breaks <- function(scale_x, scale_y, bbox, crs) { + + has_x <- !is.null(scale_x$breaks) || !is.null(scale_x$n.breaks) + has_y <- !is.null(scale_y$breaks) || !is.null(scale_y$n.breaks) + + x_breaks <- if (has_x) waiver() else NULL + y_breaks <- if (has_y) waiver() else NULL + + + if (has_x || has_y) { + if (!is.null(crs)) { + # Atomic breaks input are assumed to be in long/lat coordinates. + # To preserve that assumption for function breaks, the bounding box + # needs to be translated to long/lat coordinates. + if (!is_named(bbox)) { + names(bbox) <- c("xmin", "ymin", "xmax", "ymax") + } + # Convert bounding box to long/lat coordinates + bbox <- sf::st_as_sfc(sf::st_bbox(bbox, crs = crs)) + bbox <- sf::st_bbox(sf::st_transform(bbox, 4326)) + bbox <- as.numeric(bbox) + + # If any bbox is NA the transformation has probably failed. + # (.e.g from IGH to long/lat). In this case, just provide full long/lat. + bbox[is.na(bbox)] <- c(-180, -90, 180, 90)[is.na(bbox)] + } + + if (!(is.waive(scale_x$breaks) && is.null(scale_x$n.breaks))) { + x_breaks <- scale_x$get_breaks(limits = bbox[c(1, 3)]) + finite <- is.finite(x_breaks) + x_breaks <- if (any(finite)) x_breaks[finite] else NULL + } + + if (!(is.waive(scale_y$breaks) && is.null(scale_y$n.breaks))) { + y_breaks <- scale_y$get_breaks(limits = bbox[c(2, 4)]) + finite <- is.finite(y_breaks) + y_breaks <- if (any(finite)) y_breaks[finite] else NULL + } + } + + list(x = x_breaks, y = y_breaks) +} #' ViewScale from graticule #' diff --git a/tests/testthat/_snaps/coord_sf/no-breaks.svg b/tests/testthat/_snaps/coord_sf/no-breaks.svg new file mode 100644 index 0000000000..67455011bb --- /dev/null +++ b/tests/testthat/_snaps/coord_sf/no-breaks.svg @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +x +y +no breaks + + diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index bbb90e0243..c668b3ec79 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -30,6 +30,20 @@ test_that("graticule lines can be removed via theme", { expect_doppelganger("no panel grid", plot) }) +test_that("graticule lines and axes can be removed via scales", { + skip_if_not_installed("sf") + + df <- data_frame(x = c(1, 2, 3), y = c(1, 2, 3)) + plot <- ggplot(df, aes(x, y)) + + geom_point() + + coord_sf() + + theme_gray() + + scale_x_continuous(breaks = NULL) + + scale_y_continuous(breaks = NULL) + + expect_doppelganger("no breaks", plot) +}) + test_that("axis labels are correct for manual breaks", { skip_if_not_installed("sf") @@ -300,6 +314,31 @@ test_that("sf_transform_xy() works", { }) +test_that("coord_sf() can use function breaks and n.breaks", { + + polygon <- sf::st_sfc( + sf::st_polygon(list(matrix(c(-80, -76, -76, -80, -80, 35, 35, 40, 40, 35), ncol = 2))), + crs = 4326 # basic long-lat crs + ) + polygon <- sf::st_transform(polygon, crs = 3347) + + p <- ggplot(polygon) + geom_sf(fill = NA) + + scale_x_continuous(breaks = breaks_width(0.5)) + + scale_y_continuous(n.breaks = 4) + + b <- ggplot_build(p) + grat <- b$layout$panel_params[[1]]$graticule + + expect_equal( + vec_slice(grat$degree, grat$type == "E"), + seq(-81, -74.5, by = 0.5) + ) + expect_equal( + vec_slice(grat$degree, grat$type == "N"), + seq(34, 40, by = 2) + ) +}) + test_that("coord_sf() uses the guide system", { skip_if_not_installed("sf") polygon <- sf::st_sfc( From 9202a47d0c26a7e3f22c735a7717a4a309d1e4e0 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 10:48:49 +0200 Subject: [PATCH 023/264] Alt text label can be function (#5079) * Allow functions as `labs(alt = ...)` input * Alt functions are called with plot as input * Add test for alt text functions * Add NEWS bullet * Avoid recursion * deal with changes in {glue} --- NEWS.md | 2 ++ R/labels.R | 32 ++++++++++++++++++++++---------- man/labs.Rd | 4 +++- tests/testthat/_snaps/labels.md | 7 +++++++ tests/testthat/test-labels.R | 6 ++++++ 5 files changed, 40 insertions(+), 11 deletions(-) diff --git a/NEWS.md b/NEWS.md index 2b32681c31..50544dcce6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* A function can be provided to `labs(alt = <...>)` that takes the plot as input + and returns text as output (@teunbrand, #4795). * Position scales combined with `coord_sf()` can now use functions in the `breaks` argument. In addition, `n.breaks` works as intended and `breaks = NULL` removes grid lines and axes (@teunbrand, #4622). diff --git a/R/labels.R b/R/labels.R index a70d6d535c..66401683cb 100644 --- a/R/labels.R +++ b/R/labels.R @@ -44,7 +44,9 @@ update_labels <- function(p, labels) { #' @param tag The text for the tag label which will be displayed at the #' top-left of the plot by default. #' @param alt,alt_insight Text used for the generation of alt-text for the plot. -#' See [get_alt_text] for examples. +#' See [get_alt_text] for examples. `alt` can also be a function that +#' takes the plot as input and returns text as output. `alt` also accepts +#' rlang [lambda][rlang::as_function()] function notation. #' @param ... A list of new name-value pairs. The name should be an aesthetic. #' @export #' @@ -76,7 +78,8 @@ labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), tag = waiver(), alt = waiver(), alt_insight = waiver()) { # .ignore_empty = "all" is needed to allow trailing commas, which is NOT a trailing comma for dots_list() as it's in ... args <- dots_list(..., title = title, subtitle = subtitle, caption = caption, - tag = tag, alt = alt, alt_insight = alt_insight, .ignore_empty = "all") + tag = tag, alt = allow_lambda(alt), alt_insight = alt_insight, + .ignore_empty = "all") is_waive <- vapply(args, is.waive, logical(1)) args <- args[!is_waive] @@ -140,11 +143,15 @@ get_alt_text <- function(p, ...) { } #' @export get_alt_text.ggplot <- function(p, ...) { - p$labels[["alt"]] %||% "" + alt <- p$labels[["alt"]] %||% "" + p$labels[["alt"]] <- NULL + if (is.function(alt)) alt(p) else alt } #' @export get_alt_text.ggplot_built <- function(p, ...) { - p$plot$labels[["alt"]] %||% "" + alt <- p$plot$labels[["alt"]] %||% "" + p$plot$labels[["alt"]] <- NULL + if (is.function(alt)) alt(p$plot) else alt } #' @export get_alt_text.gtable <- function(p, ...) { @@ -197,11 +204,16 @@ get_alt_text.gtable <- function(p, ...) { #' generate_alt_text <- function(p) { # Combine titles - title <- glue(glue_collapse( - sub("\\.?$", "", c(p$labels$title, p$labels$subtitle)), - last = ": " - ), ". ") - title <- safe_string(title) + if (!is.null(p$label$title %||% p$labels$subtitle)) { + title <- glue(glue_collapse( + sub("\\.?$", "", c(p$labels$title, p$labels$subtitle)), + last = ": " + ), ". ") + title <- safe_string(title) + } else { + title <- "" + } + # Get axes descriptions axes <- glue(" showing ", glue_collapse( @@ -218,7 +230,7 @@ generate_alt_text <- function(p) { if (length(layers) == 1) "a " else "", glue_collapse(layers, sep = ", ", last = " and "), " layer", - if (length(layers) == 1) "" else "s", + if (length(layers) == 1) "" else "s" ) layers <- safe_string(layers) diff --git a/man/labs.Rd b/man/labs.Rd index 3f1687a0f6..6fc7e9aa08 100644 --- a/man/labs.Rd +++ b/man/labs.Rd @@ -38,7 +38,9 @@ bottom-right of the plot by default.} top-left of the plot by default.} \item{alt, alt_insight}{Text used for the generation of alt-text for the plot. -See \link{get_alt_text} for examples.} +See \link{get_alt_text} for examples. \code{alt} can also be a function that +takes the plot as input and returns text as output. \code{alt} also accepts +rlang \link[rlang:as_function]{lambda} function notation.} \item{label}{The title of the respective axis (for \code{xlab()} or \code{ylab()}) or of the plot (for \code{ggtitle()}).} diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index 8c027dae53..8c673cfe11 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -1,3 +1,10 @@ +# alt text can take a function + + Code + get_alt_text(p) + Output + [1] "A plot showing class on the x-axis and count on the y-axis using a bar layer" + # plot.tag.position rejects invalid input The `plot.tag.position` theme element must be a object. diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index 78a77db663..e119637f94 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -69,6 +69,12 @@ test_that("alt text is returned", { expect_equal(get_alt_text(p), "An alt text") }) +test_that("alt text can take a function", { + p <- ggplot(mpg, aes(class)) + + geom_bar() + + labs(alt = ~ generate_alt_text(.x)) + expect_snapshot(get_alt_text(p)) +}) test_that("plot.tag.position rejects invalid input", { p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() + labs(tag = "Fig. A)") From e94283380f078e2fd1cd0a9cb612796e24ffed9f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:09:25 +0200 Subject: [PATCH 024/264] Weighted eCDF (#5119) * Add weighted ecdf * Update docs * Add tests for weighted ecdf * Add NEWS.md bullet * Fix typo * Don't fallback to `ecdf()` * Add clarification in docs * use wecdf * cleanup news --- NEWS.md | 3 +- R/stat-ecdf.R | 84 +++++++++++++++++++++++++++++++-- man/stat_ecdf.Rd | 34 +++++++++++++ tests/testthat/test-stat-ecdf.R | 48 +++++++++++++++++++ 4 files changed, 164 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index 50544dcce6..8a31cd598a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,6 @@ # ggplot2 (development version) -* A function can be provided to `labs(alt = <...>)` that takes the plot as input - and returns text as output (@teunbrand, #4795). +* `stat_ecdf()` now has an optional `weight` aesthetic (@teunbrand, #5058). * Position scales combined with `coord_sf()` can now use functions in the `breaks` argument. In addition, `n.breaks` works as intended and `breaks = NULL` removes grid lines and axes (@teunbrand, #4622). diff --git a/R/stat-ecdf.R b/R/stat-ecdf.R index 5f7e5fdd30..fc55dc2e04 100644 --- a/R/stat-ecdf.R +++ b/R/stat-ecdf.R @@ -12,6 +12,10 @@ #' and one of them must be unused. The ECDF will be calculated on the given aesthetic #' and will be output on the unused one. #' +#' If the `weight` aesthetic is provided, a weighted ECDF will be computed. In +#' this case, the ECDF is incremented by `weight / sum(weight)` instead of +#' `1 / length(x)` for each observation. +#' #' @inheritParams layer #' @inheritParams geom_point #' @param na.rm If `FALSE` (the default), removes missing values with @@ -20,10 +24,16 @@ #' of points to interpolate with. #' @param pad If `TRUE`, pad the ecdf with additional points (-Inf, 0) #' and (Inf, 1) +#' @eval rd_aesthetics("stat", "ecdf") #' @eval rd_computed_vars( #' ecdf = "Cumulative density corresponding to `x`.", #' y = "`r lifecycle::badge('superseded')` For backward compatibility." #' ) +#' @section Dropped variables: +#' \describe{ +#' \item{weight}{After calculation, weights of individual observations (if +#' supplied), are no longer available.} +#' } #' @export #' @examples #' set.seed(1) @@ -41,6 +51,17 @@ #' # Multiple ECDFs #' ggplot(df, aes(x, colour = g)) + #' stat_ecdf() +#' +#' # Using weighted eCDF +#' weighted <- data.frame(x = 1:10, weights = c(1:5, 5:1)) +#' plain <- data.frame(x = rep(weighted$x, weighted$weights)) +#' +#' ggplot(plain, aes(x)) + +#' stat_ecdf(linewidth = 1) + +#' stat_ecdf( +#' aes(weight = weights), +#' data = weighted, colour = "green" +#' ) stat_ecdf <- function(mapping = NULL, data = NULL, geom = "step", position = "identity", ..., @@ -74,7 +95,7 @@ stat_ecdf <- function(mapping = NULL, data = NULL, StatEcdf <- ggproto("StatEcdf", Stat, required_aes = c("x|y"), - default_aes = aes(x = after_stat(ecdf), y = after_stat(ecdf)), + default_aes = aes(x = after_stat(ecdf), y = after_stat(ecdf), weight = NULL), setup_params = function(self, data, params) { params$flipped_aes <- has_flipped_aes(data, params, main_is_orthogonal = FALSE, main_is_continuous = TRUE) @@ -100,7 +121,7 @@ StatEcdf <- ggproto("StatEcdf", Stat, if (pad) { x <- c(-Inf, x, Inf) } - data_ecdf <- stats::ecdf(data$x)(x) + data_ecdf <- wecdf(data$x, data$weight)(x) df_ecdf <- data_frame0( x = x, @@ -110,6 +131,63 @@ StatEcdf <- ggproto("StatEcdf", Stat, ) df_ecdf$flipped_aes <- flipped_aes flip_data(df_ecdf, flipped_aes) - } + }, + + dropped_aes = "weight" ) +# Weighted eCDF function +wecdf <- function(x, weights = NULL) { + + weights <- weights %||% 1 + weights <- vec_recycle(weights, length(x)) + + # Sort vectors + ord <- order(x, na.last = NA) + x <- x[ord] + weights <- weights[ord] + + if (any(!is.finite(weights))) { + cli::cli_warn(c(paste0( + "The {.field weight} aesthetic does not support non-finite or ", + "{.code NA} values." + ), "i" = "These weights were replaced by {.val 0}.")) + weights[!is.finite(weights)] <- 0 + } + + # `total` replaces `length(x)` + total <- sum(weights) + + if (abs(total) < 1000 * .Machine$double.eps) { + if (total == 0) { + cli::cli_abort(paste0( + "Cannot compute eCDF when the {.field weight} aesthetic sums up to ", + "{.val 0}." + )) + } + cli::cli_warn(c( + "The sum of the {.field weight} aesthetic is close to {.val 0}.", + "i" = "Computed eCDF might be unstable." + )) + } + + # Link each observation to unique value + vals <- unique0(x) + matched <- match(x, vals) + + # Instead of tabulating `matched`, as we would for unweighted `ecdf(x)`, + # we sum weights per unique value of `x` + agg_weights <- vapply( + split(weights, matched), + sum, numeric(1) + ) + + # Like `ecdf(x)`, we return an approx function + approxfun( + vals, + cumsum(agg_weights) / total, + method = "constant", + yleft = 0, yright = 1, + f = 0, ties = "ordered" + ) +} diff --git a/man/stat_ecdf.Rd b/man/stat_ecdf.Rd index 2a8e6c80e7..d0941b2b56 100644 --- a/man/stat_ecdf.Rd +++ b/man/stat_ecdf.Rd @@ -125,7 +125,22 @@ The statistic relies on the aesthetics assignment to guess which variable to use as the input and which to use as the output. Either x or y must be provided and one of them must be unused. The ECDF will be calculated on the given aesthetic and will be output on the unused one. + +If the \code{weight} aesthetic is provided, a weighted ECDF will be computed. In +this case, the ECDF is incremented by \code{weight / sum(weight)} instead of +\code{1 / length(x)} for each observation. +} +\section{Aesthetics}{ + +\code{stat_ecdf()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \strong{\code{\link[=aes_position]{x}} \emph{or} \code{\link[=aes_position]{y}}} +\item \code{\link[=aes_group_order]{group}} +\item \code{weight} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } + \section{Computed variables}{ These are calculated by the 'stat' part of layers and can be accessed with \link[=aes_eval]{delayed evaluation}. @@ -135,6 +150,14 @@ These are calculated by the 'stat' part of layers and can be accessed with \link } } +\section{Dropped variables}{ + +\describe{ +\item{weight}{After calculation, weights of individual observations (if +supplied), are no longer available.} +} +} + \examples{ set.seed(1) df <- data.frame( @@ -151,4 +174,15 @@ ggplot(df, aes(x)) + # Multiple ECDFs ggplot(df, aes(x, colour = g)) + stat_ecdf() + +# Using weighted eCDF +weighted <- data.frame(x = 1:10, weights = c(1:5, 5:1)) +plain <- data.frame(x = rep(weighted$x, weighted$weights)) + +ggplot(plain, aes(x)) + + stat_ecdf(linewidth = 1) + + stat_ecdf( + aes(weight = weights), + data = weighted, colour = "green" + ) } diff --git a/tests/testthat/test-stat-ecdf.R b/tests/testthat/test-stat-ecdf.R index 6fd8297e18..399dfbebb0 100644 --- a/tests/testthat/test-stat-ecdf.R +++ b/tests/testthat/test-stat-ecdf.R @@ -15,6 +15,54 @@ test_that("stat_ecdf works in both directions", { expect_snapshot_error(ggplot_build(p)) }) +test_that("weighted ecdf computes sensible results", { + + set.seed(42) + x <- rpois(100, 5) + ux <- sort(unique0(x)) + + # Absent weights should be the same as the original + expect_equal( + ecdf(x)(ux), + wecdf(x, NULL)(ux) + ) + + # Uniform weights should be the same as the original + expect_equal( + ecdf(x)(ux), + wecdf(x, pi)(ux) + ) + + # Tabulated weights should be the same as the original + tab <- as.data.frame(table(x), stringsAsFactors = FALSE) + tab$x <- as.numeric(tab$x) + expect_equal( + ecdf(x)(ux), + wecdf(tab$x, tab$Freq)(ux) + ) +}) + +test_that("weighted ecdf warns about weird weights", { + + # Should warn when provided with illegal weights + expect_warning( + wecdf(1:10, c(NA, rep(1, 9))), + "does not support non-finite" + ) + + # Should warn when provided with near-0 weights + expect_warning( + wecdf(1:10, .Machine$double.eps), + "might be unstable" + ) + + # Should error when weights sum to 0 + expect_error( + wecdf(1:10, rep(c(-1, 1), 5)), + "Cannot compute eCDF" + ) +}) + # See #5113 and #5112 test_that("stat_ecdf responds to axis transformations", { n <- 4 From 1df93c43a255aec68a0c0ca102ab5e98c9bbce51 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:21:28 +0200 Subject: [PATCH 025/264] Weighted density (#5254) * Add weighted density computed variable * Add NEWS bullet * Fix typo --- NEWS.md | 2 ++ R/stat-density.R | 14 ++++++++++---- man/geom_density.Rd | 1 + tests/testthat/test-stat-density.R | 18 +++++++++++++----- 4 files changed, 26 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8a31cd598a..47e99f6589 100644 --- a/NEWS.md +++ b/NEWS.md @@ -29,6 +29,8 @@ * `scale_{x/y}_discrete()` can now accept a `sec.axis`. It is recommended to only use `dup_axis()` to set custom breaks or labels, as discrete variables cannot be transformed (@teunbrand, #3171). +* `stat_density()` has the new computed variable: `wdensity`, which is + calculated as the density times the sum of weights (@teunbrand, #4176). # ggplot2 3.5.1 diff --git a/R/stat-density.R b/R/stat-density.R index 4bf28f797b..1b84f2cdb4 100644 --- a/R/stat-density.R +++ b/R/stat-density.R @@ -24,6 +24,8 @@ #' @eval rd_computed_vars( #' density = "density estimate.", #' count = "density * number of points - useful for stacked density plots.", +#' wdensity = "density * sum of weights. In absence of weights, the same as +#' `count`.", #' scaled = "density estimate, scaled to maximum of 1.", #' n = "number of points.", #' ndensity = "alias for `scaled`, to mirror the syntax of [`stat_bin()`]." @@ -113,17 +115,19 @@ StatDensity <- ggproto("StatDensity", Stat, compute_density <- function(x, w, from, to, bw = "nrd0", adjust = 1, kernel = "gaussian", n = 512, bounds = c(-Inf, Inf)) { - nx <- length(x) + nx <- w_sum <- length(x) if (is.null(w)) { w <- rep(1 / nx, nx) } else { - w <- w / sum(w) + w_sum <- sum(w) + w <- w / w_sum } # Adjust data points and weights to all fit inside bounds sample_data <- fit_data_to_bounds(bounds, x, w) x <- sample_data$x w <- sample_data$w + w_sum <- sample_data$w_sum * w_sum nx <- length(x) # if less than 2 points return data frame of NAs and a warning @@ -135,6 +139,7 @@ compute_density <- function(x, w, from, to, bw = "nrd0", adjust = 1, scaled = NA_real_, ndensity = NA_real_, count = NA_real_, + wdensity = NA_real_, n = NA_integer_, .size = 1 )) @@ -158,6 +163,7 @@ compute_density <- function(x, w, from, to, bw = "nrd0", adjust = 1, scaled = dens$y / max(dens$y, na.rm = TRUE), ndensity = dens$y / max(dens$y, na.rm = TRUE), count = dens$y * nx, + wdensity = dens$y * w_sum, n = nx, .size = length(dens$x) ) @@ -166,7 +172,7 @@ compute_density <- function(x, w, from, to, bw = "nrd0", adjust = 1, # Check if all data points are inside bounds. If not, warn and remove them. fit_data_to_bounds <- function(bounds, x, w) { is_inside_bounds <- (bounds[1] <= x) & (x <= bounds[2]) - + w_sum <- 1 if (!all(is_inside_bounds)) { cli::cli_warn("Some data points are outside of `bounds`. Removing them.") x <- x[is_inside_bounds] @@ -177,7 +183,7 @@ fit_data_to_bounds <- function(bounds, x, w) { } } - return(list(x = x, w = w)) + return(list(x = x, w = w, w_sum = w_sum)) } # Update density estimation to mitigate boundary effect at known `bounds`: diff --git a/man/geom_density.Rd b/man/geom_density.Rd index cd119edcb3..26f2554e1c 100644 --- a/man/geom_density.Rd +++ b/man/geom_density.Rd @@ -188,6 +188,7 @@ These are calculated by the 'stat' part of layers and can be accessed with \link \itemize{ \item \code{after_stat(density)}\cr density estimate. \item \code{after_stat(count)}\cr density * number of points - useful for stacked density plots. +\item \code{after_stat(wdensity)}\cr density * sum of weights. In absence of weights, the same as \code{count} \item \code{after_stat(scaled)}\cr density estimate, scaled to maximum of 1. \item \code{after_stat(n)}\cr number of points. \item \code{after_stat(ndensity)}\cr alias for \code{scaled}, to mirror the syntax of \code{\link[=stat_bin]{stat_bin()}}. diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 677dfe5100..0274d83d40 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -17,13 +17,16 @@ test_that("stat_density actually computes density", { test_that("stat_density can make weighted density estimation", { df <- mtcars - df$weight <- mtcars$cyl / sum(mtcars$cyl) + df$weight <- mtcars$cyl - dens <- stats::density(df$mpg, weights = df$weight, bw = bw.nrd0(df$mpg)) + dens <- stats::density( + df$mpg, weights = df$weight / sum(df$weight), + bw = bw.nrd0(df$mpg) + ) expected_density_fun <- stats::approxfun(data.frame(x = dens$x, y = dens$y)) - plot <- ggplot(df, aes(mpg, weight = weight)) + stat_density() - actual_density_fun <- stats::approxfun(layer_data(plot)[, c("x", "y")]) + plot <- layer_data(ggplot(df, aes(mpg, weight = weight)) + stat_density()) + actual_density_fun <- stats::approxfun(plot[, c("x", "y")]) test_sample <- unique(df$mpg) expect_equal( @@ -31,6 +34,11 @@ test_that("stat_density can make weighted density estimation", { actual_density_fun(test_sample), tolerance = 1e-3 ) + + expect_equal( + plot$wdensity, + plot$density * sum(mtcars$cyl) + ) }) test_that("stat_density uses `bounds`", { @@ -115,7 +123,7 @@ test_that("compute_density returns useful df and throws warning when <2 values", expect_warning(dens <- compute_density(1, NULL, from = 0, to = 0)) expect_equal(nrow(dens), 1) - expect_equal(names(dens), c("x", "density", "scaled", "ndensity", "count", "n")) + expect_equal(names(dens), c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) expect_type(dens$x, "double") }) From 1654df1ec8b7aa1d2076b325486993f6b39fcde7 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:32:47 +0200 Subject: [PATCH 026/264] `geom_raster()` fallback for non-Cartesian coords (#5627) * fallback mechanism * add tests * add news bullet * put bullet in appropriate place --- NEWS.md | 2 + R/geom-raster.R | 9 ++- tests/testthat/_snaps/geom-raster.md | 7 -- .../_snaps/geom-raster/rectangle-fallback.svg | 78 +++++++++++++++++++ tests/testthat/test-geom-raster.R | 10 ++- 5 files changed, 96 insertions(+), 10 deletions(-) create mode 100644 tests/testthat/_snaps/geom-raster/rectangle-fallback.svg diff --git a/NEWS.md b/NEWS.md index 47e99f6589..a7fcf92b4a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_raster()` now falls back to rendering as `geom_rect()` when coordinates + are not Cartesian (#5503). * `stat_ecdf()` now has an optional `weight` aesthetic (@teunbrand, #5058). * Position scales combined with `coord_sf()` can now use functions in the `breaks` argument. In addition, `n.breaks` works as intended and diff --git a/R/geom-raster.R b/R/geom-raster.R index 2cd591d879..2d4ecd85d2 100644 --- a/R/geom-raster.R +++ b/R/geom-raster.R @@ -88,9 +88,14 @@ GeomRaster <- ggproto("GeomRaster", Geom, draw_panel = function(self, data, panel_params, coord, interpolate = FALSE, hjust = 0.5, vjust = 0.5) { if (!inherits(coord, "CoordCartesian")) { - cli::cli_abort(c( - "{.fn {snake_class(self)}} only works with {.fn coord_cartesian}." + cli::cli_inform(c( + "{.fn {snake_class(self)}} only works with {.fn coord_cartesian}.", + i = "Falling back to drawing as {.fn {snake_class(GeomRect)}}." )) + data$linewidth <- 0.3 # preventing anti-aliasing artefacts + data$colour <- data$fill + grob <- GeomRect$draw_panel(data, panel_params, coord) + return(grob) } # Convert vector of data to raster diff --git a/tests/testthat/_snaps/geom-raster.md b/tests/testthat/_snaps/geom-raster.md index 16da7d9d54..4deac92872 100644 --- a/tests/testthat/_snaps/geom-raster.md +++ b/tests/testthat/_snaps/geom-raster.md @@ -14,13 +14,6 @@ `vjust` must be a number, not the string "a". ---- - - Problem while converting geom to grob. - i Error occurred in the 1st layer. - Caused by error in `draw_panel()`: - ! `geom_raster()` only works with `coord_cartesian()`. - # geom_raster() fails with pattern fills Problem while converting geom to grob. diff --git a/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg b/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg new file mode 100644 index 0000000000..efb96b5c87 --- /dev/null +++ b/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1.0 +1.5 +2.0 +0.5/2.5 + + + +0.5 +1.0 +1.5 +2.0 +2.5 + + + + + +x +y + +fill + + + + + + + + +A +B +C +D +rectangle fallback + + diff --git a/tests/testthat/test-geom-raster.R b/tests/testthat/test-geom-raster.R index 2dfa1106e3..2a3ed66a31 100644 --- a/tests/testthat/test-geom-raster.R +++ b/tests/testthat/test-geom-raster.R @@ -6,7 +6,7 @@ test_that("geom_raster() checks input and coordinate system", { df <- data_frame(x = rep(c(-1, 1), each = 3), y = rep(-1:1, 2), z = 1:6) p <- ggplot(df, aes(x, y, fill = z)) + geom_raster() + coord_polar() - expect_snapshot_error(ggplotGrob(p)) + expect_message(ggplotGrob(p), "only works with") }) test_that("geom_raster() fails with pattern fills", { @@ -66,6 +66,14 @@ test_that("geom_raster draws correctly", { geom_point(colour = "red") ) + # In non-linear coordinates + df <- data.frame(x = c(1, 2, 1, 2), y = c(1, 1, 2, 2), fill = LETTERS[1:4]) + suppressMessages( + expect_doppelganger("rectangle fallback", + ggplot(df, aes(x, y, fill = fill)) + geom_raster() + coord_polar() + ) + ) + # Categorical fill, irregular swatches --------------------------------------- df <- expand.grid(x = 1:10, y = 1:10) From ea6b799ced36994e7e50770d9d56bb2ad2709e15 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:44:42 +0200 Subject: [PATCH 027/264] Add debugger (#5723) --- R/ggproto.R | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/R/ggproto.R b/R/ggproto.R index 48b1fcf96f..0af8a5a5ab 100644 --- a/R/ggproto.R +++ b/R/ggproto.R @@ -359,3 +359,38 @@ format.ggproto_method <- function(x, ...) { # proto2 TODO: better way of getting formals for self$draw ggproto_formals <- function(x) formals(environment(x)$f) + +#' Debug wrapper for ggproto methods +#' +#' @param method A ggproto method or function to debug. +#' @param debug One of the following: +#' * `"once"` for invoking `debugonce()` (default). +#' * `"always"` for invoking `debug()`. +#' * `"never"` for invoking `undebug()`. +#' @param ... Arguments passed to the function invoked by the `debug` argument. +#' +#' @return `NULL`, this function is called for its side-effects. +#' @noRd +#' +#' @examples +#' p <- ggplot(mpg, aes(displ, hwy)) + +#' geom_point() +#' +#' if (interactive()) { +#' ggproto_debug(GeomPoint$draw_panel) +#' } +#' +#' p +ggproto_debug <- function(method, debug = c("once", "always", "never"), ...) { + if (inherits(method, "ggproto_method")) { + method <- environment(method)$f + } + check_function(method) + switch( + arg_match0(debug, c("once", "always", "never")), + once = debugonce(method, ...), + always = debug(method, ...), + never = undebug(method, ...) + ) +} + From b3d5071badfd3a2ef6f09e0c9dfce2d6fcc7f884 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:54:43 +0200 Subject: [PATCH 028/264] New `spacing` and `margins` root theme elements (#5631) * add missing `calc_element()`s * declare new theme elements * rewire inheritance * Use theme for `legend.ticks.length` * fix bug * adapt theme_test() * temp * add visual tests * fix panel spacing in vignette * use `margin()` in vignette * reformat news bullet --- NEWS.md | 2 + R/facet-grid-.R | 10 +- R/facet-wrap.R | 9 +- R/guide-legend.R | 4 +- R/guides-.R | 2 +- R/plot-build.R | 8 +- R/theme-defaults.R | 55 ++++++----- R/theme-elements.R | 25 ++--- R/theme.R | 34 ++++--- man/geom_density.Rd | 2 +- man/theme.Rd | 37 ++++--- tests/testthat/_snaps/theme/large-margins.svg | 96 +++++++++++++++++++ tests/testthat/_snaps/theme/large-spacing.svg | 96 +++++++++++++++++++ tests/testthat/test-theme.R | 13 +++ vignettes/articles/faq-axes.Rmd | 4 +- vignettes/extending-ggplot2.Rmd | 18 +--- 16 files changed, 316 insertions(+), 99 deletions(-) create mode 100644 tests/testthat/_snaps/theme/large-margins.svg create mode 100644 tests/testthat/_snaps/theme/large-spacing.svg diff --git a/NEWS.md b/NEWS.md index a7fcf92b4a..ad02761703 100644 --- a/NEWS.md +++ b/NEWS.md @@ -33,6 +33,8 @@ cannot be transformed (@teunbrand, #3171). * `stat_density()` has the new computed variable: `wdensity`, which is calculated as the density times the sum of weights (@teunbrand, #4176). +* `theme()` gets new `spacing` and `margins` arguments that all other spacings + and (non-text) margins inherit from (@teunbrand, #5622). # ggplot2 3.5.1 diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 54c4b8f971..0854b5299b 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -412,10 +412,10 @@ FacetGrid <- ggproto("FacetGrid", Facet, panel_widths, panel_heights, respect = respect, clip = coord$clip, z = mtx(1)) panel_table$layout$name <- paste0('panel-', rep(seq_len(nrow), ncol), '-', rep(seq_len(ncol), each = nrow)) - panel_table <- gtable_add_col_space(panel_table, - theme$panel.spacing.x %||% theme$panel.spacing) - panel_table <- gtable_add_row_space(panel_table, - theme$panel.spacing.y %||% theme$panel.spacing) + spacing_x <- calc_element("panel.spacing.x", theme) + spacing_y <- calc_element("panel.spacing.y", theme) + panel_table <- gtable_add_col_space(panel_table, spacing_x) + panel_table <- gtable_add_row_space(panel_table, spacing_y) # Add axes if (params$draw_axes$x) { @@ -445,7 +445,7 @@ FacetGrid <- ggproto("FacetGrid", Facet, switch_y <- !is.null(params$switch) && params$switch %in% c("both", "y") inside_x <- (theme$strip.placement.x %||% theme$strip.placement %||% "inside") == "inside" inside_y <- (theme$strip.placement.y %||% theme$strip.placement %||% "inside") == "inside" - strip_padding <- convertUnit(theme$strip.switch.pad.grid, "cm") + strip_padding <- convertUnit(calc_element("strip.switch.pad.grid", theme), "cm") panel_pos_col <- panel_cols(panel_table) if (switch_x) { if (!is.null(strips$x$bottom)) { diff --git a/R/facet-wrap.R b/R/facet-wrap.R index f69cdd8f95..720e2e8e37 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -325,10 +325,9 @@ FacetWrap <- ggproto("FacetWrap", Facet, heights = unit(rep(abs(aspect_ratio), nrow), "null"), respect = respect, clip = coord$clip, z = matrix(1, ncol = ncol, nrow = nrow)) panel_table$layout$name <- paste0('panel-', rep(seq_len(ncol), nrow), '-', rep(seq_len(nrow), each = ncol)) - panel_table <- gtable_add_col_space(panel_table, - theme$panel.spacing.x %||% theme$panel.spacing) - panel_table <- gtable_add_row_space(panel_table, - theme$panel.spacing.y %||% theme$panel.spacing) + + panel_table <- gtable_add_col_space(panel_table, calc_element("panel.spacing.x", theme)) + panel_table <- gtable_add_row_space(panel_table, calc_element("panel.spacing.y", theme)) # Add axes axis_mat_x_top <- empty_table @@ -442,7 +441,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, axis_size <- panel_table$sizes panel_table <- panel_table$panels - strip_padding <- convertUnit(theme$strip.switch.pad.wrap, "cm") + strip_padding <- convertUnit(calc_element("strip.switch.pad.wrap", theme), "cm") strip_name <- paste0("strip-", substr(params$strip.position, 1, 1)) strip_mat <- empty_table strip_mat[panel_pos] <- unlist(unname(strips), recursive = FALSE)[[params$strip.position]] diff --git a/R/guide-legend.R b/R/guide-legend.R index c685cdd8c7..157018dc48 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -313,8 +313,8 @@ GuideLegend <- ggproto( arg_match0(title_position, .trbl, arg_nm = "legend.title.position") # Set default spacing - theme$legend.key.spacing <- theme$legend.key.spacing %||% unit(5.5, "pt") - gap <- calc_element("legend.key.spacing", theme) + theme$legend.key.spacing <- calc_element("legend.key.spacing", theme) + gap <- theme$legend.key.spacing # For backward compatibility, default vertical spacing is no spacing if (params$direction == "vertical") { diff --git a/R/guides-.R b/R/guides-.R index 2280c40def..8a0117dc75 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -608,7 +608,7 @@ Guides <- ggproto( box_xjust <- box_just[1] box_yjust <- box_just[2] - margin <- theme$legend.box.margin %||% margin() + margin <- calc_element("legend.box.margin", theme) %||% margin() # setting that is different for vertical and horizontal guide-boxes. if (identical(theme$legend.box, "horizontal")) { diff --git a/R/plot-build.R b/R/plot-build.R index d53f16ba85..55c419d1e9 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -261,10 +261,8 @@ ggplot_gtable.ggplot_built <- function(data) { plot_table <- table_add_tag(plot_table, plot$labels$tag, theme) # Margins - plot_table <- gtable_add_rows(plot_table, theme$plot.margin[1], pos = 0) - plot_table <- gtable_add_cols(plot_table, theme$plot.margin[2]) - plot_table <- gtable_add_rows(plot_table, theme$plot.margin[3]) - plot_table <- gtable_add_cols(plot_table, theme$plot.margin[4], pos = 0) + plot_margin <- calc_element("plot.margin", theme) + plot_table <- gtable_add_padding(plot_table, plot_margin) if (inherits(theme$plot.background, "element")) { plot_table <- gtable_add_grob(plot_table, @@ -443,7 +441,7 @@ table_add_legends <- function(table, legends, theme) { empty <- vapply(legends, is.zero, logical(1)) widths[!empty] <- lapply(legends[!empty], gtable_width) heights[!empty] <- lapply(legends[!empty], gtable_height) - spacing <- theme$legend.box.spacing %||% unit(0.2, "cm") + spacing <- calc_element("legend.box.spacing", theme) %||% unit(0.2, "cm") # If legend is missing, set spacing to zero for that legend zero <- unit(0, "pt") diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 05260557e9..2066679533 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -133,6 +133,8 @@ theme_grey <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + spacing = unit(half_line, "pt"), + margins = margin(half_line, half_line, half_line, half_line), axis.line = element_blank(), axis.line.x = NULL, @@ -145,7 +147,7 @@ theme_grey <- function(base_size = 11, base_family = "", axis.text.r = element_text(margin = margin(l = 0.8 * half_line / 2, r = 0.8 * half_line / 2), hjust = 0.5), axis.ticks = element_line(colour = "grey20"), - axis.ticks.length = unit(half_line / 2, "pt"), + axis.ticks.length = rel(0.5), axis.ticks.length.x = NULL, axis.ticks.length.x.top = NULL, axis.ticks.length.x.bottom = NULL, @@ -173,15 +175,15 @@ theme_grey <- function(base_size = 11, base_family = "", ), legend.background = element_rect(colour = NA), - legend.spacing = unit(2 * half_line, "pt"), + legend.spacing = rel(2), legend.spacing.x = NULL, legend.spacing.y = NULL, - legend.margin = margin(half_line, half_line, half_line, half_line), + legend.margin = NULL, legend.key = NULL, legend.key.size = unit(1.2, "lines"), legend.key.height = NULL, legend.key.width = NULL, - legend.key.spacing = unit(half_line, "pt"), + legend.key.spacing = NULL, legend.text = element_text(size = rel(0.8)), legend.title = element_text(hjust = 0), legend.ticks.length = rel(0.2), @@ -189,15 +191,15 @@ theme_grey <- function(base_size = 11, base_family = "", legend.direction = NULL, legend.justification = "center", legend.box = NULL, - legend.box.margin = margin(0, 0, 0, 0, "cm"), + legend.box.margin = rel(0), legend.box.background = element_blank(), - legend.box.spacing = unit(2 * half_line, "pt"), + legend.box.spacing = rel(2), panel.background = element_rect(fill = "grey92", colour = NA), panel.border = element_blank(), panel.grid = element_line(colour = "white"), panel.grid.minor = element_line(linewidth = rel(0.5)), - panel.spacing = unit(half_line, "pt"), + panel.spacing = NULL, panel.spacing.x = NULL, panel.spacing.y = NULL, panel.ontop = FALSE, @@ -240,7 +242,7 @@ theme_grey <- function(base_size = 11, base_family = "", hjust = 0.5, vjust = 0.5 ), plot.tag.position = 'topleft', - plot.margin = margin(half_line, half_line, half_line, half_line), + plot.margin = NULL, complete = TRUE ) @@ -466,30 +468,35 @@ theme_void <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + spacing = unit(half_line, "pt"), + margins = margin(half_line, half_line, half_line, half_line), axis.text = element_blank(), axis.title = element_blank(), - axis.ticks.length = unit(0, "pt"), + axis.ticks.length = rel(0), axis.ticks.length.x = NULL, axis.ticks.length.x.top = NULL, axis.ticks.length.x.bottom = NULL, axis.ticks.length.y = NULL, axis.ticks.length.y.left = NULL, axis.ticks.length.y.right = NULL, - axis.minor.ticks.length = unit(0, "pt"), + axis.minor.ticks.length = NULL, legend.box = NULL, legend.key.size = unit(1.2, "lines"), legend.position = "right", legend.text = element_text(size = rel(0.8)), legend.title = element_text(hjust = 0), - legend.key.spacing = unit(half_line, "pt"), + legend.key.spacing = rel(1), + legend.margin = rel(0), + legend.box.margin = rel(0), + legend.box.spacing = unit(0.2, "cm"), legend.ticks.length = rel(0.2), strip.clip = "inherit", strip.text = element_text(size = rel(0.8)), - strip.switch.pad.grid = unit(half_line / 2, "pt"), - strip.switch.pad.wrap = unit(half_line / 2, "pt"), + strip.switch.pad.grid = rel(0.5), + strip.switch.pad.wrap = rel(0.5), panel.ontop = FALSE, - panel.spacing = unit(half_line, "pt"), - plot.margin = unit(c(0, 0, 0, 0), "lines"), + panel.spacing = NULL, + plot.margin = rel(0), plot.title = element_text( size = rel(1.2), hjust = 0, vjust = 1, @@ -542,6 +549,8 @@ theme_test <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + spacing = unit(half_line, "pt"), + margins = margin(half_line, half_line, half_line, half_line), axis.line = element_blank(), axis.line.x = NULL, @@ -552,7 +561,7 @@ theme_test <- function(base_size = 11, base_family = "", axis.text.y = element_text(margin = margin(r = 0.8 * half_line / 2), hjust = 1), axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line / 2), hjust = 0), axis.ticks = element_line(colour = "grey20"), - axis.ticks.length = unit(half_line / 2, "pt"), + axis.ticks.length = rel(0.5), axis.ticks.length.x = NULL, axis.ticks.length.x.top = NULL, axis.ticks.length.x.bottom = NULL, @@ -580,7 +589,7 @@ theme_test <- function(base_size = 11, base_family = "", ), legend.background = element_rect(colour = NA), - legend.spacing = unit(2 * half_line, "pt"), + legend.spacing = rel(2), legend.spacing.x = NULL, legend.spacing.y = NULL, legend.margin = margin(0, 0, 0, 0, "cm"), @@ -588,7 +597,7 @@ theme_test <- function(base_size = 11, base_family = "", legend.key.size = unit(1.2, "lines"), legend.key.height = NULL, legend.key.width = NULL, - legend.key.spacing = unit(half_line, "pt"), + legend.key.spacing = NULL, legend.key.spacing.x = NULL, legend.key.spacing.y = NULL, legend.text = element_text(size = rel(0.8)), @@ -600,13 +609,13 @@ theme_test <- function(base_size = 11, base_family = "", legend.box = NULL, legend.box.margin = margin(0, 0, 0, 0, "cm"), legend.box.background = element_blank(), - legend.box.spacing = unit(2 * half_line, "pt"), + legend.box.spacing = rel(2), panel.background = element_rect(fill = "white", colour = NA), panel.border = element_rect(fill = NA, colour = "grey20"), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), - panel.spacing = unit(half_line, "pt"), + panel.spacing = NULL, panel.spacing.x = NULL, panel.spacing.y = NULL, panel.ontop = FALSE, @@ -624,8 +633,8 @@ theme_test <- function(base_size = 11, base_family = "", strip.placement = "inside", strip.placement.x = NULL, strip.placement.y = NULL, - strip.switch.pad.grid = unit(half_line / 2, "pt"), - strip.switch.pad.wrap = unit(half_line / 2, "pt"), + strip.switch.pad.grid = rel(0.5), + strip.switch.pad.wrap = rel(0.5), plot.background = element_rect(colour = "white"), plot.title = element_text( @@ -649,7 +658,7 @@ theme_test <- function(base_size = 11, base_family = "", hjust = 0.5, vjust = 0.5 ), plot.tag.position = 'topleft', - plot.margin = margin(half_line, half_line, half_line, half_line), + plot.margin = NULL, complete = TRUE ) diff --git a/R/theme-elements.R b/R/theme-elements.R index 41b989df7e..23bf79bd6e 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -419,11 +419,14 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { rect = el_def("element_rect"), text = el_def("element_text"), title = el_def("element_text", "text"), + spacing = el_def("unit"), + margins = el_def("margin"), + axis.line = el_def("element_line", "line"), axis.text = el_def("element_text", "text"), axis.title = el_def("element_text", "title"), axis.ticks = el_def("element_line", "line"), - legend.key.size = el_def("unit"), + legend.key.size = el_def(c("unit", "rel"), "spacing"), panel.grid = el_def("element_line", "line"), panel.grid.major = el_def("element_line", "panel.grid"), panel.grid.minor = el_def("element_line", "panel.grid"), @@ -447,7 +450,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { axis.text.theta = el_def("element_text", "axis.text.x"), axis.text.r = el_def("element_text", "axis.text.y"), - axis.ticks.length = el_def("unit"), + axis.ticks.length = el_def(c("unit", "rel"), "spacing"), axis.ticks.length.x = el_def(c("unit", "rel"), "axis.ticks.length"), axis.ticks.length.x.top = el_def(c("unit", "rel"), "axis.ticks.length.x"), axis.ticks.length.x.bottom = el_def(c("unit", "rel"), "axis.ticks.length.x"), @@ -503,14 +506,14 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { ), legend.background = el_def("element_rect", "rect"), - legend.margin = el_def("margin"), - legend.spacing = el_def("unit"), + legend.margin = el_def(c("margin", "rel"), "margins"), + legend.spacing = el_def(c("unit", "rel"), "spacing"), legend.spacing.x = el_def(c("unit", "rel"), "legend.spacing"), legend.spacing.y = el_def(c("unit", "rel"), "legend.spacing"), legend.key = el_def("element_rect", "panel.background"), legend.key.height = el_def(c("unit", "rel"), "legend.key.size"), legend.key.width = el_def(c("unit", "rel"), "legend.key.size"), - legend.key.spacing = el_def("unit"), + legend.key.spacing = el_def(c("unit", "rel"), "spacing"), legend.key.spacing.x = el_def(c("unit", "rel"), "legend.key.spacing"), legend.key.spacing.y = el_def(c("unit", "rel"), "legend.key.spacing"), legend.frame = el_def("element_rect", "rect"), @@ -552,13 +555,13 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { legend.box = el_def("character"), legend.box.just = el_def("character"), - legend.box.margin = el_def("margin"), + legend.box.margin = el_def(c("margin", "rel"), "margins"), legend.box.background = el_def("element_rect", "rect"), - legend.box.spacing = el_def("unit"), + legend.box.spacing = el_def(c("unit", "rel"), "spacing"), panel.background = el_def("element_rect", "rect"), panel.border = el_def("element_rect", "rect"), - panel.spacing = el_def("unit"), + panel.spacing = el_def(c("unit", "rel"), "spacing"), panel.spacing.x = el_def(c("unit", "rel"), "panel.spacing"), panel.spacing.y = el_def(c("unit", "rel"), "panel.spacing"), panel.grid.major.x = el_def("element_line", "panel.grid.major"), @@ -580,8 +583,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { strip.placement = el_def("character"), strip.placement.x = el_def("character", "strip.placement"), strip.placement.y = el_def("character", "strip.placement"), - strip.switch.pad.grid = el_def("unit"), - strip.switch.pad.wrap = el_def("unit"), + strip.switch.pad.grid = el_def(c("unit", "rel"), "spacing"), + strip.switch.pad.wrap = el_def(c("unit", "rel"), "spacing"), plot.background = el_def("element_rect", "rect"), plot.title = el_def("element_text", "title"), @@ -592,7 +595,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { plot.tag = el_def("element_text", "title"), plot.tag.position = el_def(c("character", "numeric", "integer")), # Need to also accept numbers plot.tag.location = el_def("character"), - plot.margin = el_def("margin"), + plot.margin = el_def(c("margin", "rel"), "margins"), aspect.ratio = el_def(c("numeric", "integer")) ) diff --git a/R/theme.R b/R/theme.R index 3611af323e..f03d2a67ef 100644 --- a/R/theme.R +++ b/R/theme.R @@ -25,6 +25,8 @@ #' @param text all text elements ([element_text()]) #' @param title all title elements: plot, axes, legends ([element_text()]; #' inherits from `text`) +#' @param spacing all spacings ([`unit()`][grid::unit]) +#' @param margins all margins ([margin()]) #' @param aspect.ratio aspect ratio of the panel #' #' @param axis.title,axis.title.x,axis.title.y,axis.title.x.top,axis.title.x.bottom,axis.title.y.left,axis.title.y.right @@ -52,7 +54,7 @@ #' minor tick marks along axes ([element_line()]). `axis.minor.ticks.*.*` #' inherit from the corresponding major ticks `axis.ticks.*.*`. #' @param axis.ticks.length,axis.ticks.length.x,axis.ticks.length.x.top,axis.ticks.length.x.bottom,axis.ticks.length.y,axis.ticks.length.y.left,axis.ticks.length.y.right,axis.ticks.length.theta,axis.ticks.length.r -#' length of tick marks (`unit`) +#' length of tick marks (`unit`). `axis.ticks.length` inherits from `spacing`. #' @param axis.minor.ticks.length,axis.minor.ticks.length.x,axis.minor.ticks.length.x.top,axis.minor.ticks.length.x.bottom,axis.minor.ticks.length.y,axis.minor.ticks.length.y.left,axis.minor.ticks.length.y.right,axis.minor.ticks.length.theta,axis.minor.ticks.length.r #' length of minor tick marks (`unit`), or relative to `axis.ticks.length` when provided with `rel()`. #' @param axis.line,axis.line.x,axis.line.x.top,axis.line.x.bottom,axis.line.y,axis.line.y.left,axis.line.y.right,axis.line.theta,axis.line.r @@ -65,22 +67,26 @@ #' #' @param legend.background background of legend ([element_rect()]; inherits #' from `rect`) -#' @param legend.margin the margin around each legend ([margin()]) +#' @param legend.margin the margin around each legend ([margin()]); inherits +#' from `margins`. #' @param legend.spacing,legend.spacing.x,legend.spacing.y #' the spacing between legends (`unit`). `legend.spacing.x` & `legend.spacing.y` -#' inherit from `legend.spacing` or can be specified separately +#' inherit from `legend.spacing` or can be specified separately. +#' `legend.spacing` inherits from `spacing`. #' @param legend.key background underneath legend keys ([element_rect()]; #' inherits from `rect`) #' @param legend.key.size,legend.key.height,legend.key.width #' size of legend keys (`unit`); key background height & width inherit from -#' `legend.key.size` or can be specified separately +#' `legend.key.size` or can be specified separately. In turn `legend.key.size` +#' inherits from `spacing`. #' @param legend.key.spacing,legend.key.spacing.x,legend.key.spacing.y spacing #' between legend keys given as a `unit`. Spacing in the horizontal (x) and #' vertical (y) direction inherit from `legend.key.spacing` or can be -#' specified separately. +#' specified separately. `legend.key.spacing` inherits from `spacing`. #' @param legend.frame frame drawn around the bar ([element_rect()]). #' @param legend.ticks tick marks shown along bars or axes ([element_line()]) -#' @param legend.ticks.length length of tick marks in legend (`unit`) +#' @param legend.ticks.length length of tick marks in legend +#' ([`unit()`][grid::unit]); inherits from `legend.key.size`. #' @param legend.axis.line lines along axes in legends ([element_line()]) #' @param legend.text legend item labels ([element_text()]; inherits from #' `text`) @@ -113,11 +119,11 @@ #' bounding box, when there are multiple legends ("top", "bottom", "left", or #' "right") #' @param legend.box.margin margins around the full legend area, as specified -#' using [margin()] +#' using [margin()]; inherits from `margins`. #' @param legend.box.background background of legend area ([element_rect()]; #' inherits from `rect`) #' @param legend.box.spacing The spacing between the plotting area and the -#' legend box (`unit`) +#' legend box (`unit`); inherits from `spacing`. #' #' @param panel.background background of plotting area, drawn underneath plot #' ([element_rect()]; inherits from `rect`) @@ -127,7 +133,7 @@ #' ([element_rect()]; inherits from `rect`) #' @param panel.spacing,panel.spacing.x,panel.spacing.y spacing between facet #' panels (`unit`). `panel.spacing.x` & `panel.spacing.y` inherit from `panel.spacing` -#' or can be specified separately. +#' or can be specified separately. `panel.spacing` inherits from `spacing`. #' @param panel.grid,panel.grid.major,panel.grid.minor,panel.grid.major.x,panel.grid.major.y,panel.grid.minor.x,panel.grid.minor.y #' grid lines ([element_line()]). Specify major grid lines, #' or minor grid lines separately (using `panel.grid.major` or `panel.grid.minor`) @@ -166,7 +172,7 @@ #' set the x,y-coordinate relative to the whole plot. The coordinate option #' is unavailable for `plot.tag.location = "margin"`. #' @param plot.margin margin around entire plot (`unit` with the sizes of -#' the top, right, bottom, and left margins) +#' the top, right, bottom, and left margins); inherits from `margin`. #' #' @param strip.background,strip.background.x,strip.background.y #' background of facet labels ([element_rect()]; @@ -188,10 +194,8 @@ #' that inherit from `strip.text.x` and `strip.text.y`, respectively. #' As a consequence, some theme stylings need to be applied to #' the position-dependent elements rather than to the parent elements -#' @param strip.switch.pad.grid space between strips and axes when strips are -#' switched (`unit`) -#' @param strip.switch.pad.wrap space between strips and axes when strips are -#' switched (`unit`) +#' @param strip.switch.pad.grid,strip.switch.pad.wrap space between strips and +#' axes when strips are switched (`unit`); inherits from `spacing`. #' #' @param ... additional element specifications not part of base ggplot2. In general, #' these should also be defined in the `element tree` argument. [Splicing][rlang::splice] a list is also supported. @@ -311,6 +315,8 @@ theme <- function(..., rect, text, title, + spacing, + margins, aspect.ratio, axis.title, axis.title.x, diff --git a/man/geom_density.Rd b/man/geom_density.Rd index 26f2554e1c..86bf57d6e9 100644 --- a/man/geom_density.Rd +++ b/man/geom_density.Rd @@ -188,7 +188,7 @@ These are calculated by the 'stat' part of layers and can be accessed with \link \itemize{ \item \code{after_stat(density)}\cr density estimate. \item \code{after_stat(count)}\cr density * number of points - useful for stacked density plots. -\item \code{after_stat(wdensity)}\cr density * sum of weights. In absence of weights, the same as \code{count} +\item \code{after_stat(wdensity)}\cr density * sum of weights. In absence of weights, the same as \code{count}. \item \code{after_stat(scaled)}\cr density estimate, scaled to maximum of 1. \item \code{after_stat(n)}\cr number of points. \item \code{after_stat(ndensity)}\cr alias for \code{scaled}, to mirror the syntax of \code{\link[=stat_bin]{stat_bin()}}. diff --git a/man/theme.Rd b/man/theme.Rd index 5d51fd8643..13a88a2e2a 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -10,6 +10,8 @@ theme( rect, text, title, + spacing, + margins, aspect.ratio, axis.title, axis.title.x, @@ -159,6 +161,10 @@ these should also be defined in the \verb{element tree} argument. \link[rlang:sp \item{title}{all title elements: plot, axes, legends (\code{\link[=element_text]{element_text()}}; inherits from \code{text})} +\item{spacing}{all spacings (\code{\link[grid:unit]{unit()}})} + +\item{margins}{all margins (\code{\link[=margin]{margin()}})} + \item{aspect.ratio}{aspect ratio of the panel} \item{axis.title, axis.title.x, axis.title.y, axis.title.x.top, axis.title.x.bottom, axis.title.y.left, axis.title.y.right}{labels of axes (\code{\link[=element_text]{element_text()}}). Specify all axes' labels (\code{axis.title}), @@ -185,7 +191,7 @@ from \code{line}} \item{axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r, }{minor tick marks along axes (\code{\link[=element_line]{element_line()}}). \verb{axis.minor.ticks.*.*} inherit from the corresponding major ticks \verb{axis.ticks.*.*}.} -\item{axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r}{length of tick marks (\code{unit})} +\item{axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r}{length of tick marks (\code{unit}). \code{axis.ticks.length} inherits from \code{spacing}.} \item{axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r}{length of minor tick marks (\code{unit}), or relative to \code{axis.ticks.length} when provided with \code{rel()}.} @@ -199,27 +205,31 @@ from \code{line}} \item{legend.background}{background of legend (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect})} -\item{legend.margin}{the margin around each legend (\code{\link[=margin]{margin()}})} +\item{legend.margin}{the margin around each legend (\code{\link[=margin]{margin()}}); inherits +from \code{margins}.} \item{legend.spacing, legend.spacing.x, legend.spacing.y}{the spacing between legends (\code{unit}). \code{legend.spacing.x} & \code{legend.spacing.y} -inherit from \code{legend.spacing} or can be specified separately} +inherit from \code{legend.spacing} or can be specified separately. +\code{legend.spacing} inherits from \code{spacing}.} \item{legend.key}{background underneath legend keys (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect})} \item{legend.key.size, legend.key.height, legend.key.width}{size of legend keys (\code{unit}); key background height & width inherit from -\code{legend.key.size} or can be specified separately} +\code{legend.key.size} or can be specified separately. In turn \code{legend.key.size} +inherits from \code{spacing}.} \item{legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y}{spacing between legend keys given as a \code{unit}. Spacing in the horizontal (x) and vertical (y) direction inherit from \code{legend.key.spacing} or can be -specified separately.} +specified separately. \code{legend.key.spacing} inherits from \code{spacing}.} \item{legend.frame}{frame drawn around the bar (\code{\link[=element_rect]{element_rect()}}).} \item{legend.ticks}{tick marks shown along bars or axes (\code{\link[=element_line]{element_line()}})} -\item{legend.ticks.length}{length of tick marks in legend (\code{unit})} +\item{legend.ticks.length}{length of tick marks in legend +(\code{\link[grid:unit]{unit()}}); inherits from \code{legend.key.size}.} \item{legend.axis.line}{lines along axes in legends (\code{\link[=element_line]{element_line()}})} @@ -266,13 +276,13 @@ bounding box, when there are multiple legends ("top", "bottom", "left", or "right")} \item{legend.box.margin}{margins around the full legend area, as specified -using \code{\link[=margin]{margin()}}} +using \code{\link[=margin]{margin()}}; inherits from \code{margins}.} \item{legend.box.background}{background of legend area (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect})} \item{legend.box.spacing}{The spacing between the plotting area and the -legend box (\code{unit})} +legend box (\code{unit}); inherits from \code{spacing}.} \item{panel.background}{background of plotting area, drawn underneath plot (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect})} @@ -284,7 +294,7 @@ it covers tick marks and grid lines. This should be used with \item{panel.spacing, panel.spacing.x, panel.spacing.y}{spacing between facet panels (\code{unit}). \code{panel.spacing.x} & \code{panel.spacing.y} inherit from \code{panel.spacing} -or can be specified separately.} +or can be specified separately. \code{panel.spacing} inherits from \code{spacing}.} \item{panel.grid, panel.grid.major, panel.grid.minor, panel.grid.major.x, panel.grid.major.y, panel.grid.minor.x, panel.grid.minor.y}{grid lines (\code{\link[=element_line]{element_line()}}). Specify major grid lines, or minor grid lines separately (using \code{panel.grid.major} or \code{panel.grid.minor}) @@ -332,7 +342,7 @@ inside the panel space, anywhere in the plot as a whole, or in the margin around the panel space.} \item{plot.margin}{margin around entire plot (\code{unit} with the sizes of -the top, right, bottom, and left margins)} +the top, right, bottom, and left margins); inherits from \code{margin}.} \item{strip.background, strip.background.x, strip.background.y}{background of facet labels (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect}). Horizontal facet background (\code{strip.background.x}) @@ -356,11 +366,8 @@ that inherit from \code{strip.text.x} and \code{strip.text.y}, respectively. As a consequence, some theme stylings need to be applied to the position-dependent elements rather than to the parent elements} -\item{strip.switch.pad.grid}{space between strips and axes when strips are -switched (\code{unit})} - -\item{strip.switch.pad.wrap}{space between strips and axes when strips are -switched (\code{unit})} +\item{strip.switch.pad.grid, strip.switch.pad.wrap}{space between strips and +axes when strips are switched (\code{unit}); inherits from \code{spacing}.} \item{complete}{set this to \code{TRUE} if this is a complete theme, such as the one returned by \code{\link[=theme_grey]{theme_grey()}}. Complete themes behave diff --git a/tests/testthat/_snaps/theme/large-margins.svg b/tests/testthat/_snaps/theme/large-margins.svg new file mode 100644 index 0000000000..1e4bfb10db --- /dev/null +++ b/tests/testthat/_snaps/theme/large-margins.svg @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1 + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + +x +y + +z + + + + +a +b +large margins + + diff --git a/tests/testthat/_snaps/theme/large-spacing.svg b/tests/testthat/_snaps/theme/large-spacing.svg new file mode 100644 index 0000000000..1680934c61 --- /dev/null +++ b/tests/testthat/_snaps/theme/large-spacing.svg @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1 + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + +x +y + +z + + + + +a +b +large spacing + + diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 895d4cf9fc..1200a56d99 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -649,6 +649,19 @@ test_that("themes look decent at larger base sizes", { expect_doppelganger("theme_linedraw_large", plot + theme_linedraw(base_size = 33)) }) +test_that("setting 'spacing' and 'margins' affect the whole plot", { + + df <- data_frame(x = 1:3, y = 1:3, z = c("a", "b", "a"), a = 1) + plot <- ggplot(df, aes(x, y, colour = z)) + + geom_point() + + facet_wrap(~ a) + + theme_gray() + + expect_doppelganger("large spacing", plot + theme(spacing = unit(1, "cm"))) + expect_doppelganger("large margins", plot + theme(margins = margin(1, 1, 1, 1, "cm"))) + +}) + test_that("axes can be styled independently", { plot <- ggplot() + geom_point(aes(1:10, 1:10)) + diff --git a/vignettes/articles/faq-axes.Rmd b/vignettes/articles/faq-axes.Rmd index 6a9ed45521..f9868cdf8e 100644 --- a/vignettes/articles/faq-axes.Rmd +++ b/vignettes/articles/faq-axes.Rmd @@ -193,7 +193,7 @@ ggplot(sales, aes(x = interaction(quarter, year), y = value, group = 1)) + geom_line() + coord_cartesian(ylim = c(9, 32), expand = FALSE, clip = "off") + theme( - plot.margin = unit(c(1, 1, 3, 1), "lines"), + plot.margin = margin(1, 1, 3, 1, "lines"), axis.title.x = element_blank(), axis.text.x = element_blank() ) + @@ -215,7 +215,7 @@ ggplot(sales, aes(x = interaction(quarter, year), y = value)) + annotate(geom = "text", x = seq_len(nrow(sales)), y = -1, label = sales$quarter, size = 3) + annotate(geom = "text", x = c(2.5, 6.5), y = -3, label = unique(sales$year), size = 4) + theme( - plot.margin = unit(c(1, 1, 3, 1), "lines"), + plot.margin = margin(1, 1, 3, 1, "lines"), axis.title.x = element_blank(), axis.text.x = element_blank() ) diff --git a/vignettes/extending-ggplot2.Rmd b/vignettes/extending-ggplot2.Rmd index 01383378bc..6ee65ae718 100644 --- a/vignettes/extending-ggplot2.Rmd +++ b/vignettes/extending-ggplot2.Rmd @@ -724,11 +724,7 @@ render <- function(panels, layout, x_scales, y_scales, ranges, coord, data, panel_table <- gtable::gtable_matrix("layout", panels, widths = unit(c(1, 1), "null"), heights = unit(1, "null"), clip = "on") # Add spacing according to theme - panel_spacing <- if (is.null(theme$panel.spacing.x)) { - theme$panel.spacing - } else { - theme$panel.spacing.x - } + panel_spacing <- calc_element("panel.spacing.x", theme) panel_table <- gtable::gtable_add_col_space(panel_table, panel_spacing) } else { panels <- matrix(panels, ncol = 1) @@ -909,21 +905,13 @@ FacetTrans <- ggproto("FacetTrans", Facet, panel_table <- gtable::gtable_matrix("layout", panels, widths = unit(c(1, 1), "null"), heights = unit(1, "null"), clip = "on") # Add spacing according to theme - panel_spacing <- if (is.null(theme$panel.spacing.x)) { - theme$panel.spacing - } else { - theme$panel.spacing.x - } + panel_spacing <- calc_element("panel.spacing.x", theme) panel_table <- gtable::gtable_add_col_space(panel_table, panel_spacing) } else { panels <- matrix(panels, ncol = 1) panel_table <- gtable::gtable_matrix("layout", panels, widths = unit(1, "null"), heights = unit(c(1, 1), "null"), clip = "on") - panel_spacing <- if (is.null(theme$panel.spacing.y)) { - theme$panel.spacing - } else { - theme$panel.spacing.y - } + panel_spacing <- calc_element("panel.spacing.y", theme) panel_table <- gtable::gtable_add_row_space(panel_table, panel_spacing) } # Name panel grobs so they can be found later From e22cff2c20af8c47d22c526d206cc52f010aef75 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 11:57:29 +0200 Subject: [PATCH 029/264] Avoid bounded density discontinuity (#5642) * widen range of unbounded estimation * increase test tolerance * add news bullet * move bullet --- NEWS.md | 2 ++ R/stat-density.R | 19 ++++++++++++++++--- tests/testthat/test-stat-density.R | 4 ++-- 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index ad02761703..a8c8dd0867 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* The bounded density option in `stat_density()` uses a wider range to + prevent discontinuities (#5641). * `geom_raster()` now falls back to rendering as `geom_rect()` when coordinates are not Cartesian (#5503). * `stat_ecdf()` now has an optional `weight` aesthetic (@teunbrand, #5058). diff --git a/R/stat-density.R b/R/stat-density.R index 1b84f2cdb4..27cafd4b6d 100644 --- a/R/stat-density.R +++ b/R/stat-density.R @@ -148,10 +148,23 @@ compute_density <- function(x, w, from, to, bw = "nrd0", adjust = 1, bw <- precompute_bw(x, bw) # Decide whether to use boundary correction if (any(is.finite(bounds))) { - dens <- stats::density(x, weights = w, bw = bw, adjust = adjust, - kernel = kernel, n = n) + # To prevent discontinuities, we widen the range before calling the + # unbounded estimator (#5641). + bounds <- sort(bounds) + range <- range(from, to) + width <- diff(range) + range[1] <- range[1] - width * as.numeric(is.finite(bounds[1])) + range[2] <- range[2] + width * as.numeric(is.finite(bounds[2])) + n <- n * (sum(is.finite(bounds)) + 1) - dens <- reflect_density(dens = dens, bounds = bounds, from = from, to = to) + dens <- stats::density( + x, weights = w, bw = bw, adjust = adjust, + kernel = kernel, n = n, from = range[1], to = range[2] + ) + dens <- reflect_density( + dens = dens, bounds = bounds, + from = range[1], to = range[2] + ) } else { dens <- stats::density(x, weights = w, bw = bw, adjust = adjust, kernel = kernel, n = n, from = from, to = to) diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 0274d83d40..8a772b8873 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -66,7 +66,7 @@ test_that("stat_density uses `bounds`", { expect_equal( orig_density(test_sample) + left_reflection + right_reflection, plot_density(test_sample), - tolerance = 1e-4 + tolerance = 1e-3 ) } @@ -94,7 +94,7 @@ test_that("stat_density handles data outside of `bounds`", { stat_density(bounds = c(cutoff, Inf)) ) - expect_equal(data_actual, data_expected) + expect_equal(data_actual, data_expected, tolerance = 1e-4) }) test_that("compute_density succeeds when variance is zero", { From f8dac9d4170feea1ed94b4b8816e70b08a1258be Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 12:18:31 +0200 Subject: [PATCH 030/264] Gradients in ribbons (#5699) * support alpha/fill gradients in `geom_ribbon()` * add test * Add news bullet * Fix error messages * More aggressively enforce device capabilities * add missing newline --- NEWS.md | 2 ++ R/geom-ribbon.R | 41 +++++++++++++++++++++++++--- tests/testthat/_snaps/geom-ribbon.md | 2 +- tests/testthat/test-geom-ribbon.R | 18 +++++++++++- 4 files changed, 57 insertions(+), 6 deletions(-) diff --git a/NEWS.md b/NEWS.md index a8c8dd0867..9d2a5eb033 100644 --- a/NEWS.md +++ b/NEWS.md @@ -37,6 +37,8 @@ calculated as the density times the sum of weights (@teunbrand, #4176). * `theme()` gets new `spacing` and `margins` arguments that all other spacings and (non-text) margins inherit from (@teunbrand, #5622). +* `geom_ribbon()` can have varying `fill` or `alpha` in linear coordinate + systems (@teunbrand, #4690) # ggplot2 3.5.1 diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 11774c97f5..4170d87d21 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -135,11 +135,44 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, data <- data[order(data$group), ] # Check that aesthetics are constant - aes <- unique0(data[names(data) %in% c("colour", "fill", "linewidth", "linetype", "alpha")]) - if (nrow(aes) > 1) { - cli::cli_abort("Aesthetics can not vary along a ribbon.") + aes <- lapply( + data[names(data) %in% c("colour", "fill", "linewidth", "linetype", "alpha")], + unique0 + ) + non_constant <- names(aes)[lengths(aes) > 1] + if (coord$is_linear()) { + if (any(c("fill", "alpha") %in% non_constant)) { + check_device("gradients", action = "abort", maybe = TRUE) + } + # For linear coords, we can make a fill/alpha gradient, so we allow + # these to vary + non_constant <- setdiff(non_constant, c("fill", "alpha")) + } + if (length(non_constant) > 0) { + cli::cli_abort( + "Aesthetics can not vary along a ribbon: {.and {.field {non_constant}}}." + ) + } + if ((length(aes$fill) > 1 || length(aes$alpha) > 1)) { + transformed <- coord$transform(flip_data(data, flipped_aes), panel_params) + if (flipped_aes) { + keep <- is.finite(tranformed$y) + args <- list( + colours = alpha(data$fill, data$alpha)[keep], + stops = rescale(transformed$y)[keep], + y1 = 0, y2 = 1, x1 = 0.5, x2 = 0.5 + ) + } else { + keep <- is.finite(transformed$x) + args <- list( + colours = alpha(data$fill, data$alpha)[keep], + stops = rescale(transformed$x)[keep], + x1 = 0, x2 = 1, y1 = 0.5, y2 = 0.5 + ) + } + aes$fill <- inject(linearGradient(!!!args)) + aes$alpha <- NA } - aes <- as.list(aes) # Instead of removing NA values from the data and plotting a single # polygon, we want to "stop" plotting the polygon whenever we're diff --git a/tests/testthat/_snaps/geom-ribbon.md b/tests/testthat/_snaps/geom-ribbon.md index ae45d533f0..a2db3d427d 100644 --- a/tests/testthat/_snaps/geom-ribbon.md +++ b/tests/testthat/_snaps/geom-ribbon.md @@ -17,7 +17,7 @@ Problem while converting geom to grob. i Error occurred in the 1st layer. Caused by error in `draw_group()`: - ! Aesthetics can not vary along a ribbon. + ! Aesthetics can not vary along a ribbon: linewidth. --- diff --git a/tests/testthat/test-geom-ribbon.R b/tests/testthat/test-geom-ribbon.R index bcc04bf6eb..22e98a81c2 100644 --- a/tests/testthat/test-geom-ribbon.R +++ b/tests/testthat/test-geom-ribbon.R @@ -7,7 +7,7 @@ test_that("geom_ribbon() checks the aesthetics", { geom_ribbon(aes(y = year, xmin = level - 5, xmax = level + 5), orientation = "x") expect_snapshot_error(ggplotGrob(p)) p <- ggplot(huron) + - geom_ribbon(aes(year, ymin = level - 5, ymax = level + 5, fill = year)) + geom_ribbon(aes(year, ymin = level - 5, ymax = level + 5, linewidth = year)) expect_snapshot_error(ggplotGrob(p)) expect_snapshot_error(geom_ribbon(aes(year, ymin = level - 5, ymax = level + 5), outline.type = "test")) @@ -74,3 +74,19 @@ test_that("outline.type option works", { expect_s3_class(g_area_default$children[[1]]$children[[2]], "polyline") expect_equal(g_area_default$children[[1]]$children[[2]]$id, rep(1L, each = 4)) }) + +test_that("ribbons can have gradients", { + skip_if_not( + check_device("gradients", action = "test"), + "graphics device does not support gradients." + ) + + df <- data.frame(x = 1:2, ymin = c(-1:-2), ymax = 1:2) + p <- ggplot(df, aes(x, ymin = ymin, ymax = ymax, fill = x)) + + geom_ribbon(outline.type = "full") + + scale_fill_gradientn(colours = c("red", "blue")) + fill <- layer_grob(p)[[1]]$children[[1]]$gp$fill + + expect_s3_class(fill, "GridLinearGradient") + expect_equal(fill$colours, alpha(c("red", "blue"), NA)) +}) From e72d1a17f2cf5fcf138cf22e2c3aaef04bf0bb1d Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 12:26:54 +0200 Subject: [PATCH 031/264] Fill in missing `se` parameter (#5700) * fill in missing `se` * account for flipped aesthetics * add news bullet --- NEWS.md | 4 ++++ R/geom-smooth.R | 7 +++++++ 2 files changed, 11 insertions(+) diff --git a/NEWS.md b/NEWS.md index 9d2a5eb033..7b6bf44182 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* The default `se` parameter in layers with `geom = "smooth"` will be `TRUE` + when the data has `ymin` and `ymax` parameters and `FALSE` if these are + absent. Note that this does not affect the default of `geom_smooth()` or + `stat_smooth()` (@teunbrand, #5572). * The bounded density option in `stat_density()` uses a wider range to prevent discontinuities (#5641). * `geom_raster()` now falls back to rendering as `geom_rect()` when coordinates diff --git a/R/geom-smooth.R b/R/geom-smooth.R index 535b8965a8..0c3432620c 100644 --- a/R/geom-smooth.R +++ b/R/geom-smooth.R @@ -125,6 +125,13 @@ geom_smooth <- function(mapping = NULL, data = NULL, GeomSmooth <- ggproto("GeomSmooth", Geom, setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params, range_is_orthogonal = TRUE, ambiguous = TRUE) + params$se <- params$se %||% + if (params$flipped_aes) { + all(c("xmin", "xmax") %in% names(data)) + } else { + all(c("ymin", "ymax") %in% names(data)) + } + params }, From ae02c681e568d777639cfdd46b0ff60de4fbad9a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 12:47:44 +0200 Subject: [PATCH 032/264] Resolution of `geom_tile()` per panel (#5764) * compute resolution per panel * add news bullet * add test --- NEWS.md | 4 +++- R/geom-tile.R | 7 +++++-- tests/testthat/test-geom-tile.R | 15 +++++++++++++++ 3 files changed, 23 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 7b6bf44182..633a46172b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -42,7 +42,9 @@ * `theme()` gets new `spacing` and `margins` arguments that all other spacings and (non-text) margins inherit from (@teunbrand, #5622). * `geom_ribbon()` can have varying `fill` or `alpha` in linear coordinate - systems (@teunbrand, #4690) + systems (@teunbrand, #4690). +* `geom_tile()` computes default widths and heights per panel instead of + per layer (@teunbrand, #5740). # ggplot2 3.5.1 diff --git a/R/geom-tile.R b/R/geom-tile.R index 139d6f733e..ad01b1248f 100644 --- a/R/geom-tile.R +++ b/R/geom-tile.R @@ -109,8 +109,11 @@ GeomTile <- ggproto("GeomTile", GeomRect, extra_params = c("na.rm"), setup_data = function(data, params) { - data$width <- data$width %||% params$width %||% resolution(data$x, FALSE, TRUE) - data$height <- data$height %||% params$height %||% resolution(data$y, FALSE, TRUE) + + data$width <- data$width %||% params$width %||% + stats::ave(data$x, data$PANEL, FUN = function(x) resolution(x, FALSE, TRUE)) + data$height <- data$height %||% params$height %||% + stats::ave(data$y, data$PANEL, FUN = function(y) resolution(y, FALSE, TRUE)) transform(data, xmin = x - width / 2, xmax = x + width / 2, width = NULL, diff --git a/tests/testthat/test-geom-tile.R b/tests/testthat/test-geom-tile.R index d0c8a6f073..f63602bf66 100644 --- a/tests/testthat/test-geom-tile.R +++ b/tests/testthat/test-geom-tile.R @@ -34,3 +34,18 @@ test_that("accepts linejoin parameter", { gp2 <- layer_grob(ggplot(df, aes(x, y)) + geom_tile(linejoin = "round"))[[1]]$gp expect_equal(gp2$linejoin, "round") }) + +test_that("width and height are inferred per panel", { + df <- data_frame0( + x = c(1, 2, 3, 10, 20, 30), + y = c(10, 10.5, 11, 100, 200, 300), + f = rep(c("A", "B"), each = 3) + ) + + ld <- layer_data( + ggplot(df, aes(x, y)) + geom_tile() + facet_wrap(~f, scales = "free") + ) + + expect_equal(ld$xmax - ld$xmin, c(1, 1, 1, 10, 10, 10)) + expect_equal(ld$ymax - ld$ymin, c(0.5, 0.5, 0.5, 100, 100, 100)) +}) From 7a006da07c9b89976cfdcf6546a5a4d3c4e1047f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 13:42:30 +0200 Subject: [PATCH 033/264] Palettes for discrete scales (#5771) * Discrete position scales use palette * Plumbing for `palette` argument * discrete range derived from mapped limits * adjust test * add tests * palettes take `n` just like other scales * reoxygenate * rephrase palette arg * add news bullet --- NEWS.md | 2 ++ R/coord-transform.R | 2 +- R/scale-discrete-.R | 35 ++++++++++++++++------ R/scale-expansion.R | 19 +++++++----- man/scale_discrete.Rd | 9 ++++-- tests/testthat/test-scale-discrete.R | 42 +++++++++++++++++++++++++++ tests/testthat/test-scale-expansion.R | 2 +- 7 files changed, 89 insertions(+), 22 deletions(-) diff --git a/NEWS.md b/NEWS.md index 633a46172b..4e8216504e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Discrete position scales now expose the `palette` argument, which can be used + to customise spacings between levels (@teunbrand, #5770). * The default `se` parameter in layers with `geom = "smooth"` will be `TRUE` when the data has `ymin` and `ymax` parameters and `FALSE` if these are absent. Note that this does not affect the default of `geom_smooth()` or diff --git a/R/coord-transform.R b/R/coord-transform.R index 81f06afad3..83ffd7b9ee 100644 --- a/R/coord-transform.R +++ b/R/coord-transform.R @@ -198,7 +198,7 @@ view_scales_from_scale_with_coord_trans <- function(scale, coord_limits, trans, if (scale$is_discrete()) { continuous_ranges <- expand_limits_discrete_trans( - scale_limits, + scale$map(scale_limits), expansion, coord_limits, trans, diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index 60bcc3f8b7..b957b97b97 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -12,6 +12,9 @@ #' #' @inheritDotParams discrete_scale -scale_name #' @inheritParams discrete_scale +#' @param palette A palette function that when called with a single integer +#' argument (the number of levels in the scale) returns the numerical values +#' that they should take. #' @param sec.axis [dup_axis()] is used to specify a secondary axis. #' @rdname scale_discrete #' @family position scales @@ -64,12 +67,12 @@ #' geom_point() + #' scale_x_discrete(labels = abbreviate) #' } -scale_x_discrete <- function(name = waiver(), ..., expand = waiver(), - guide = waiver(), position = "bottom", - sec.axis = waiver()) { +scale_x_discrete <- function(name = waiver(), ..., palette = seq_len, + expand = waiver(), guide = waiver(), + position = "bottom", sec.axis = waiver()) { sc <- discrete_scale( aesthetics = c("x", "xmin", "xmax", "xend"), name = name, - palette = identity, ..., + palette = palette, ..., expand = expand, guide = guide, position = position, super = ScaleDiscretePosition ) @@ -79,12 +82,12 @@ scale_x_discrete <- function(name = waiver(), ..., expand = waiver(), } #' @rdname scale_discrete #' @export -scale_y_discrete <- function(name = waiver(), ..., expand = waiver(), - guide = waiver(), position = "left", - sec.axis = waiver()) { +scale_y_discrete <- function(name = waiver(), ..., palette = seq_len, + expand = waiver(), guide = waiver(), + position = "left", sec.axis = waiver()) { sc <- discrete_scale( aesthetics = c("y", "ymin", "ymax", "yend"), name = name, - palette = identity, ..., + palette = palette, ..., expand = expand, guide = guide, position = position, super = ScaleDiscretePosition ) @@ -137,7 +140,21 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, map = function(self, x, limits = self$get_limits()) { if (is.discrete(x)) { - x <- seq_along(limits)[match(as.character(x), limits)] + values <- self$palette(length(limits)) + if (!is.numeric(values)) { + cli::cli_abort( + "The {.arg palette} function must return a {.cls numeric} vector.", + call = self$call + ) + } + if (length(values) < length(limits)) { + cli::cli_abort( + "The {.arg palette} function must return at least \\ + {length(limits)} values.", + call = self$call + ) + } + x <- values[match(as.character(x), limits)] } mapped_discrete(x) }, diff --git a/R/scale-expansion.R b/R/scale-expansion.R index 9ede4c1400..8ec72c2a78 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -137,7 +137,7 @@ expand_limits_scale <- function(scale, expand = expansion(0, 0), limits = waiver if (scale$is_discrete()) { coord_limits <- coord_limits %||% c(NA_real_, NA_real_) expand_limits_discrete( - limits, + scale$map(limits), expand, coord_limits, range_continuous = scale$range_c$range @@ -201,14 +201,17 @@ expand_limits_continuous_trans <- function(limits, expand = expansion(0, 0), expand_limits_discrete_trans <- function(limits, expand = expansion(0, 0), coord_limits = c(NA, NA), trans = transform_identity(), range_continuous = NULL) { - if (is.discrete(limits)) { - n_discrete_limits <- length(limits) - } else { - n_discrete_limits <- 0 + discrete_limits <- NULL + if (length(limits) > 0) { + if (is.discrete(limits)) { + discrete_limits <- c(1, length(limits)) # for backward compatibility + } else { + discrete_limits <- range(limits) + } } is_empty <- is.null(limits) && is.null(range_continuous) - is_only_continuous <- n_discrete_limits == 0 + is_only_continuous <- is.null(discrete_limits) is_only_discrete <- is.null(range_continuous) if (is_empty) { @@ -216,10 +219,10 @@ expand_limits_discrete_trans <- function(limits, expand = expansion(0, 0), } else if (is_only_continuous) { expand_limits_continuous_trans(range_continuous, expand, coord_limits, trans) } else if (is_only_discrete) { - expand_limits_continuous_trans(c(1, n_discrete_limits), expand, coord_limits, trans) + expand_limits_continuous_trans(discrete_limits, expand, coord_limits, trans) } else { # continuous and discrete - limit_info_discrete <- expand_limits_continuous_trans(c(1, n_discrete_limits), expand, coord_limits, trans) + limit_info_discrete <- expand_limits_continuous_trans(discrete_limits, expand, coord_limits, trans) # don't expand continuous range if there is also a discrete range limit_info_continuous <- expand_limits_continuous_trans( diff --git a/man/scale_discrete.Rd b/man/scale_discrete.Rd index e92179a921..381c09254e 100644 --- a/man/scale_discrete.Rd +++ b/man/scale_discrete.Rd @@ -8,6 +8,7 @@ scale_x_discrete( name = waiver(), ..., + palette = seq_len, expand = waiver(), guide = waiver(), position = "bottom", @@ -17,6 +18,7 @@ scale_x_discrete( scale_y_discrete( name = waiver(), ..., + palette = seq_len, expand = waiver(), guide = waiver(), position = "left", @@ -32,9 +34,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks @@ -79,6 +78,10 @@ notation. \item{\code{super}}{The super class to use for the constructed scale} }} +\item{palette}{A palette function that when called with a single integer +argument (the number of levels in the scale) returns the numerical values +that they should take.} + \item{expand}{For position scales, a vector of range expansion constants used to add some padding around the data to ensure that they are placed some distance away from the axes. Use the convenience function \code{\link[=expansion]{expansion()}} diff --git a/tests/testthat/test-scale-discrete.R b/tests/testthat/test-scale-discrete.R index d9ce98c494..cd8c2da933 100644 --- a/tests/testthat/test-scale-discrete.R +++ b/tests/testthat/test-scale-discrete.R @@ -162,3 +162,45 @@ test_that("mapped_discrete vectors behaves as predicted", { x[5:7] <- mapped_discrete(seq_len(3)) expect_s3_class(x, "mapped_discrete") }) + +# Palettes ---------------------------------------------------------------- + +test_that("palettes work for discrete scales", { + + df <- data.frame(x = c("A", "B", "C"), y = 1:3) + values <- c(1, 10, 100) + + p <- ggplot(df, aes(x, y)) + + geom_point() + + scale_x_discrete(palette = function(x) values) + + # Check limits are translated to correct values + ld <- layer_data(p) + expect_equal(ld$x, values, ignore_attr = TRUE) + + # Check discsrete expansion is applied + b <- ggplot_build(p) + expect_equal( + b$layout$panel_params[[1]]$x.range, + range(values) + c(-0.6, 0.6) + ) +}) + +test_that("invalid palettes trigger errors", { + + df <- data.frame(x = c("A", "B", "C"), y = 1:3) + + p <- ggplot(df, aes(x, y)) + + geom_point() + + expect_error( + ggplot_build(p + scale_x_discrete(palette = function(x) LETTERS[1:3])), + "must return a .+ vector\\." + ) + + expect_error( + ggplot_build(p + scale_x_discrete(palette = function(x) 1:2)), + "must return at least 3 values" + ) +}) + diff --git a/tests/testthat/test-scale-expansion.R b/tests/testthat/test-scale-expansion.R index 7d1b5b30ae..26d25abfdc 100644 --- a/tests/testthat/test-scale-expansion.R +++ b/tests/testthat/test-scale-expansion.R @@ -116,6 +116,6 @@ test_that("expand_limits_scale_discrete() begrudgingly handles numeric limits", coord_limits = c(NA, NA), range_continuous = c(-15, -2) ), - c(-15, -2) + c(-16, -1) ) }) From d3adf172decaa0feec8e7a3b75a497d2f5c83415 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 13:42:45 +0200 Subject: [PATCH 034/264] Transparent fill of panel borders (#5784) * Force `fill = NA` * remove superfluous `fill = NA` * add news bullet --- NEWS.md | 2 ++ R/coord-.R | 4 +++- R/coord-polar.R | 4 ++-- R/coord-radial.R | 6 ++++-- R/theme-defaults.R | 8 ++++---- R/theme.R | 2 +- man/theme.Rd | 2 +- 7 files changed, 17 insertions(+), 11 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4e8216504e..4c9fb2f09c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -47,6 +47,8 @@ systems (@teunbrand, #4690). * `geom_tile()` computes default widths and heights per panel instead of per layer (@teunbrand, #5740). +* The `fill` of the `panel.border` theme setting is ignored and forced to be + transparent (#5782). # ggplot2 3.5.1 diff --git a/R/coord-.R b/R/coord-.R index dc7090c352..ced1257b42 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -65,7 +65,9 @@ Coord <- ggproto("Coord", labels }, - render_fg = function(panel_params, theme) element_render(theme, "panel.border"), + render_fg = function(panel_params, theme) { + element_render(theme, "panel.border", fill = NA) + }, render_bg = function(self, panel_params, theme) { cli::cli_abort("{.fn {snake_class(self)}} has not implemented a {.fn render_bg} method.") diff --git a/R/coord-polar.R b/R/coord-polar.R index 6c8b4813b4..e0712760fb 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -265,7 +265,7 @@ CoordPolar <- ggproto("CoordPolar", Coord, render_fg = function(self, panel_params, theme) { if (is.null(panel_params$theta.major)) { - return(element_render(theme, "panel.border")) + return(element_render(theme, "panel.border", fill = NA)) } arc <- self$start + c(0, 2 * pi) dir <- self$direction @@ -297,7 +297,7 @@ CoordPolar <- ggproto("CoordPolar", Coord, unit(0.45 * cos(theta) + 0.5, "native"), hjust = 0.5, vjust = 0.5 ), - element_render(theme, "panel.border") + element_render(theme, "panel.border", fill = NA) ) }, diff --git a/R/coord-radial.R b/R/coord-radial.R index 89c84dd5dc..b5ad621beb 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -357,11 +357,13 @@ CoordRadial <- ggproto("CoordRadial", Coord, render_fg = function(self, panel_params, theme) { + border <- element_render(theme, "panel.border", fill = NA) + if (!self$r_axis_inside) { out <- grobTree( panel_guides_grob(panel_params$guides, "theta", theme), panel_guides_grob(panel_params$guides, "theta.sec", theme), - element_render(theme, "panel.border") + border ) return(out) } @@ -381,7 +383,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, panel_guides_grob(panel_params$guides, "theta", theme), panel_guides_grob(panel_params$guides, "theta.sec", theme), left, right, - element_render(theme, "panel.border") + border ) }, diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 2066679533..6ecd6d68c0 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -269,7 +269,7 @@ theme_bw <- function(base_size = 11, base_family = "", theme( # white background and dark border panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(fill = NA, colour = "grey20"), + panel.border = element_rect(colour = "grey20"), # make gridlines dark, same contrast with white as in theme_grey panel.grid = element_line(colour = "grey92"), panel.grid.minor = element_line(linewidth = rel(0.5)), @@ -303,7 +303,7 @@ theme_linedraw <- function(base_size = 11, base_family = "", # 0.5 clipped looks like 0.25 # pure black panel border and grid lines, but thinner - panel.border = element_rect(fill = NA, colour = "black", linewidth = rel(1)), + panel.border = element_rect(colour = "black", linewidth = rel(1)), panel.grid = element_line(colour = "black"), panel.grid.major = element_line(linewidth = rel(0.1)), panel.grid.minor = element_line(linewidth = rel(0.05)), @@ -337,7 +337,7 @@ theme_light <- function(base_size = 11, base_family = "", theme( # white panel with light grey border panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(fill = NA, colour = "grey70", linewidth = rel(1)), + panel.border = element_rect(colour = "grey70", linewidth = rel(1)), # light grey, thinner gridlines # => make them slightly darker to keep acceptable contrast panel.grid = element_line(colour = "grey87"), @@ -612,7 +612,7 @@ theme_test <- function(base_size = 11, base_family = "", legend.box.spacing = rel(2), panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(fill = NA, colour = "grey20"), + panel.border = element_rect(colour = "grey20"), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.spacing = NULL, diff --git a/R/theme.R b/R/theme.R index f03d2a67ef..f151a316a7 100644 --- a/R/theme.R +++ b/R/theme.R @@ -226,7 +226,7 @@ #' # Panels -------------------------------------------------------------------- #' #' p1 + theme(panel.background = element_rect(fill = "white", colour = "grey50")) -#' p1 + theme(panel.border = element_rect(linetype = "dashed", fill = NA)) +#' p1 + theme(panel.border = element_rect(linetype = "dashed")) #' p1 + theme(panel.grid.major = element_line(colour = "black")) #' p1 + theme( #' panel.grid.major.y = element_blank(), diff --git a/man/theme.Rd b/man/theme.Rd index 13a88a2e2a..5635049b5c 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -412,7 +412,7 @@ p1 + theme(plot.background = element_rect(fill = "green")) # Panels -------------------------------------------------------------------- p1 + theme(panel.background = element_rect(fill = "white", colour = "grey50")) -p1 + theme(panel.border = element_rect(linetype = "dashed", fill = NA)) +p1 + theme(panel.border = element_rect(linetype = "dashed")) p1 + theme(panel.grid.major = element_line(colour = "black")) p1 + theme( panel.grid.major.y = element_blank(), From 0b348cd201af7ce8f2858f51f743643d56639452 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 14:20:54 +0200 Subject: [PATCH 035/264] Skip alignment/stacking when possible (#5789) * skip alignment if there is just one group * add extra group to test * skip stacking if every x position is unique * add news bullets --- NEWS.md | 4 ++++ R/position-stack.R | 4 ++++ R/stat-align.R | 21 +++++++++------------ tests/testthat/test-stat-align.R | 13 +++++++------ 4 files changed, 24 insertions(+), 18 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4c9fb2f09c..191b0701a2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -49,6 +49,10 @@ per layer (@teunbrand, #5740). * The `fill` of the `panel.border` theme setting is ignored and forced to be transparent (#5782). +* `stat_align()` skips computation when there is only 1 group and therefore + alignment is not necessary (#5788). +* `position_stack()` skips computation when all `x` values are unique and + therefore stacking is not necessary (#5788). # ggplot2 3.5.1 diff --git a/R/position-stack.R b/R/position-stack.R index ac445be071..2da5c91ef6 100644 --- a/R/position-stack.R +++ b/R/position-stack.R @@ -187,6 +187,10 @@ PositionStack <- ggproto("PositionStack", Position, if (is.null(params$var)) { return(data) } + if (!vec_duplicate_any(data$x)) { + # Every x is unique, nothing to stack here + return(flip_data(data, params$flipped_aes)) + } negative <- data$ymax < 0 negative[is.na(negative)] <- FALSE diff --git a/R/stat-align.R b/R/stat-align.R index 5f49b29152..3187ca28c0 100644 --- a/R/stat-align.R +++ b/R/stat-align.R @@ -40,22 +40,19 @@ StatAlign <- ggproto("StatAlign", Stat, if (empty(data)) { return(data_frame0()) } - + if (is_unique(data$group)) { + return(data) + } names <- flipped_names(flipped_aes) x <- data[[names$x]] y <- data[[names$y]] - if (is_unique(data$group)) { - # No need for interpolation - cross <- x[0] - } else { - # Find positions where 0 is crossed - pivot <- vec_unrep(data_frame0(group = data$group, y = y < 0)) - group_ends <- cumsum(vec_unrep(pivot$key$group)$times) - pivot <- cumsum(pivot$times)[-group_ends] - cross <- -y[pivot] * (x[pivot + 1] - x[pivot]) / - (y[pivot + 1] - y[pivot]) + x[pivot] - } + # Find positions where 0 is crossed + pivot <- vec_unrep(data_frame0(group = data$group, y = y < 0)) + group_ends <- cumsum(vec_unrep(pivot$key$group)$times) + pivot <- cumsum(pivot$times)[-group_ends] + cross <- -y[pivot] * (x[pivot + 1] - x[pivot]) / + (y[pivot + 1] - y[pivot]) + x[pivot] unique_loc <- unique(sort(c(x, cross))) adjust <- diff(range(unique_loc, na.rm = TRUE)) * 0.001 diff --git a/tests/testthat/test-stat-align.R b/tests/testthat/test-stat-align.R index 411e29b2b8..87a69cbba7 100644 --- a/tests/testthat/test-stat-align.R +++ b/tests/testthat/test-stat-align.R @@ -48,19 +48,20 @@ test_that("alignment adjusts per panel", { # data into account (#5227) df <- data_frame0( - x = c(0, 1, 1000, 1001), - y = c(-1, 1, -1, 1), - g = c("A", "A", "B", "B") + x = c(0, 1, 1000, 1001, 0, 1, 1000, 1001), + y = c(-1, 1, -1, 1, -1, 1, -1, 1), + f = c("A", "A", "B", "B", "A", "A", "B", "B"), + g = c("a", "a", "b", "b", "c", "c", "d", "d") ) - p <- ggplot(df, aes(x, y)) + p <- ggplot(df, aes(x, y, group = g)) # Here, x-range is large, so adjustment should be larger - ld <- layer_data(p + geom_area(aes(fill = g))) + ld <- layer_data(p + geom_area(aes(fill = f))) expect_equal(diff(ld$x[1:2]), 1/6, tolerance = 1e-4) # Here, x-ranges are smaller, so adjustment should be smaller instead of # considering the data as a whole - ld <- layer_data(p + geom_area() + facet_wrap(vars(g), scales = "free_x")) + ld <- layer_data(p + geom_area() + facet_wrap(vars(f), scales = "free_x")) expect_equal(diff(ld$x[1:2]), 1e-3, tolerance = 1e-4) }) From f89a00751668b3ec39f2d83304c3d2fc104c0ca9 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 14:32:32 +0200 Subject: [PATCH 036/264] Discrete minor ticks (#5777) * plumbing for `minor_breaks` * proper `get_breaks_minor()` method * view scales treat minor breaks equally * tweak param docs * Add news bullet * protect axis against mixing types * remove duplicate news entry * accept new underscore argument --- NEWS.md | 3 ++ R/guide-axis.R | 5 +++ R/scale-.R | 40 ++++++++++++++++--- R/scale-view.R | 9 ++--- man/continuous_scale.Rd | 6 +-- man/discrete_scale.Rd | 13 ++++++ man/scale_continuous.Rd | 6 +-- man/scale_discrete.Rd | 11 +++++ man/scale_gradient.Rd | 6 +-- man/scale_grey.Rd | 11 +++++ man/scale_hue.Rd | 11 +++++ man/scale_linetype.Rd | 11 +++++ man/scale_manual.Rd | 11 +++++ man/scale_shape.Rd | 11 +++++ man/scale_size.Rd | 6 +-- tests/testthat/_snaps/prohibited-functions.md | 2 +- 16 files changed, 139 insertions(+), 23 deletions(-) diff --git a/NEWS.md b/NEWS.md index 191b0701a2..75b5efef11 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* Discrete scales now support `minor_breaks`. This may only make sense in + discrete position scales, where it affects the placement of minor ticks + and minor gridlines (#5434). * Discrete position scales now expose the `palette` argument, which can be used to customise spacings between levels (@teunbrand, #5770). * The default `se` parameter in layers with `geom = "smooth"` will be `TRUE` diff --git a/R/guide-axis.R b/R/guide-axis.R index 8eafccf114..dc57ffd23e 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -136,6 +136,11 @@ GuideAxis <- ggproto( if (nrow(major) > 0) { major$.type <- "major" + if (!vec_is(minor$.value, major$.value)) { + # If we have mixed types of values, which may happen in discrete scales, + # discard minor values in favour of the major values. + minor$.value <- NULL + } vec_rbind(major, minor) } else { minor diff --git a/R/scale-.R b/R/scale-.R index 6233caf54f..9eaa153590 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -23,13 +23,13 @@ #' Also accepts rlang [lambda][rlang::as_function()] function notation. #' @param minor_breaks One of: #' - `NULL` for no minor breaks -#' - `waiver()` for the default breaks (one minor break between -#' each major break) +#' - `waiver()` for the default breaks (none for discrete, one minor break +#' between each major break for continuous) #' - A numeric vector of positions #' - A function that given the limits returns a vector of minor breaks. Also #' accepts rlang [lambda][rlang::as_function()] function notation. When #' the function has two arguments, it will be given the limits and major -#' breaks. +#' break positions. #' @param n.breaks An integer guiding the number of major breaks. The algorithm #' may choose a slightly different number to ensure nice break labels. Will #' only have an effect if `breaks = waiver()`. Use `NULL` to use the default @@ -200,7 +200,8 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam #' The `r link_book("new scales section", "extensions#sec-new-scales")` #' @keywords internal discrete_scale <- function(aesthetics, scale_name = deprecated(), palette, name = waiver(), - breaks = waiver(), labels = waiver(), limits = NULL, expand = waiver(), + breaks = waiver(), minor_breaks = waiver(), + labels = waiver(), limits = NULL, expand = waiver(), na.translate = TRUE, na.value = NA, drop = TRUE, guide = "legend", position = "left", call = caller_call(), @@ -218,6 +219,7 @@ discrete_scale <- function(aesthetics, scale_name = deprecated(), palette, name limits <- allow_lambda(limits) breaks <- allow_lambda(breaks) labels <- allow_lambda(labels) + minor_breaks <- allow_lambda(minor_breaks) if (!is.function(limits) && (length(limits) > 0) && !is.discrete(limits)) { cli::cli_warn(c( @@ -247,6 +249,7 @@ discrete_scale <- function(aesthetics, scale_name = deprecated(), palette, name name = name, breaks = breaks, + minor_breaks = minor_breaks, labels = labels, drop = drop, guide = guide, @@ -1022,7 +1025,34 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, structure(in_domain, pos = match(in_domain, breaks)) }, - get_breaks_minor = function(...) NULL, + get_breaks_minor = function(self, n = 2, b = self$break_positions(), + limits = self$get_limits()) { + breaks <- self$minor_breaks + # The default is to draw no minor ticks + if (is.null(breaks %|W|% NULL)) { + return(NULL) + } + if (is.function(breaks)) { + # Ensure function gets supplied numeric limits and breaks + if (!is.numeric(b)) { + b <- self$map(b) + } + if (!is.numeric(limits)) { + limits <- self$map(limits) + limits <- self$dimension(self$expand, limits) + } + + # Allow for two types of minor breaks specifications + break_fun <- fetch_ggproto(self, "minor_breaks") + arg_names <- fn_fmls_names(break_fun) + if (length(arg_names) == 1L) { + breaks <- break_fun(limits) + } else { + breaks <- break_fun(limits, b) + } + } + breaks + }, get_labels = function(self, breaks = self$get_breaks()) { if (self$is_empty()) { diff --git a/R/scale-view.R b/R/scale-view.R index 3a068ea81c..de78ebffb6 100644 --- a/R/scale-view.R +++ b/R/scale-view.R @@ -15,17 +15,16 @@ view_scale_primary <- function(scale, limits = scale$get_limits(), continuous_range = scale$dimension(limits = limits)) { + # continuous_range can be specified in arbitrary order, but + # scales expect the one in ascending order. + continuous_scale_sorted <- sort(continuous_range) if(!scale$is_discrete()) { - # continuous_range can be specified in arbitrary order, but - # continuous scales expect the one in ascending order. - continuous_scale_sorted <- sort(continuous_range) breaks <- scale$get_breaks(continuous_scale_sorted) - minor_breaks <- scale$get_breaks_minor(b = breaks, limits = continuous_scale_sorted) breaks <- censor(breaks, continuous_scale_sorted, only.finite = FALSE) } else { breaks <- scale$get_breaks(limits) - minor_breaks <- scale$get_breaks_minor(b = breaks, limits = limits) } + minor_breaks <- scale$get_breaks_minor(b = breaks, limits = continuous_scale_sorted) minor_breaks <- censor(minor_breaks, continuous_range, only.finite = FALSE) ggproto(NULL, ViewScale, diff --git a/man/continuous_scale.Rd b/man/continuous_scale.Rd index dc4abffbce..a572ec2bf7 100644 --- a/man/continuous_scale.Rd +++ b/man/continuous_scale.Rd @@ -56,13 +56,13 @@ Also accepts rlang \link[rlang:as_function]{lambda} function notation. \item{minor_breaks}{One of: \itemize{ \item \code{NULL} for no minor breaks -\item \code{waiver()} for the default breaks (one minor break between -each major break) +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) \item A numeric vector of positions \item A function that given the limits returns a vector of minor breaks. Also accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major -breaks. +break positions. }} \item{n.breaks}{An integer guiding the number of major breaks. The algorithm diff --git a/man/discrete_scale.Rd b/man/discrete_scale.Rd index 0fd213cd30..ae349cdf1f 100644 --- a/man/discrete_scale.Rd +++ b/man/discrete_scale.Rd @@ -10,6 +10,7 @@ discrete_scale( palette, name = waiver(), breaks = waiver(), + minor_breaks = waiver(), labels = waiver(), limits = NULL, expand = waiver(), @@ -47,6 +48,18 @@ as output. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} +\item{minor_breaks}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} + \item{labels}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_continuous.Rd b/man/scale_continuous.Rd index 56c23639a6..153bb325f5 100644 --- a/man/scale_continuous.Rd +++ b/man/scale_continuous.Rd @@ -78,13 +78,13 @@ Also accepts rlang \link[rlang:as_function]{lambda} function notation. \item{minor_breaks}{One of: \itemize{ \item \code{NULL} for no minor breaks -\item \code{waiver()} for the default breaks (one minor break between -each major break) +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) \item A numeric vector of positions \item A function that given the limits returns a vector of minor breaks. Also accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major -breaks. +break positions. }} \item{n.breaks}{An integer guiding the number of major breaks. The algorithm diff --git a/man/scale_discrete.Rd b/man/scale_discrete.Rd index 381c09254e..0bab3ad985 100644 --- a/man/scale_discrete.Rd +++ b/man/scale_discrete.Rd @@ -63,6 +63,17 @@ from a discrete scale, specify \code{na.translate = FALSE}.} missing values be displayed as? Does not apply to position scales where \code{NA} is always placed at the far right.} \item{\code{aesthetics}}{The names of the aesthetics that this scale works with.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_gradient.Rd b/man/scale_gradient.Rd index cbc5427282..368ef16509 100644 --- a/man/scale_gradient.Rd +++ b/man/scale_gradient.Rd @@ -120,13 +120,13 @@ Also accepts rlang \link[rlang:as_function]{lambda} function notation. \item{\code{minor_breaks}}{One of: \itemize{ \item \code{NULL} for no minor breaks -\item \code{waiver()} for the default breaks (one minor break between -each major break) +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) \item A numeric vector of positions \item A function that given the limits returns a vector of minor breaks. Also accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major -breaks. +break positions. }} \item{\code{n.breaks}}{An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will diff --git a/man/scale_grey.Rd b/man/scale_grey.Rd index e085fa0016..6b04f40688 100644 --- a/man/scale_grey.Rd +++ b/man/scale_grey.Rd @@ -61,6 +61,17 @@ every level in a legend, the layer should use \code{show.legend = TRUE}.} \item{\code{na.translate}}{Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify \code{na.translate = FALSE}.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_hue.Rd b/man/scale_hue.Rd index 0ec49fd123..99776d95d3 100644 --- a/man/scale_hue.Rd +++ b/man/scale_hue.Rd @@ -67,6 +67,17 @@ every level in a legend, the layer should use \code{show.legend = TRUE}.} \item{\code{na.translate}}{Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify \code{na.translate = FALSE}.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index 94eeb93927..da4cf2b7c3 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -53,6 +53,17 @@ every level in a legend, the layer should use \code{show.legend = TRUE}.} missing values, and do so by default. If you want to remove missing values from a discrete scale, specify \code{na.translate = FALSE}.} \item{\code{aesthetics}}{The names of the aesthetics that this scale works with.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_manual.Rd b/man/scale_manual.Rd index 9857dcbc65..92205f3013 100644 --- a/man/scale_manual.Rd +++ b/man/scale_manual.Rd @@ -64,6 +64,17 @@ from a discrete scale, specify \code{na.translate = FALSE}.} \code{waiver()}, the default, the name of the scale is taken from the first mapping used for that aesthetic. If \code{NULL}, the legend title will be omitted.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index 65deec3ea2..ffbb381481 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -53,6 +53,17 @@ from a discrete scale, specify \code{na.translate = FALSE}.} missing values be displayed as? Does not apply to position scales where \code{NA} is always placed at the far right.} \item{\code{aesthetics}}{The names of the aesthetics that this scale works with.} + \item{\code{minor_breaks}}{One of: +\itemize{ +\item \code{NULL} for no minor breaks +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) +\item A numeric vector of positions +\item A function that given the limits returns a vector of minor breaks. Also +accepts rlang \link[rlang:as_function]{lambda} function notation. When +the function has two arguments, it will be given the limits and major +break positions. +}} \item{\code{labels}}{One of: \itemize{ \item \code{NULL} for no labels diff --git a/man/scale_size.Rd b/man/scale_size.Rd index c1c7d8dd05..753ecfa790 100644 --- a/man/scale_size.Rd +++ b/man/scale_size.Rd @@ -134,13 +134,13 @@ breaks are given explicitly.} \item{\code{minor_breaks}}{One of: \itemize{ \item \code{NULL} for no minor breaks -\item \code{waiver()} for the default breaks (one minor break between -each major break) +\item \code{waiver()} for the default breaks (none for discrete, one minor break +between each major break for continuous) \item A numeric vector of positions \item A function that given the limits returns a vector of minor breaks. Also accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major -breaks. +break positions. }} \item{\code{oob}}{One of: \itemize{ diff --git a/tests/testthat/_snaps/prohibited-functions.md b/tests/testthat/_snaps/prohibited-functions.md index 87c26e26a8..f2aa9bf4d2 100644 --- a/tests/testthat/_snaps/prohibited-functions.md +++ b/tests/testthat/_snaps/prohibited-functions.md @@ -29,7 +29,7 @@ [4] "date_minor_breaks" $discrete_scale - [1] "scale_name" + [1] "scale_name" "minor_breaks" $geom_density2d [1] "contour_var" From f7cf2af28dba72327188c1c112994f2e53809f07 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 14:53:24 +0200 Subject: [PATCH 037/264] Standardise `get_*`, `set_*`, `update_*` and `replace_*` prefixes. (#5802) * standardise layer getters * standardise theme accessors * Make `get_last_plot()` * propagate changes throughout * adjust docs * add news bullet * missed a few replacements * propagate to recent PRs --- NAMESPACE | 8 +++ NEWS.md | 15 +++++ R/guides-.R | 2 +- R/plot-build.R | 27 +++++--- R/plot-last.R | 6 +- R/save.R | 2 +- R/theme-current.R | 78 +++++++++++++--------- R/theme.R | 2 +- man/get_guide_data.Rd | 2 +- man/{last_plot.Rd => get_last_plot.Rd} | 5 +- man/{theme_get.Rd => get_theme.Rd} | 56 ++++++++++------ man/ggplot_build.Rd | 25 ++++--- man/ggsave.Rd | 2 +- tests/testthat/test-aes-grouping.R | 2 +- tests/testthat/test-aes-setting.R | 16 ++--- tests/testthat/test-aes.R | 6 +- tests/testthat/test-annotate.R | 2 +- tests/testthat/test-build.R | 10 +-- tests/testthat/test-coord-polar.R | 8 +-- tests/testthat/test-empty-data.R | 46 ++++++------- tests/testthat/test-facet-.R | 16 ++--- tests/testthat/test-geom-bar.R | 4 +- tests/testthat/test-geom-boxplot.R | 12 ++-- tests/testthat/test-geom-col.R | 10 +-- tests/testthat/test-geom-dotplot.R | 6 +- tests/testthat/test-geom-freqpoly.R | 2 +- tests/testthat/test-geom-hex.R | 4 +- tests/testthat/test-geom-label.R | 2 +- tests/testthat/test-geom-quantile.R | 2 +- tests/testthat/test-geom-ribbon.R | 18 ++--- tests/testthat/test-geom-rug.R | 8 +-- tests/testthat/test-geom-rule.R | 20 +++--- tests/testthat/test-geom-sf.R | 4 +- tests/testthat/test-geom-smooth.R | 14 ++-- tests/testthat/test-geom-text.R | 4 +- tests/testthat/test-geom-tile.R | 12 ++-- tests/testthat/test-geom-violin.R | 10 +-- tests/testthat/test-layer.R | 12 ++-- tests/testthat/test-position-dodge2.R | 12 ++-- tests/testthat/test-position-nudge.R | 12 ++-- tests/testthat/test-position-stack.R | 12 ++-- tests/testthat/test-position_dodge.R | 4 +- tests/testthat/test-qplot.R | 2 +- tests/testthat/test-scale-brewer.R | 4 +- tests/testthat/test-scale-date.R | 16 ++--- tests/testthat/test-scale-discrete.R | 44 ++++++------ tests/testthat/test-scale-gradient.R | 2 +- tests/testthat/test-scale-manual.R | 4 +- tests/testthat/test-scales-breaks-labels.R | 5 +- tests/testthat/test-scales.R | 16 ++--- tests/testthat/test-sec-axis.R | 28 ++++---- tests/testthat/test-stat-align.R | 4 +- tests/testthat/test-stat-bin.R | 28 ++++---- tests/testthat/test-stat-bin2d.R | 8 +-- tests/testthat/test-stat-contour.R | 6 +- tests/testthat/test-stat-count.R | 2 +- tests/testthat/test-stat-density.R | 14 ++-- tests/testthat/test-stat-density2d.R | 22 +++--- tests/testthat/test-stat-ecdf.R | 8 +-- tests/testthat/test-stat-ellipsis.R | 2 +- tests/testthat/test-stat-function.R | 38 +++++------ tests/testthat/test-stat-hex.R | 2 +- tests/testthat/test-stat-sf-coordinates.R | 2 +- tests/testthat/test-stat-sum.R | 14 ++-- tests/testthat/test-stat-summary.R | 16 ++--- tests/testthat/test-stat-ydensity.R | 6 +- tests/testthat/test-theme.R | 6 +- tests/testthat/test-viridis.R | 6 +- vignettes/articles/faq-customising.Rmd | 4 +- vignettes/ggplot2-in-packages.Rmd | 2 +- 70 files changed, 456 insertions(+), 375 deletions(-) rename man/{last_plot.Rd => get_last_plot.Rd} (84%) rename man/{theme_get.Rd => get_theme.Rd} (60%) diff --git a/NAMESPACE b/NAMESPACE index 3dbc9d5ca6..74fc47431f 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -421,6 +421,11 @@ export(geom_vline) export(get_alt_text) export(get_element_tree) export(get_guide_data) +export(get_last_plot) +export(get_layer_data) +export(get_layer_grob) +export(get_panel_scales) +export(get_theme) export(gg_dep) export(ggpar) export(ggplot) @@ -504,6 +509,7 @@ export(rel) export(remove_missing) export(render_axes) export(render_strips) +export(replace_theme) export(reset_theme_settings) export(resolution) export(scale_alpha) @@ -639,6 +645,7 @@ export(scale_y_sqrt) export(scale_y_time) export(sec_axis) export(set_last_plot) +export(set_theme) export(sf_transform_xy) export(should_stop) export(stage) @@ -704,6 +711,7 @@ export(unit) export(update_geom_defaults) export(update_labels) export(update_stat_defaults) +export(update_theme) export(vars) export(waiver) export(wrap_dims) diff --git a/NEWS.md b/NEWS.md index 75b5efef11..df77db8c95 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,20 @@ # ggplot2 (development version) +* Special getter and setter functions have been renamed for consistency, allowing + for better tab-completion with `get_*`- and `set_*`-prefixes. The old names + remain available for backward compatibility (@teunbrand, #5568). + + | New name | Old name | + | -------------------- | ----------------- | + | `get_theme()` | `theme_get()` | + | `set_theme()` | `theme_set()` | + | `replace_theme()` | `theme_replace()` | + | `update_theme()` | `theme_update()` | + | `get_last_plot()` | `last_plot()` | + | `get_layer_data()` | `layer_data()` | + | `get_layer_grob()` | `layer_grob()` | + | `get_panel_scales()` | `layer_scales()` | + * Discrete scales now support `minor_breaks`. This may only make sense in discrete position scales, where it affects the placement of minor ticks and minor gridlines (#5434). diff --git a/R/guides-.R b/R/guides-.R index 8a0117dc75..8a7396fab0 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -787,7 +787,7 @@ Guides <- ggproto( #' # Coord polar doesn't support proper guides, so we get a list #' polar <- p + coord_polar() #' get_guide_data(polar, "theta", panel = 2) -get_guide_data <- function(plot = last_plot(), aesthetic, panel = 1L) { +get_guide_data <- function(plot = get_last_plot(), aesthetic, panel = 1L) { check_string(aesthetic, allow_empty = FALSE) aesthetic <- standardise_aes_names(aesthetic) diff --git a/R/plot-build.R b/R/plot-build.R index 55c419d1e9..e2cc519823 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -5,15 +5,15 @@ #' a list of data frames (one for each layer), and a panel object, which #' contain all information about axis limits, breaks etc. #' -#' `layer_data()`, `layer_grob()`, and `layer_scales()` are helper +#' `get_layer_data()`, `get_layer_grob()`, and `get_panel_scales()` are helper #' functions that return the data, grob, or scales associated with a given #' layer. These are useful for tests. #' #' @param plot ggplot object -#' @param i An integer. In `layer_data()`, the data to return (in the order added to the -#' plot). In `layer_grob()`, the grob to return (in the order added to the -#' plot). In `layer_scales()`, the row of a facet to return scales for. -#' @param j An integer. In `layer_scales()`, the column of a facet to return +#' @param i An integer. In `get_layer_data()`, the data to return (in the order added to the +#' plot). In `get_layer_grob()`, the grob to return (in the order added to the +#' plot). In `get_panel_scales()`, the row of a facet to return scales for. +#' @param j An integer. In `get_panel_scales()`, the column of a facet to return #' scales for. #' @seealso #' [print.ggplot()] and [benchplot()] for @@ -125,13 +125,16 @@ ggplot_build.ggplot <- function(plot) { #' @export #' @rdname ggplot_build -layer_data <- function(plot = last_plot(), i = 1L) { +get_layer_data <- function(plot = get_last_plot(), i = 1L) { ggplot_build(plot)$data[[i]] } +#' @export +#' @rdname ggplot_build +layer_data <- get_layer_data #' @export #' @rdname ggplot_build -layer_scales <- function(plot = last_plot(), i = 1L, j = 1L) { +get_panel_scales <- function(plot = get_last_plot(), i = 1L, j = 1L) { b <- ggplot_build(plot) layout <- b$layout$layout @@ -145,12 +148,20 @@ layer_scales <- function(plot = last_plot(), i = 1L, j = 1L) { #' @export #' @rdname ggplot_build -layer_grob <- function(plot = last_plot(), i = 1L) { +layer_scales <- get_panel_scales + +#' @export +#' @rdname ggplot_build +get_layer_grob <- function(plot = get_last_plot(), i = 1L) { b <- ggplot_build(plot) b$plot$layers[[i]]$draw_geom(b$data[[i]], b$layout) } +#' @export +#' @rdname ggplot_build +layer_grob <- get_layer_grob + #' Build a plot with all the usual bits and pieces. #' #' This function builds all grobs necessary for displaying the plot, and diff --git a/R/plot-last.R b/R/plot-last.R index 81f15d57aa..3a67f978ba 100644 --- a/R/plot-last.R +++ b/R/plot-last.R @@ -21,4 +21,8 @@ set_last_plot <- function(value) .store$set(value) #' @seealso [ggsave()] #' @export #' @keywords internal -last_plot <- function() .store$get() +get_last_plot <- function() .store$get() + +#' @export +#' @rdname get_last_plot +last_plot <- get_last_plot diff --git a/R/save.R b/R/save.R index dc71365c25..2f28c49418 100644 --- a/R/save.R +++ b/R/save.R @@ -89,7 +89,7 @@ #' dev.off() #' #' } -ggsave <- function(filename, plot = last_plot(), +ggsave <- function(filename, plot = get_last_plot(), device = NULL, path = NULL, scale = 1, width = NA, height = NA, units = c("in", "cm", "mm", "px"), dpi = 300, limitsize = TRUE, bg = NULL, diff --git a/R/theme-current.R b/R/theme-current.R index b56b2e1651..ac24ec4724 100644 --- a/R/theme-current.R +++ b/R/theme-current.R @@ -5,8 +5,8 @@ NULL #' Get, set, and modify the active theme #' #' The current/active theme (see [theme()]) is automatically applied to every -#' plot you draw. Use `theme_get()` to get the current theme, and `theme_set()` to -#' completely override it. `theme_update()` and `theme_replace()` are shorthands for +#' plot you draw. Use `get_theme()` to get the current theme, and `set_theme()` to +#' completely override it. `update_theme()` and `replace_theme()` are shorthands for #' changing individual elements. #' #' @section Adding on to a theme: @@ -14,30 +14,30 @@ NULL #' `+` and `%+replace%` can be used to modify elements in themes. #' #' `+` updates the elements of e1 that differ from elements specified (not -#' NULL) in e2. Thus this operator can be used to incrementally add or modify +#' `NULL`) in e2. Thus this operator can be used to incrementally add or modify #' attributes of a ggplot theme. #' #' In contrast, `%+replace%` replaces the entire element; any element of a #' theme not specified in e2 will not be present in the resulting theme (i.e. -#' NULL). Thus this operator can be used to overwrite an entire theme. +#' `NULL`). Thus this operator can be used to overwrite an entire theme. #' -#' `theme_update()` uses the `+` operator, so that any unspecified values in the +#' `update_theme()` uses the `+` operator, so that any unspecified values in the #' theme element will default to the values they are set in the theme. -#' `theme_replace()` uses `%+replace%` to completely replace the element, so any +#' `replace_theme()` uses `%+replace%` to completely replace the element, so any #' unspecified values will overwrite the current value in the theme with #' `NULL`. #' -#' In summary, the main differences between `theme_set()`, `theme_update()`, -#' and `theme_replace()` are: -#' * `theme_set()` completely overrides the current theme. -#' * `theme_update()` modifies a particular element of the current theme +#' In summary, the main differences between `set_theme()`, `update_theme()`, +#' and `replace_theme()` are: +#' * `set_theme()` completely overrides the current theme. +#' * `update_theme()` modifies a particular element of the current theme #' using the `+` operator. -#' * `theme_replace()` modifies a particular element of the current theme +#' * `replace_theme()` modifies a particular element of the current theme #' using the `%+replace%` operator. #' #' @param ... named list of theme settings #' @param e1,e2 Theme and element to combine -#' @return `theme_set()`, `theme_update()`, and `theme_replace()` +#' @return `set_theme()`, `update_theme()`, and `replace_theme()` #' invisibly return the previous theme so you can easily save it, then #' later restore it. #' @seealso [+.gg()] @@ -47,25 +47,25 @@ NULL #' geom_point() #' p #' -#' # Use theme_set() to completely override the current theme. -#' # theme_update() and theme_replace() are similar except they +#' # Use set_theme() to completely override the current theme. +#' # update_theme() and replace_theme() are similar except they #' # apply directly to the current/active theme. -#' # theme_update() modifies a particular element of the current theme. +#' # update_theme() modifies a particular element of the current theme. #' # Here we have the old theme so we can later restore it. #' # Note that the theme is applied when the plot is drawn, not #' # when it is created. -#' old <- theme_set(theme_bw()) +#' old <- set_theme(theme_bw()) #' p #' -#' theme_set(old) -#' theme_update(panel.grid.minor = element_line(colour = "red")) +#' set_theme(old) +#' update_theme(panel.grid.minor = element_line(colour = "red")) #' p #' -#' theme_set(old) -#' theme_replace(panel.grid.minor = element_line(colour = "red")) +#' set_theme(old) +#' replace_theme(panel.grid.minor = element_line(colour = "red")) #' p #' -#' theme_set(old) +#' set_theme(old) #' p #' #' @@ -82,33 +82,49 @@ NULL #' theme(text = element_text(family = "Times")) #' rep_el$text #' -theme_get <- function() { +get_theme <- function() { ggplot_global$theme_current } -#' @rdname theme_get +#' @export +#' @rdname get_theme +theme_get <- get_theme + +#' @rdname get_theme #' @param new new theme (a list of theme elements) #' @export -theme_set <- function(new) { +set_theme <- function(new) { check_object(new, is.theme, "a {.cls theme} object") old <- ggplot_global$theme_current ggplot_global$theme_current <- new invisible(old) } -#' @rdname theme_get #' @export -theme_update <- function(...) { - theme_set(theme_get() + theme(...)) +#' @rdname get_theme +theme_set <- set_theme + +#' @rdname get_theme +#' @export +update_theme <- function(...) { + set_theme(get_theme() + theme(...)) } -#' @rdname theme_get #' @export -theme_replace <- function(...) { - theme_set(theme_get() %+replace% theme(...)) +#' @rdname get_theme +theme_update <- update_theme + +#' @rdname get_theme +#' @export +replace_theme <- function(...) { + set_theme(get_theme() %+replace% theme(...)) } -#' @rdname theme_get +#' @export +#' @rdname get_theme +theme_replace <- replace_theme + +#' @rdname get_theme #' @export "%+replace%" <- function(e1, e2) { if (!is.theme(e1) || !is.theme(e2)) { diff --git a/R/theme.R b/R/theme.R index f151a316a7..28d9cf1008 100644 --- a/R/theme.R +++ b/R/theme.R @@ -561,7 +561,7 @@ validate_theme <- function(theme, tree = get_element_tree(), call = caller_env() } # Combine plot defaults with current theme to get complete theme for a plot -plot_theme <- function(x, default = theme_get()) { +plot_theme <- function(x, default = get_theme()) { theme <- x$theme # apply theme defaults appropriately if needed diff --git a/man/get_guide_data.Rd b/man/get_guide_data.Rd index ece14cf284..5b15ad2b50 100644 --- a/man/get_guide_data.Rd +++ b/man/get_guide_data.Rd @@ -4,7 +4,7 @@ \alias{get_guide_data} \title{Extract tick information from guides} \usage{ -get_guide_data(plot = last_plot(), aesthetic, panel = 1L) +get_guide_data(plot = get_last_plot(), aesthetic, panel = 1L) } \arguments{ \item{plot}{A \code{ggplot} or \code{ggplot_build} object.} diff --git a/man/last_plot.Rd b/man/get_last_plot.Rd similarity index 84% rename from man/last_plot.Rd rename to man/get_last_plot.Rd index 6d47629391..0da1c83a54 100644 --- a/man/last_plot.Rd +++ b/man/get_last_plot.Rd @@ -1,9 +1,12 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/plot-last.R -\name{last_plot} +\name{get_last_plot} +\alias{get_last_plot} \alias{last_plot} \title{Retrieve the last plot to be modified or created.} \usage{ +get_last_plot() + last_plot() } \description{ diff --git a/man/theme_get.Rd b/man/get_theme.Rd similarity index 60% rename from man/theme_get.Rd rename to man/get_theme.Rd index 2246f1146b..d3283d0e67 100644 --- a/man/theme_get.Rd +++ b/man/get_theme.Rd @@ -1,19 +1,31 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/theme-current.R -\name{theme_get} +\name{get_theme} +\alias{get_theme} \alias{theme_get} +\alias{set_theme} \alias{theme_set} +\alias{update_theme} \alias{theme_update} +\alias{replace_theme} \alias{theme_replace} \alias{\%+replace\%} \title{Get, set, and modify the active theme} \usage{ +get_theme() + theme_get() +set_theme(new) + theme_set(new) +update_theme(...) + theme_update(...) +replace_theme(...) + theme_replace(...) e1 \%+replace\% e2 @@ -26,14 +38,14 @@ e1 \%+replace\% e2 \item{e1, e2}{Theme and element to combine} } \value{ -\code{theme_set()}, \code{theme_update()}, and \code{theme_replace()} +\code{set_theme()}, \code{update_theme()}, and \code{replace_theme()} invisibly return the previous theme so you can easily save it, then later restore it. } \description{ The current/active theme (see \code{\link[=theme]{theme()}}) is automatically applied to every -plot you draw. Use \code{theme_get()} to get the current theme, and \code{theme_set()} to -completely override it. \code{theme_update()} and \code{theme_replace()} are shorthands for +plot you draw. Use \code{get_theme()} to get the current theme, and \code{set_theme()} to +completely override it. \code{update_theme()} and \code{replace_theme()} are shorthands for changing individual elements. } \section{Adding on to a theme}{ @@ -42,26 +54,26 @@ changing individual elements. \code{+} and \verb{\%+replace\%} can be used to modify elements in themes. \code{+} updates the elements of e1 that differ from elements specified (not -NULL) in e2. Thus this operator can be used to incrementally add or modify +\code{NULL}) in e2. Thus this operator can be used to incrementally add or modify attributes of a ggplot theme. In contrast, \verb{\%+replace\%} replaces the entire element; any element of a theme not specified in e2 will not be present in the resulting theme (i.e. -NULL). Thus this operator can be used to overwrite an entire theme. +\code{NULL}). Thus this operator can be used to overwrite an entire theme. -\code{theme_update()} uses the \code{+} operator, so that any unspecified values in the +\code{update_theme()} uses the \code{+} operator, so that any unspecified values in the theme element will default to the values they are set in the theme. -\code{theme_replace()} uses \verb{\%+replace\%} to completely replace the element, so any +\code{replace_theme()} uses \verb{\%+replace\%} to completely replace the element, so any unspecified values will overwrite the current value in the theme with \code{NULL}. -In summary, the main differences between \code{theme_set()}, \code{theme_update()}, -and \code{theme_replace()} are: +In summary, the main differences between \code{set_theme()}, \code{update_theme()}, +and \code{replace_theme()} are: \itemize{ -\item \code{theme_set()} completely overrides the current theme. -\item \code{theme_update()} modifies a particular element of the current theme +\item \code{set_theme()} completely overrides the current theme. +\item \code{update_theme()} modifies a particular element of the current theme using the \code{+} operator. -\item \code{theme_replace()} modifies a particular element of the current theme +\item \code{replace_theme()} modifies a particular element of the current theme using the \verb{\%+replace\%} operator. } } @@ -71,25 +83,25 @@ p <- ggplot(mtcars, aes(mpg, wt)) + geom_point() p -# Use theme_set() to completely override the current theme. -# theme_update() and theme_replace() are similar except they +# Use set_theme() to completely override the current theme. +# update_theme() and replace_theme() are similar except they # apply directly to the current/active theme. -# theme_update() modifies a particular element of the current theme. +# update_theme() modifies a particular element of the current theme. # Here we have the old theme so we can later restore it. # Note that the theme is applied when the plot is drawn, not # when it is created. -old <- theme_set(theme_bw()) +old <- set_theme(theme_bw()) p -theme_set(old) -theme_update(panel.grid.minor = element_line(colour = "red")) +set_theme(old) +update_theme(panel.grid.minor = element_line(colour = "red")) p -theme_set(old) -theme_replace(panel.grid.minor = element_line(colour = "red")) +set_theme(old) +replace_theme(panel.grid.minor = element_line(colour = "red")) p -theme_set(old) +set_theme(old) p diff --git a/man/ggplot_build.Rd b/man/ggplot_build.Rd index 0c03c1c0b4..239677f6ce 100644 --- a/man/ggplot_build.Rd +++ b/man/ggplot_build.Rd @@ -2,27 +2,36 @@ % Please edit documentation in R/plot-build.R \name{ggplot_build} \alias{ggplot_build} +\alias{get_layer_data} \alias{layer_data} +\alias{get_panel_scales} \alias{layer_scales} +\alias{get_layer_grob} \alias{layer_grob} \title{Build ggplot for rendering.} \usage{ ggplot_build(plot) -layer_data(plot = last_plot(), i = 1L) +get_layer_data(plot = get_last_plot(), i = 1L) -layer_scales(plot = last_plot(), i = 1L, j = 1L) +layer_data(plot = get_last_plot(), i = 1L) -layer_grob(plot = last_plot(), i = 1L) +get_panel_scales(plot = get_last_plot(), i = 1L, j = 1L) + +layer_scales(plot = get_last_plot(), i = 1L, j = 1L) + +get_layer_grob(plot = get_last_plot(), i = 1L) + +layer_grob(plot = get_last_plot(), i = 1L) } \arguments{ \item{plot}{ggplot object} -\item{i}{An integer. In \code{layer_data()}, the data to return (in the order added to the -plot). In \code{layer_grob()}, the grob to return (in the order added to the -plot). In \code{layer_scales()}, the row of a facet to return scales for.} +\item{i}{An integer. In \code{get_layer_data()}, the data to return (in the order added to the +plot). In \code{get_layer_grob()}, the grob to return (in the order added to the +plot). In \code{get_panel_scales()}, the row of a facet to return scales for.} -\item{j}{An integer. In \code{layer_scales()}, the column of a facet to return +\item{j}{An integer. In \code{get_panel_scales()}, the column of a facet to return scales for.} } \description{ @@ -32,7 +41,7 @@ a list of data frames (one for each layer), and a panel object, which contain all information about axis limits, breaks etc. } \details{ -\code{layer_data()}, \code{layer_grob()}, and \code{layer_scales()} are helper +\code{get_layer_data()}, \code{get_layer_grob()}, and \code{get_panel_scales()} are helper functions that return the data, grob, or scales associated with a given layer. These are useful for tests. } diff --git a/man/ggsave.Rd b/man/ggsave.Rd index 6c6f97d16d..2e06df38ea 100644 --- a/man/ggsave.Rd +++ b/man/ggsave.Rd @@ -6,7 +6,7 @@ \usage{ ggsave( filename, - plot = last_plot(), + plot = get_last_plot(), device = NULL, path = NULL, scale = 1, diff --git a/tests/testthat/test-aes-grouping.R b/tests/testthat/test-aes-grouping.R index 204128f197..bea15e2630 100644 --- a/tests/testthat/test-aes-grouping.R +++ b/tests/testthat/test-aes-grouping.R @@ -4,7 +4,7 @@ df <- data_frame( b = c("a", "b", "a", "b") ) -group <- function(x) as.vector(layer_data(x, 1)$group) +group <- function(x) as.vector(get_layer_data(x, 1)$group) groups <- function(x) vec_unique_count(group(x)) diff --git a/tests/testthat/test-aes-setting.R b/tests/testthat/test-aes-setting.R index 4c3e055ea8..422032017f 100644 --- a/tests/testthat/test-aes-setting.R +++ b/tests/testthat/test-aes-setting.R @@ -3,7 +3,7 @@ test_that("aesthetic parameters match length of data", { p <- ggplot(df, aes(x, y)) set_colours <- function(colours) { - layer_data(p + geom_point(colour = colours)) + get_layer_data(p + geom_point(colour = colours)) } set_colours("red") @@ -19,7 +19,7 @@ test_that("Length 1 aesthetics are recycled to 0", { expect_silent(plot(p)) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(nrow(data), 0) }) @@ -45,11 +45,11 @@ test_that("alpha affects only fill colour of solid geoms", { ribb <- ggplot(df, aes(x = x, ymin = 1, ymax = y + 1)) + geom_ribbon(fill = "red", colour = "red", alpha = 0.5) - expect_equal(layer_grob(poly)[[1]]$gp$col[[1]], "red") - expect_equal(layer_grob(rect)[[1]]$gp$col[[1]], "red") - expect_equal(layer_grob(ribb)[[1]]$children[[1]]$children[[2]]$gp$col[[1]], "red") + expect_equal(get_layer_grob(poly)[[1]]$gp$col[[1]], "red") + expect_equal(get_layer_grob(rect)[[1]]$gp$col[[1]], "red") + expect_equal(get_layer_grob(ribb)[[1]]$children[[1]]$children[[2]]$gp$col[[1]], "red") - expect_equal(layer_grob(poly)[[1]]$gp$fill[[1]], "#FF000080") - expect_equal(layer_grob(rect)[[1]]$gp$fill[[1]], "#FF000080") - expect_equal(layer_grob(ribb)[[1]]$children[[1]]$children[[1]]$gp$fill[[1]], "#FF000080") + expect_equal(get_layer_grob(poly)[[1]]$gp$fill[[1]], "#FF000080") + expect_equal(get_layer_grob(rect)[[1]]$gp$fill[[1]], "#FF000080") + expect_equal(get_layer_grob(ribb)[[1]]$children[[1]]$children[[1]]$gp$fill[[1]], "#FF000080") }) diff --git a/tests/testthat/test-aes.R b/tests/testthat/test-aes.R index 92b51b94e8..e407562082 100644 --- a/tests/testthat/test-aes.R +++ b/tests/testthat/test-aes.R @@ -49,18 +49,18 @@ test_that("aes evaluated in environment where plot created", { p <- ggplot(df, aes(foo, y)) + geom_point() # Accessing an undefined variable should result in error - expect_error(layer_data(p), "'foo' not found") + expect_error(get_layer_data(p), "'foo' not found") # Once it's defined we should get it back foo <- 0 - expect_equal(layer_data(p)$x, 0) + expect_equal(get_layer_data(p)$x, 0) # And regular variable shadowing should work f <- function() { foo <- 10 ggplot(df, aes(foo, y)) + geom_point() } - expect_equal(layer_data(f())$x, 10) + expect_equal(get_layer_data(f())$x, 10) }) test_that("constants are not wrapped in quosures", { diff --git a/tests/testthat/test-annotate.R b/tests/testthat/test-annotate.R index 8646433a92..129b5b6720 100644 --- a/tests/testthat/test-annotate.R +++ b/tests/testthat/test-annotate.R @@ -13,7 +13,7 @@ test_that("dates in segment annotation work", { yend = 10 ) - expect_true(all(c("xend", "yend") %in% names(layer_data(p, 2)))) + expect_true(all(c("xend", "yend") %in% names(get_layer_data(p, 2)))) }) test_that("segment annotations transform with scales", { diff --git a/tests/testthat/test-build.R b/tests/testthat/test-build.R index 24930a0373..cdcbe0c6ac 100644 --- a/tests/testthat/test-build.R +++ b/tests/testthat/test-build.R @@ -15,13 +15,13 @@ test_that("there is one data frame for each layer", { test_that("position aesthetics are coerced to correct type", { l1 <- ggplot(df, aes(x, y)) + geom_point() - d1 <- layer_data(l1, 1) + d1 <- get_layer_data(l1, 1) expect_type(d1$x, "double") expect_type(d1$y, "double") l2 <- ggplot(df, aes(x, z)) + geom_point() + scale_x_discrete() - d2 <- layer_data(l2, 1) + d2 <- get_layer_data(l2, 1) expect_s3_class(d2$x, "mapped_discrete") expect_s3_class(d2$y, "mapped_discrete") @@ -32,7 +32,7 @@ test_that("non-position aesthetics are mapped", { geom_point() expect_named( - layer_data(l1, 1), + get_layer_data(l1, 1), c( "x", "y", "fill", "group", "colour", "shape", "size", "PANEL", "alpha", "stroke" @@ -41,7 +41,7 @@ test_that("non-position aesthetics are mapped", { ) l2 <- l1 + scale_colour_manual(values = c("blue", "red", "yellow")) - d2 <- layer_data(l2, 1) + d2 <- get_layer_data(l2, 1) expect_equal(d2$colour, c("blue", "red", "yellow")) }) @@ -50,5 +50,5 @@ test_that("strings are not converted to factors", { p <- ggplot(df, aes(x, y)) + geom_text(aes(label = label), parse = TRUE) - expect_type(layer_data(p)$label, "character") + expect_type(get_layer_data(p)$label, "character") }) diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index 2a9b15867a..6e5f435d60 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -85,16 +85,16 @@ test_that("coord_polar can have free scales in facets", { geom_col() + coord_polar(theta = "y") - sc <- layer_scales(p + facet_wrap(~ x), 1, 1) + sc <- get_panel_scales(p + facet_wrap(~ x), 1, 1) expect_equal(sc$y$get_limits(), c(0, 2)) - sc <- layer_scales(p + facet_wrap(~ x, scales = "free"), 1, 1) + sc <- get_panel_scales(p + facet_wrap(~ x, scales = "free"), 1, 1) expect_equal(sc$y$get_limits(), c(0, 1)) - sc <- layer_scales(p + facet_grid(x ~ .), 1, 1) + sc <- get_panel_scales(p + facet_grid(x ~ .), 1, 1) expect_equal(sc$y$get_limits(), c(0, 2)) - sc <- layer_scales(p + facet_grid(x ~ ., scales = "free"), 1, 1) + sc <- get_panel_scales(p + facet_grid(x ~ ., scales = "free"), 1, 1) expect_equal(sc$y$get_limits(), c(0, 1)) }) diff --git a/tests/testthat/test-empty-data.R b/tests/testthat/test-empty-data.R index b9c72ced1b..3d7c27c52d 100644 --- a/tests/testthat/test-empty-data.R +++ b/tests/testthat/test-empty-data.R @@ -3,30 +3,30 @@ df0 <- data_frame(mpg = numeric(0), wt = numeric(0), am = numeric(0), cyl = nume test_that("layers with empty data are silently omitted", { # Empty data (no visible points) d <- ggplot(df0, aes(mpg,wt)) + geom_point() - expect_equal(nrow(layer_data(d)), 0) + expect_equal(nrow(get_layer_data(d)), 0) d <- ggplot() + geom_point(data = df0, aes(mpg,wt)) - expect_equal(nrow(layer_data(d)), 0) + expect_equal(nrow(get_layer_data(d)), 0) # Regular mtcars data, x=mpg, y=wt, normal points and points from empty data frame d <- ggplot(mtcars, aes(mpg, wt)) + geom_point() + geom_point(data = df0) - expect_equal(nrow(layer_data(d, 1)), nrow(mtcars)) - expect_equal(nrow(layer_data(d, 2)), 0) + expect_equal(nrow(get_layer_data(d, 1)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d, 2)), 0) # Regular mtcars data, but points only from empty data frame d <- ggplot(mtcars, aes(mpg, wt)) + geom_point(data = df0) - expect_equal(nrow(layer_data(d, 1)), 0) + expect_equal(nrow(get_layer_data(d, 1)), 0) }) test_that("plots with empty data and vectors for aesthetics work", { d <- ggplot(NULL, aes(1:5, 1:5)) + geom_point() - expect_equal(nrow(layer_data(d)), 5) + expect_equal(nrow(get_layer_data(d)), 5) d <- ggplot(data_frame(), aes(1:5, 1:5)) + geom_point() - expect_equal(nrow(layer_data(d)), 5) + expect_equal(nrow(get_layer_data(d)), 5) d <- ggplot() + geom_point(aes(1:5, 1:5)) - expect_equal(nrow(layer_data(d)), 5) + expect_equal(nrow(get_layer_data(d)), 5) }) test_that("layers with empty data are silently omitted with facet_wrap", { @@ -34,22 +34,22 @@ test_that("layers with empty data are silently omitted with facet_wrap", { d <- ggplot(df0, aes(mpg, wt)) + geom_point() + facet_wrap(~cyl) - expect_error(layer_data(d), "must have at least one value") + expect_error(get_layer_data(d), "must have at least one value") d <- d + geom_point(data = mtcars) - expect_equal(nrow(layer_data(d, 1)), 0) - expect_equal(nrow(layer_data(d, 2)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d, 1)), 0) + expect_equal(nrow(get_layer_data(d, 2)), nrow(mtcars)) }) test_that("layers with empty data are silently omitted with facet_grid", { d <- ggplot(df0, aes(mpg, wt)) + geom_point() + facet_grid(am ~ cyl) - expect_error(layer_data(d), "must have at least one value") + expect_error(get_layer_data(d), "must have at least one value") d <- d + geom_point(data = mtcars) - expect_equal(nrow(layer_data(d, 1)), 0) - expect_equal(nrow(layer_data(d, 2)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d, 1)), 0) + expect_equal(nrow(get_layer_data(d, 2)), nrow(mtcars)) }) test_that("empty data overrides plot defaults", { @@ -57,27 +57,27 @@ test_that("empty data overrides plot defaults", { d <- ggplot(mtcars, aes(mpg, wt)) + geom_point() + geom_point(data = data_frame()) - expect_error(layer_data(d), "not found") + expect_error(get_layer_data(d), "not found") # No extra points when x and y vars don't exist but are set d <- ggplot(mtcars, aes(mpg, wt)) + geom_point() + geom_point(data = data_frame(), x = 20, y = 3) - expect_equal(nrow(layer_data(d, 1)), nrow(mtcars)) - expect_equal(nrow(layer_data(d, 2)), 0) + expect_equal(nrow(get_layer_data(d, 1)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d, 2)), 0) # No extra points when x and y vars are empty, even when aesthetics are set d <- ggplot(mtcars, aes(mpg, wt)) + geom_point() + geom_point(data = df0, x = 20, y = 3) - expect_equal(nrow(layer_data(d, 1)), nrow(mtcars)) - expect_equal(nrow(layer_data(d, 2)), 0) + expect_equal(nrow(get_layer_data(d, 1)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d, 2)), 0) }) test_that("layer inherits data from plot when data = NULL", { d <- ggplot(mtcars, aes(mpg, wt)) + geom_point(data = NULL) - expect_equal(nrow(layer_data(d)), nrow(mtcars)) + expect_equal(nrow(get_layer_data(d)), nrow(mtcars)) }) test_that("empty layers still generate one grob per panel", { @@ -88,13 +88,13 @@ test_that("empty layers still generate one grob per panel", { geom_point() + facet_wrap(~y) - expect_equal(length(layer_grob(d)), 3) + expect_equal(length(get_layer_grob(d)), 3) }) test_that("missing layers generate one grob per panel", { df <- data_frame(x = 1:4, y = rep(1:2, 2), g = rep(1:2, 2)) base <- ggplot(df, aes(x, y)) + geom_point(shape = NA, na.rm = TRUE) - expect_equal(length(layer_grob(base)), 1) - expect_equal(length(layer_grob(base + facet_wrap(~ g))), 2) + expect_equal(length(get_layer_grob(base)), 1) + expect_equal(length(get_layer_grob(base + facet_wrap(~ g))), 2) }) diff --git a/tests/testthat/test-facet-.R b/tests/testthat/test-facet-.R index 5d4b176b6b..8573ef80d5 100644 --- a/tests/testthat/test-facet-.R +++ b/tests/testthat/test-facet-.R @@ -92,9 +92,9 @@ test_that("facets split up the data", { l2 <- p + facet_grid(. ~ z) l3 <- p + facet_grid(z ~ .) - d1 <- layer_data(l1) - d2 <- layer_data(l2) - d3 <- layer_data(l3) + d1 <- get_layer_data(l1) + d2 <- get_layer_data(l2) + d3 <- get_layer_data(l3) expect_equal(d1, d2) expect_equal(d1, d3) @@ -105,8 +105,8 @@ test_that("facets split up the data", { l4 <- p_empty + facet_wrap(~z) l5 <- p_empty + facet_grid(. ~ z) - d4 <- layer_data(l4) - d5 <- layer_data(l5) + d4 <- get_layer_data(l4) + d5 <- get_layer_data(l5) expect_equal(d1, d4) expect_equal(d1, d5) @@ -120,7 +120,7 @@ test_that("facet_wrap() accepts vars()", { p1 <- p + facet_wrap(~z) p2 <- p + facet_wrap(vars(Z = z), labeller = label_both) - expect_identical(layer_data(p1), layer_data(p2)) + expect_identical(get_layer_data(p1), get_layer_data(p2)) }) test_that("facet_grid() accepts vars()", { @@ -165,14 +165,14 @@ test_that("facet_wrap()/facet_grid() compact the facet spec, and accept empty sp # facet_wrap() p_wrap <- p + facet_wrap(vars(NULL)) - d_wrap <- layer_data(p_wrap) + d_wrap <- get_layer_data(p_wrap) expect_equal(d_wrap$PANEL, factor(c(1L, 1L, 1L))) expect_equal(d_wrap$group, structure(c(-1L, -1L, -1L), n = 1L)) # facet_grid() p_grid <- p + facet_grid(vars(NULL)) - d_grid <- layer_data(p_grid) + d_grid <- get_layer_data(p_grid) expect_equal(d_grid$PANEL, factor(c(1L, 1L, 1L))) expect_equal(d_grid$group, structure(c(-1L, -1L, -1L), n = 1L)) diff --git a/tests/testthat/test-geom-bar.R b/tests/testthat/test-geom-bar.R index b21a2f5a64..28d2430c09 100644 --- a/tests/testthat/test-geom-bar.R +++ b/tests/testthat/test-geom-bar.R @@ -13,11 +13,11 @@ test_that("geom_bar works in both directions", { dat <- data_frame(x = c("a", "b", "b", "c", "c", "c")) p <- ggplot(dat, aes(x)) + geom_bar() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(dat, aes(y = x)) + geom_bar() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL diff --git a/tests/testthat/test-geom-boxplot.R b/tests/testthat/test-geom-boxplot.R index e6cfa26416..195a3d9ade 100644 --- a/tests/testthat/test-geom-boxplot.R +++ b/tests/testthat/test-geom-boxplot.R @@ -23,11 +23,11 @@ test_that("geom_boxplot works in both directions", { dat <- data_frame(x = 1, y = c(-(1:20) ^ 3, (1:20) ^ 3) ) p <- ggplot(dat, aes(x, y)) + geom_boxplot() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(dat, aes(y, x)) + geom_boxplot() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -57,7 +57,7 @@ test_that("can use US spelling of colour", { df <- data_frame(x = 1, y = c(1:5, 100)) plot <- ggplot(df, aes(x, y)) + geom_boxplot(outlier.color = "red") - gpar <- layer_grob(plot)[[1]]$children[[1]]$children[[1]]$gp + gpar <- get_layer_grob(plot)[[1]]$children[[1]]$children[[1]]$gp expect_equal(gpar$col, "#FF0000FF") }) @@ -70,7 +70,7 @@ test_that("boxes with variable widths do not overlap", { p <- ggplot(df, aes(group, value, colour = subgroup)) + geom_boxplot(varwidth = TRUE) - d <- layer_data(p)[c("xmin", "xmax")] + d <- get_layer_data(p)[c("xmin", "xmax")] xid <- find_x_overlaps(d) expect_false(any(duplicated(xid))) @@ -83,8 +83,8 @@ test_that("boxplots with a group size >1 error", { ) + geom_boxplot(stat = "identity") - expect_equal(nrow(layer_data(p, 1)), 3) - expect_snapshot_error(layer_grob(p, 1)) + expect_equal(nrow(get_layer_data(p, 1)), 3) + expect_snapshot_error(get_layer_grob(p, 1)) }) # Visual tests ------------------------------------------------------------ diff --git a/tests/testthat/test-geom-col.R b/tests/testthat/test-geom-col.R index 17c61064d9..5849ea0bcc 100644 --- a/tests/testthat/test-geom-col.R +++ b/tests/testthat/test-geom-col.R @@ -17,11 +17,11 @@ test_that("geom_col works in both directions", { dat <- data_frame(x = c("a", "b", "c"), y = c(1.2, 2.5, 3.1)) p <- ggplot(dat, aes(x, y)) + geom_col() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(dat, aes(y, x)) + geom_col() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -33,17 +33,17 @@ test_that("geom_col supports alignment of columns", { dat <- data_frame(x = c("a", "b"), y = c(1.2, 2.5)) p <- ggplot(dat, aes(x, y)) + geom_col(just = 0.5) - y <- layer_data(p) + y <- get_layer_data(p) expect_equal(as.numeric(y$xmin), c(0.55, 1.55)) expect_equal(as.numeric(y$xmax), c(1.45, 2.45)) p <- ggplot(dat, aes(x, y)) + geom_col(just = 1.0) - y <- layer_data(p) + y <- get_layer_data(p) expect_equal(as.numeric(y$xmin), c(0.1, 1.1)) expect_equal(as.numeric(y$xmax), c(1.0, 2.0)) p <- ggplot(dat, aes(x, y)) + geom_col(just = 0.0) - y <- layer_data(p) + y <- get_layer_data(p) expect_equal(as.numeric(y$xmin), c(1.0, 2.0)) expect_equal(as.numeric(y$xmax), c(1.9, 2.9)) }) diff --git a/tests/testthat/test-geom-dotplot.R b/tests/testthat/test-geom-dotplot.R index 8f9aae6024..3cf61d4216 100644 --- a/tests/testthat/test-geom-dotplot.R +++ b/tests/testthat/test-geom-dotplot.R @@ -11,7 +11,7 @@ test_that("dodging works", { position = "dodge", stackdir = "center" ) - df <- layer_data(p) + df <- get_layer_data(p) # Number of levels in the dodged variable ndodge <- 3 @@ -37,7 +37,7 @@ test_that("dodging works", { test_that("binning works", { bp <- ggplot(dat, aes(y)) + geom_dotplot(binwidth = .4, method = "histodot") - x <- layer_data(bp)$x + x <- get_layer_data(bp)$x # Need ugly hack to make sure mod function doesn't give values like -3.99999 # due to floating point error @@ -45,7 +45,7 @@ test_that("binning works", { bp <- ggplot(dat, aes(x = y)) + geom_dotplot(binwidth = .4, method = "dotdensity") - x <- layer_data(bp)$x + x <- get_layer_data(bp)$x # This one doesn't ensure that dotdensity works, but it does check that it's not # doing fixed bin sizes diff --git a/tests/testthat/test-geom-freqpoly.R b/tests/testthat/test-geom-freqpoly.R index 762b075977..09a6b7dc27 100644 --- a/tests/testthat/test-geom-freqpoly.R +++ b/tests/testthat/test-geom-freqpoly.R @@ -2,7 +2,7 @@ test_that("can do frequency polygon with categorical x", { df <- data_frame(x = rep(letters[1:3], 3:1)) p <- ggplot(df, aes(x)) + geom_freqpoly(stat = "count") - d <- layer_data(p) + d <- get_layer_data(p) expect_s3_class(d$x, "mapped_discrete") expect_equal(d$x, mapped_discrete(1:3)) diff --git a/tests/testthat/test-geom-hex.R b/tests/testthat/test-geom-hex.R index e63e159438..0934f8fd27 100644 --- a/tests/testthat/test-geom-hex.R +++ b/tests/testthat/test-geom-hex.R @@ -5,7 +5,7 @@ test_that("density and value summaries are available", { base <- ggplot(df, aes(x, y)) + geom_hex() - out <- layer_data(base) + out <- get_layer_data(base) expect_equal(nrow(out), 2) expect_equal(out$density, c(0.75, 0.25), tolerance = 1e-7) expect_equal(out$count, c(3, 1), tolerance = 1e-7) @@ -16,7 +16,7 @@ test_that("size and linetype are applied", { plot <- ggplot(df, aes(x, y)) + geom_hex(color = "red", linewidth = 4, linetype = 2) - gpar <- layer_grob(plot)[[1]]$children[[1]]$gp + gpar <- get_layer_grob(plot)[[1]]$children[[1]]$gp expect_equal(gpar$lwd, rep(4, 2) * .pt, tolerance = 1e-7) expect_equal(gpar$lty, rep(2, 2), tolerance = 1e-7) }) diff --git a/tests/testthat/test-geom-label.R b/tests/testthat/test-geom-label.R index 2504787fd2..028c3c4980 100644 --- a/tests/testthat/test-geom-label.R +++ b/tests/testthat/test-geom-label.R @@ -16,7 +16,7 @@ test_that("geom_label() rotates labels", { geom_label(angle = angle_in) vps <- lapply( - layer_grob(p, 1)[[1]]$children, + get_layer_grob(p, 1)[[1]]$children, `[[`, "vp" ) angle_out <- unname(vapply(vps, `[[`, numeric(1), "angle")) diff --git a/tests/testthat/test-geom-quantile.R b/tests/testthat/test-geom-quantile.R index d9eaf84184..742e2850ed 100644 --- a/tests/testthat/test-geom-quantile.R +++ b/tests/testthat/test-geom-quantile.R @@ -33,7 +33,7 @@ test_that("geom_quantile matches quantile regression", { # pred_rq is a matrix; convert it to data.frame so that it can be compared pred_rq <- as.data.frame(pred_rq) - ggplot_data <- layer_data(ps) + ggplot_data <- get_layer_data(ps) pred_rq_test_25 <- pred_rq[, c("x", "Q_25")] colnames(pred_rq_test_25) <- c("x", "y") diff --git a/tests/testthat/test-geom-ribbon.R b/tests/testthat/test-geom-ribbon.R index 22e98a81c2..c923942dde 100644 --- a/tests/testthat/test-geom-ribbon.R +++ b/tests/testthat/test-geom-ribbon.R @@ -19,7 +19,7 @@ test_that("NAs are not dropped from the data", { p <- ggplot(df, aes(x))+ geom_ribbon(aes(ymin = y - 1, ymax = y + 1)) - expect_equal(layer_data(p)$ymin, c(0, 0, NA, 0, 0)) + expect_equal(get_layer_data(p)$ymin, c(0, 0, NA, 0, 0)) }) test_that("geom_ribbon works in both directions", { @@ -28,11 +28,11 @@ test_that("geom_ribbon works in both directions", { ymax = c(4, 6, 5, 4.5, 5.2)) p <- ggplot(dat, aes(x, ymin = ymin, ymax = ymax)) + geom_ribbon() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(dat, aes(y = x, xmin = ymin, xmax = ymax)) + geom_ribbon() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -45,11 +45,11 @@ test_that("outline.type option works", { p <- ggplot(df, aes(x, ymin = -y, ymax = y)) - g_ribbon_default <- layer_grob(p + geom_ribbon())[[1]] - g_ribbon_upper <- layer_grob(p + geom_ribbon(outline.type = "upper"))[[1]] - g_ribbon_lower <- layer_grob(p + geom_ribbon(outline.type = "lower"))[[1]] - g_ribbon_full <- layer_grob(p + geom_ribbon(outline.type = "full"))[[1]] - g_area_default <- layer_grob(ggplot(df, aes(x, y)) + geom_area(stat = "identity"))[[1]] + g_ribbon_default <- get_layer_grob(p + geom_ribbon())[[1]] + g_ribbon_upper <- get_layer_grob(p + geom_ribbon(outline.type = "upper"))[[1]] + g_ribbon_lower <- get_layer_grob(p + geom_ribbon(outline.type = "lower"))[[1]] + g_ribbon_full <- get_layer_grob(p + geom_ribbon(outline.type = "full"))[[1]] + g_area_default <- get_layer_grob(ggplot(df, aes(x, y)) + geom_area(stat = "identity"))[[1]] # default expect_s3_class(g_ribbon_default$children[[1]]$children[[1]], "polygon") @@ -85,7 +85,7 @@ test_that("ribbons can have gradients", { p <- ggplot(df, aes(x, ymin = ymin, ymax = ymax, fill = x)) + geom_ribbon(outline.type = "full") + scale_fill_gradientn(colours = c("red", "blue")) - fill <- layer_grob(p)[[1]]$children[[1]]$gp$fill + fill <- get_layer_grob(p)[[1]]$children[[1]]$gp$fill expect_s3_class(fill, "GridLinearGradient") expect_equal(fill$colours, alpha(c("red", "blue"), NA)) diff --git a/tests/testthat/test-geom-rug.R b/tests/testthat/test-geom-rug.R index 7171db1e10..a613e58f0d 100644 --- a/tests/testthat/test-geom-rug.R +++ b/tests/testthat/test-geom-rug.R @@ -3,8 +3,8 @@ df <- data_frame(x = 1:n, y = (1:n)^3) p <- ggplot(df, aes(x, y)) + geom_point() + geom_rug(sides = 'l') test_that("coord_flip flips the rugs", { - a <- layer_grob(p, 2) - b <- layer_grob(p + coord_flip(), 2) + a <- get_layer_grob(p, 2) + b <- get_layer_grob(p + coord_flip(), 2) # Rugs along y-axis, all x coordinates are the same expect_equal(length(a[[1]]$children[[1]]$x0), 1) @@ -25,14 +25,14 @@ test_that("Rug length needs unit object", { }) test_that("Rug lengths are correct", { - a <- layer_grob(p, 2) + a <- get_layer_grob(p, 2) # Check default lengths expect_equal(a[[1]]$children[[1]]$x0, unit(0, "npc")) expect_equal(a[[1]]$children[[1]]$x1, unit(0.03, "npc")) p <- ggplot(df, aes(x, y)) + geom_point() + geom_rug(sides = 'l', length = unit(12, "pt")) - b <- layer_grob(p, 2) + b <- get_layer_grob(p, 2) # Check default length is changed expect_equal(a[[1]]$children[[1]]$x0, unit(0, "npc")) diff --git a/tests/testthat/test-geom-rule.R b/tests/testthat/test-geom-rule.R index e41ab41103..35bac24974 100644 --- a/tests/testthat/test-geom-rule.R +++ b/tests/testthat/test-geom-rule.R @@ -6,28 +6,28 @@ p_col <- ggplot(df, aes(x, y, colour = factor(x))) + geom_point() test_that("setting parameters makes one row df", { b <- p + geom_hline(yintercept = 1.5) - expect_equal(layer_data(b, 2)$yintercept, 1.5) + expect_equal(get_layer_data(b, 2)$yintercept, 1.5) b <- p + geom_vline(xintercept = 1.5) - expect_equal(layer_data(b, 2)$xintercept, 1.5) + expect_equal(get_layer_data(b, 2)$xintercept, 1.5) b <- p + geom_abline() - expect_equal(layer_data(b, 2)$intercept, 0) - expect_equal(layer_data(b, 2)$slope, 1) + expect_equal(get_layer_data(b, 2)$intercept, 0) + expect_equal(get_layer_data(b, 2)$slope, 1) b <- p + geom_abline(slope = 0, intercept = 1) - expect_equal(layer_data(b, 2)$intercept, 1) - expect_equal(layer_data(b, 2)$slope, 0) + expect_equal(get_layer_data(b, 2)$intercept, 1) + expect_equal(get_layer_data(b, 2)$slope, 0) }) test_that("setting aesthetics generates one row for each input row", { b <- p + geom_hline(aes(yintercept = 1.5)) - expect_equal(layer_data(b, 2)$yintercept, rep(1.5, 3)) + expect_equal(get_layer_data(b, 2)$yintercept, rep(1.5, 3)) b <- p + geom_vline(aes(xintercept = 1.5)) - expect_equal(layer_data(b, 2)$xintercept, rep(1.5, 3)) + expect_equal(get_layer_data(b, 2)$xintercept, rep(1.5, 3)) b <- p + geom_abline(aes(slope = 0, intercept = 1)) - expect_equal(layer_data(b, 2)$intercept, rep(1, 3)) - expect_equal(layer_data(b, 2)$slope, rep(0, 3)) + expect_equal(get_layer_data(b, 2)$intercept, rep(1, 3)) + expect_equal(get_layer_data(b, 2)$slope, rep(0, 3)) }) diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index 1db38a1fff..d79146ff73 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -88,7 +88,7 @@ test_that("geom_sf() removes rows containing missing aes", { if (packageVersion("sf") < "0.5.3") skip("Need sf 0.5.3") grob_xy_length <- function(x) { - g <- layer_grob(x)[[1]] + g <- get_layer_grob(x)[[1]] c(length(g$x), length(g$y)) } @@ -127,7 +127,7 @@ test_that("geom_sf() handles alpha properly", { ) red <- "#FF0000FF" p <- ggplot(sfc) + geom_sf(colour = red, fill = red, alpha = 0.5) - g <- layer_grob(p)[[1]] + g <- get_layer_grob(p)[[1]] # alpha affects the colour of points and lines expect_equal(g[[1]]$gp$col, alpha(red, 0.5)) diff --git a/tests/testthat/test-geom-smooth.R b/tests/testthat/test-geom-smooth.R index c8a7f3af32..5f8282c176 100644 --- a/tests/testthat/test-geom-smooth.R +++ b/tests/testthat/test-geom-smooth.R @@ -4,18 +4,18 @@ test_that("data is ordered by x", { ps <- ggplot(df, aes(x, y))+ geom_smooth(stat = "identity", se = FALSE) - expect_equal(layer_data(ps)[c("x", "y")], df[order(df$x), ], ignore_attr = TRUE) + expect_equal(get_layer_data(ps)[c("x", "y")], df[order(df$x), ], ignore_attr = TRUE) }) test_that("geom_smooth works in both directions", { p <- ggplot(mpg, aes(displ, hwy)) + geom_smooth(method = 'loess', formula = y ~ x) - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(mpg, aes(hwy, displ)) + geom_smooth(orientation = "y", method = 'loess', formula = y ~ x) - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -45,7 +45,7 @@ test_that("default smoothing methods for small and large data sets work", { p <- ggplot(df, aes(x, y)) + geom_smooth() expect_message( - plot_data <- layer_data(p), + plot_data <- get_layer_data(p), "method = 'loess' and formula = 'y ~ x'" ) expect_equal(plot_data$y, as.numeric(out)) @@ -64,7 +64,7 @@ test_that("default smoothing methods for small and large data sets work", { p <- ggplot(df, aes(x, y)) + geom_smooth() expect_message( - plot_data <- layer_data(p), + plot_data <- get_layer_data(p), "method = 'gam' and formula = 'y ~ s\\(x, bs = \"cs\"\\)" ) expect_equal(plot_data$y, as.numeric(out)) @@ -73,7 +73,7 @@ test_that("default smoothing methods for small and large data sets work", { p <- ggplot(df, aes(x, y)) + geom_smooth(method = "auto") expect_message( - plot_data <- layer_data(p), + plot_data <- get_layer_data(p), "method = 'gam' and formula = 'y ~ s\\(x, bs = \"cs\"\\)" ) expect_equal(plot_data$y, as.numeric(out)) @@ -90,7 +90,7 @@ test_that("geom_smooth() works when one group fails", { geom_smooth(method = "loess", formula = y ~ x) suppressWarnings( - expect_warning(ld <- layer_data(p), "Failed to fit group 1") + expect_warning(ld <- get_layer_data(p), "Failed to fit group 1") ) expect_equal(unique(ld$group), 2) expect_gte(nrow(ld), 2) diff --git a/tests/testthat/test-geom-text.R b/tests/testthat/test-geom-text.R index 36c52a14a0..ca5b495968 100644 --- a/tests/testthat/test-geom-text.R +++ b/tests/testthat/test-geom-text.R @@ -21,10 +21,10 @@ test_that("geom_text() drops missing angles", { test_that("geom_text() accepts mm and pt size units", { p <- ggplot(data_frame0(x = 1, y = 1, label = "A"), aes(x, y, label = label)) - grob <- layer_grob(p + geom_text(size = 10, size.unit = "mm"))[[1]] + grob <- get_layer_grob(p + geom_text(size = 10, size.unit = "mm"))[[1]] expect_equal(grob$gp$fontsize, 10 * .pt) - grob <- layer_grob(p + geom_text(size = 10, size.unit = "pt"))[[1]] + grob <- get_layer_grob(p + geom_text(size = 10, size.unit = "pt"))[[1]] expect_equal(grob$gp$fontsize, 10) }) diff --git a/tests/testthat/test-geom-tile.R b/tests/testthat/test-geom-tile.R index f63602bf66..581963a4b2 100644 --- a/tests/testthat/test-geom-tile.R +++ b/tests/testthat/test-geom-tile.R @@ -1,11 +1,11 @@ test_that("accepts width and height params", { df <- data_frame(x = c("a", "b"), y = c("a", "b")) - out1 <- layer_data(ggplot(df, aes(x, y)) + geom_tile()) + out1 <- get_layer_data(ggplot(df, aes(x, y)) + geom_tile()) expect_equal(out1$xmin, new_mapped_discrete(c(0.5, 1.5))) expect_equal(out1$xmax, new_mapped_discrete(c(1.5, 2.5))) - out2 <- layer_data(ggplot(df, aes(x, y)) + geom_tile(width = 0.5, height = 0.5)) + out2 <- get_layer_data(ggplot(df, aes(x, y)) + geom_tile(width = 0.5, height = 0.5)) expect_equal(out2$xmin, new_mapped_discrete(c(0.75, 1.75))) expect_equal(out2$xmax, new_mapped_discrete(c(1.25, 2.25))) }) @@ -15,7 +15,7 @@ test_that("accepts width and height aesthetics", { p <- ggplot(df, aes(x, y, width = width, height = height)) + geom_tile(fill = NA, colour = "black", linewidth = 1) - out <- layer_data(p) + out <- get_layer_data(p) boundary <- as.data.frame(tibble::tribble( ~xmin, ~xmax, ~ymin, ~ymax, @@ -28,10 +28,10 @@ test_that("accepts width and height aesthetics", { test_that("accepts linejoin parameter", { df <- data_frame(x = c("a", "b"), y = c("a", "b")) - gp1 <- layer_grob(ggplot(df, aes(x, y)) + geom_tile())[[1]]$gp + gp1 <- get_layer_grob(ggplot(df, aes(x, y)) + geom_tile())[[1]]$gp expect_equal(gp1$linejoin, "mitre") - gp2 <- layer_grob(ggplot(df, aes(x, y)) + geom_tile(linejoin = "round"))[[1]]$gp + gp2 <- get_layer_grob(ggplot(df, aes(x, y)) + geom_tile(linejoin = "round"))[[1]]$gp expect_equal(gp2$linejoin, "round") }) @@ -42,7 +42,7 @@ test_that("width and height are inferred per panel", { f = rep(c("A", "B"), each = 3) ) - ld <- layer_data( + ld <- get_layer_data( ggplot(df, aes(x, y)) + geom_tile() + facet_wrap(~f, scales = "free") ) diff --git a/tests/testthat/test-geom-violin.R b/tests/testthat/test-geom-violin.R index 5633e85d8f..eabbc5c95c 100644 --- a/tests/testthat/test-geom-violin.R +++ b/tests/testthat/test-geom-violin.R @@ -10,17 +10,17 @@ test_that("range is expanded", { coord_cartesian(expand = FALSE) expand_a <- stats::bw.nrd0(df$y[df$x == "a"]) * 3 expand_b <- stats::bw.nrd0(df$y[df$x == "b"]) * 3 - expect_equal(layer_scales(p, 1)$y$dimension(), c(0 - expand_a, 1 + expand_a)) - expect_equal(layer_scales(p, 2)$y$dimension(), c(0 - expand_b, 2 + expand_b)) + expect_equal(get_panel_scales(p, 1)$y$dimension(), c(0 - expand_a, 1 + expand_a)) + expect_equal(get_panel_scales(p, 2)$y$dimension(), c(0 - expand_b, 2 + expand_b)) }) test_that("geom_violin works in both directions", { p <- ggplot(mpg) + geom_violin(aes(drv, hwy)) - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(mpg) + geom_violin(aes(hwy, drv)) - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -43,7 +43,7 @@ test_that("quantiles do not fail on zero-range data", { p <- ggplot(zero.range.data) + geom_violin(aes(1, y), draw_quantiles = 0.5) # This should return without error and have length one - expect_equal(length(layer_grob(p)), 1) + expect_equal(length(get_layer_grob(p)), 1) }) test_that("quantiles fails outside 0-1 bound", { diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 3a7de53d8c..0a89af1da8 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -43,7 +43,7 @@ test_that("column vectors are allowed (#2609)", { df <- data_frame(x = 1:10) df$y <- scale(1:10) # Returns a column vector p <- ggplot(df, aes(x, y)) - expect_s3_class(layer_data(p), "data.frame") + expect_s3_class(get_layer_data(p), "data.frame") }) test_that("missing aesthetics trigger informative error", { @@ -107,12 +107,12 @@ test_that("inherit.aes works", { test_that("retransform works on computed aesthetics in `map_statistic`", { df <- data.frame(x = rep(c(1,2), c(9, 25))) p <- ggplot(df, aes(x)) + geom_bar() + scale_y_sqrt() - expect_equal(layer_data(p)$y, c(3, 5)) + expect_equal(get_layer_data(p)$y, c(3, 5)) # To double check: should be original values when `retransform = FALSE` parent <- p$layers[[1]]$stat p$layers[[1]]$stat <- ggproto(NULL, parent, retransform = FALSE) - expect_equal(layer_data(p)$y, c(9, 25)) + expect_equal(get_layer_data(p)$y, c(9, 25)) }) test_that("layer reports the error with correct index etc", { @@ -142,13 +142,13 @@ test_that("layer warns for constant aesthetics", { test_that("AsIs data passes unmodified", { p <- ggplot() + geom_blank(aes(x = 1:2, y = 1:2)) - ld <- layer_data(p + geom_point(aes(x = I(0.5), y = I(0.5))), 2) + ld <- get_layer_data(p + geom_point(aes(x = I(0.5), y = I(0.5))), 2) expect_s3_class(ld$x, "AsIs") expect_equal(ld$y, I(0.5)) - ld <- layer_data(p + geom_point(x = I(0.5), y = I(0.5), data = mtcars), 2) + ld <- get_layer_data(p + geom_point(x = I(0.5), y = I(0.5), data = mtcars), 2) expect_s3_class(ld$x, "AsIs") expect_equal(ld$y[1], I(0.5)) - ld <- layer_data(p + annotate("point", x = I(0.5), y = I(0.5)), 2) + ld <- get_layer_data(p + annotate("point", x = I(0.5), y = I(0.5)), 2) expect_s3_class(ld$x, "AsIs") expect_equal(ld$y, I(0.5)) }) diff --git a/tests/testthat/test-position-dodge2.R b/tests/testthat/test-position-dodge2.R index 2ef17a4347..d1e54a37fc 100644 --- a/tests/testthat/test-position-dodge2.R +++ b/tests/testthat/test-position-dodge2.R @@ -32,7 +32,7 @@ test_that("rectangles are dodged", { p <- ggplot(df, aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax)) + geom_rect(aes(fill = fill), position = "dodge2", alpha = 0.8) - expect_false(any(duplicated(find_x_overlaps(layer_data(p))))) + expect_false(any(duplicated(find_x_overlaps(get_layer_data(p))))) }) test_that("cols at the same x position are dodged", { @@ -44,7 +44,7 @@ test_that("cols at the same x position are dodged", { p <- ggplot(df, aes(1, n, fill = x)) + geom_col(position = "dodge2", alpha = 0.5) - expect_false(any(duplicated(find_x_overlaps(layer_data(p))))) + expect_false(any(duplicated(find_x_overlaps(get_layer_data(p))))) }) test_that("padding argument controls space between elements", { @@ -55,8 +55,8 @@ test_that("padding argument controls space between elements", { p2 <- ggplot(df, aes(1, value, fill = group)) + geom_boxplot(position = position_dodge2(padding = 0.1)) - d1 <- layer_data(p1) - d2 <- layer_data(p2) + d1 <- get_layer_data(p1) + d2 <- get_layer_data(p2) gaps <- function(df) { gap <- vector() @@ -81,7 +81,7 @@ test_that("boxes in facetted plots keep the correct width", { facet_wrap( ~ group) + geom_boxplot() - d <- layer_data(p) + d <- get_layer_data(p) expect_true(all(d$xmax - d$xmin == 0.75)) }) @@ -97,7 +97,7 @@ test_that("width of groups is computed per facet", { geom_col(position = position_dodge2(preserve = "single")) + facet_wrap(vars(g1)) - d <- layer_data(p) + d <- get_layer_data(p) width <- d$xmax - d$xmin expect_true(all(width == (0.9 / 3) * 0.9)) diff --git a/tests/testthat/test-position-nudge.R b/tests/testthat/test-position-nudge.R index 2ec0e767e2..564595b36e 100644 --- a/tests/testthat/test-position-nudge.R +++ b/tests/testthat/test-position-nudge.R @@ -5,7 +5,7 @@ test_that("nudging works in both dimensions simultaneously", { p <- ggplot(df, aes(x, x, xmax = x, xmin = x, ymax = x, ymin = x)) + geom_point(position = position_nudge(x = 1, y = 2)) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$x, 2:4) expect_equal(data$xmin, 2:4) @@ -20,7 +20,7 @@ test_that("nudging works in both dimensions simultaneously", { p <- ggplot(df, aes(x, x, xmax = x, xmin = x, ymax = x, ymin = x)) + geom_point(position = position_nudge(x = c(0, -1, 0), y = c(0, 1, 2))) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$x, c(1, 1, 1)) expect_equal(data$xmin, c(1, 1, 1)) @@ -39,7 +39,7 @@ test_that("nudging works in individual dimensions", { p <- ggplot(df, aes(x = x, xmax = x, xmin = x)) + layer(geom = Geom, stat = StatIdentity, position = position_nudge(x = 1)) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$x, 2:4) expect_equal(data$xmin, 2:4) @@ -49,7 +49,7 @@ test_that("nudging works in individual dimensions", { p <- ggplot(df, aes(x = x, xmax = x, xmin = x)) + layer(geom = Geom, stat = StatIdentity, position = position_nudge(x = c(0, -1, -2))) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$x, c(1, 1, 1)) expect_equal(data$xmin, c(1, 1, 1)) @@ -61,7 +61,7 @@ test_that("nudging works in individual dimensions", { p <- ggplot(df, aes(y = x, ymax = x, ymin = x)) + layer(geom = Geom, stat = StatIdentity, position = position_nudge(y = 2)) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$y, 3:5) expect_equal(data$ymin, 3:5) @@ -71,7 +71,7 @@ test_that("nudging works in individual dimensions", { p <- ggplot(df, aes(y = x, ymax = x, ymin = x)) + layer(geom = Geom, stat = StatIdentity, position = position_nudge(y = c(0, -1, -2))) - data <- layer_data(p) + data <- get_layer_data(p) expect_equal(data$y, c(1, 1, 1)) expect_equal(data$ymin, c(1, 1, 1)) diff --git a/tests/testthat/test-position-stack.R b/tests/testthat/test-position-stack.R index 6b404284de..6a9353a300 100644 --- a/tests/testthat/test-position-stack.R +++ b/tests/testthat/test-position-stack.R @@ -6,7 +6,7 @@ test_that("data keeps its order after stacking", { ) p <- ggplot(df, aes(x = x, y = y, fill = var)) + geom_area(stat = "identity", position = "stack") - dat <- layer_data(p) + dat <- get_layer_data(p) expect_true(all(dat$group == rep(1:3, each = 10))) expect_true(all(dat$x == df$x)) }) @@ -18,7 +18,7 @@ test_that("negative and positive values are handled separately", { y = c(1,-1,1,2,-3) ) p <- ggplot(df, aes(x, y, fill = factor(g))) + geom_col() - dat <- layer_data(p) + dat <- get_layer_data(p) expect_equal(dat$ymin[dat$x == 1], c(1, -1, 0)) expect_equal(dat$ymax[dat$x == 1], c(2, 0, 1)) @@ -34,7 +34,7 @@ test_that("can request reverse stacking", { ) p <- ggplot(df, aes(1, y, fill = g)) + geom_col(position = position_stack(reverse = TRUE)) - dat <- layer_data(p) + dat <- get_layer_data(p) expect_equal(dat$ymin, c(-2, 0, -3, 2)) }) @@ -48,14 +48,14 @@ test_that("data with no extent is stacked correctly", { p0 <- base + geom_text(aes(label = y), position = position_stack(vjust = 0)) p1 <- base + geom_text(aes(label = y), position = position_stack(vjust = 1)) - expect_equal(layer_data(p0)$y, c(-115, -75)) - expect_equal(layer_data(p1)$y, c(-75, 0)) + expect_equal(get_layer_data(p0)$y, c(-115, -75)) + expect_equal(get_layer_data(p1)$y, c(-75, 0)) }) test_that("position_stack() can stack correctly when ymax is NA", { df <- data_frame(x = c(1, 1), y = c(1, 1)) p <- ggplot(df, aes(x, y, ymax = NA_real_)) + geom_point(position = "stack") - expect_equal(layer_data(p)$y, c(1, 2)) + expect_equal(get_layer_data(p)$y, c(1, 2)) }) # Visual tests ------------------------------------------------------------ diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index aa036c7abe..51d7b54cce 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -6,8 +6,8 @@ test_that("can control whether to preserve total or individual width", { p_single <- ggplot(df, aes(x, fill = y)) + geom_bar(position = position_dodge(preserve = "single"), width = 1) - expect_equal(layer_data(p_total)$x, new_mapped_discrete(c(1, 1.75, 2.25))) - expect_equal(layer_data(p_single)$x, new_mapped_discrete(c(0.75, 1.75, 2.25))) + expect_equal(get_layer_data(p_total)$x, new_mapped_discrete(c(1, 1.75, 2.25))) + expect_equal(get_layer_data(p_single)$x, new_mapped_discrete(c(0.75, 1.75, 2.25))) }) test_that("position_dodge() can dodge points vertically", { diff --git a/tests/testthat/test-qplot.R b/tests/testthat/test-qplot.R index 12fd2f229f..58e8fa1e14 100644 --- a/tests/testthat/test-qplot.R +++ b/tests/testthat/test-qplot.R @@ -37,7 +37,7 @@ test_that("qplot() evaluates constants in the right place", { qplot(1, 1, colour = I(paste0("re", foo))) }) ) - expect_identical(layer_data(p)$colour, I("red")) + expect_identical(get_layer_data(p)$colour, I("red")) }) test_that("qplot() evaluates layers in package environment", { diff --git a/tests/testthat/test-scale-brewer.R b/tests/testthat/test-scale-brewer.R index b838952fbe..d14edd1a8b 100644 --- a/tests/testthat/test-scale-brewer.R +++ b/tests/testthat/test-scale-brewer.R @@ -5,11 +5,11 @@ test_that("mid-point in diverging brewer color scale", { aes(x = x, y = 1, color = x) + scale_color_distiller(palette = 'RdBu', direction = 1, limits = c(-1, 1)) - expect_equal(layer_data(p)$colour, c("#B2182B", "#F7F7F7", "#2166AC")) + expect_equal(get_layer_data(p)$colour, c("#B2182B", "#F7F7F7", "#2166AC")) p <- ggplot(d) + aes(x = x, y = 1, fill = x) + scale_fill_distiller(palette = 'RdBu', direction = 1, limits = c(-1, 1)) - expect_equal(layer_data(p)$fill, c("#B2182B", "#F7F7F7", "#2166AC")) + expect_equal(get_layer_data(p)$fill, c("#B2182B", "#F7F7F7", "#2166AC")) }) diff --git a/tests/testthat/test-scale-date.R b/tests/testthat/test-scale-date.R index 8f0e1fa410..83b95c6827 100644 --- a/tests/testthat/test-scale-date.R +++ b/tests/testthat/test-scale-date.R @@ -15,14 +15,14 @@ test_that("inherits timezone from data", { # Local time p <- ggplot(df, aes(y = y)) + geom_point(aes(time1)) - sc <- layer_scales(p)$x + sc <- get_panel_scales(p)$x expect_true(identical(sc$timezone, NULL)) expect_equal(sc$get_labels()[1], "00:00") # UTC p <- ggplot(df, aes(y = y)) + geom_point(aes(time2)) - sc <- layer_scales(p)$x + sc <- get_panel_scales(p)$x expect_equal(sc$timezone, "UTC") expect_equal(sc$get_labels()[1], "00:00") }) @@ -33,7 +33,7 @@ test_that("first timezone wins", { geom_point(aes(time2)) + geom_point(aes(time3), colour = "red") + scale_x_datetime(date_breaks = "hour", date_labels = "%H:%M") - sc <- layer_scales(p)$x + sc <- get_panel_scales(p)$x expect_equal(sc$timezone, "UTC") }) @@ -43,22 +43,22 @@ test_that("not cached across calls", { p1 <- ggplot(df, aes(y = y)) + geom_point(aes(time2)) + scale_x p2 <- ggplot(df, aes(y = y)) + geom_point(aes(time3)) + scale_x - expect_equal(layer_scales(p1)$x$timezone, "UTC") - expect_equal(layer_scales(p2)$x$timezone, "Australia/Lord_Howe") + expect_equal(get_panel_scales(p1)$x$timezone, "UTC") + expect_equal(get_panel_scales(p2)$x$timezone, "Australia/Lord_Howe") }) test_that("datetime size scales work", { p <- ggplot(df, aes(y = y)) + geom_point(aes(time1, size = time1)) # Default size range is c(1, 6) - expect_equal(range(layer_data(p)$size), c(1, 6)) + expect_equal(range(get_layer_data(p)$size), c(1, 6)) }) test_that("datetime alpha scales work", { p <- ggplot(df, aes(y = y)) + geom_point(aes(time1, alpha = time1)) # Default alpha range is c(0.1, 1.0) - expect_equal(range(layer_data(p)$alpha), c(0.1, 1.0)) + expect_equal(range(get_layer_data(p)$alpha), c(0.1, 1.0)) }) test_that("datetime colour scales work", { @@ -66,5 +66,5 @@ test_that("datetime colour scales work", { geom_point(aes(time1, colour = time1)) + scale_colour_datetime() - expect_equal(range(layer_data(p)$colour), c("#132B43", "#56B1F7")) + expect_equal(range(get_layer_data(p)$colour), c("#132B43", "#56B1F7")) }) diff --git a/tests/testthat/test-scale-discrete.R b/tests/testthat/test-scale-discrete.R index cd8c2da933..084511571f 100644 --- a/tests/testthat/test-scale-discrete.R +++ b/tests/testthat/test-scale-discrete.R @@ -13,35 +13,35 @@ test_that("NAs are translated/preserved for position scales", { p2a <- ggplot(df, aes(x2, y)) + geom_point() p3a <- ggplot(df, aes(x3, y)) + geom_point() - expect_equal(layer_data(p1a)$x, new_mapped_discrete(c(1, 2, 3))) - expect_equal(layer_data(p2a)$x, new_mapped_discrete(c(1, 2, 3))) - expect_equal(layer_data(p3a)$x, new_mapped_discrete(c(1, 2, 3))) + expect_equal(get_layer_data(p1a)$x, new_mapped_discrete(c(1, 2, 3))) + expect_equal(get_layer_data(p2a)$x, new_mapped_discrete(c(1, 2, 3))) + expect_equal(get_layer_data(p3a)$x, new_mapped_discrete(c(1, 2, 3))) rm_na_x <- scale_x_discrete(na.translate = FALSE) p1b <- p1a + rm_na_x p2b <- p2a + rm_na_x p3b <- p3a + rm_na_x - expect_equal(layer_data(p1b)$x, new_mapped_discrete(c(1, 2, NA))) - expect_equal(layer_data(p2b)$x, new_mapped_discrete(c(1, 2, NA))) - expect_equal(layer_data(p3b)$x, new_mapped_discrete(c(1, 2, NA))) + expect_equal(get_layer_data(p1b)$x, new_mapped_discrete(c(1, 2, NA))) + expect_equal(get_layer_data(p2b)$x, new_mapped_discrete(c(1, 2, NA))) + expect_equal(get_layer_data(p3b)$x, new_mapped_discrete(c(1, 2, NA))) }) test_that("NAs are translated/preserved for non-position scales", { p1a <- ggplot(df, aes(y, y, colour = x1)) + geom_point() p2a <- ggplot(df, aes(y, y, colour = x2)) + geom_point() p3a <- ggplot(df, aes(y, y, colour = x3)) + geom_point() - expect_equal(layer_data(p1a)$colour, c("#F8766D", "#00BFC4", "grey50")) - expect_equal(layer_data(p2a)$colour, c("#F8766D", "#00BFC4", "grey50")) - expect_equal(layer_data(p3a)$colour, c("#F8766D", "#00BFC4", "grey50")) + expect_equal(get_layer_data(p1a)$colour, c("#F8766D", "#00BFC4", "grey50")) + expect_equal(get_layer_data(p2a)$colour, c("#F8766D", "#00BFC4", "grey50")) + expect_equal(get_layer_data(p3a)$colour, c("#F8766D", "#00BFC4", "grey50")) rm_na_colour <- scale_colour_discrete(na.translate = FALSE) p1b <- p1a + rm_na_colour p2b <- p2a + rm_na_colour p3b <- p3a + rm_na_colour - expect_equal(layer_data(p1b)$colour, c("#F8766D", "#00BFC4", NA)) - expect_equal(layer_data(p2b)$colour, c("#F8766D", "#00BFC4", NA)) - expect_equal(layer_data(p3b)$colour, c("#F8766D", "#00BFC4", NA)) + expect_equal(get_layer_data(p1b)$colour, c("#F8766D", "#00BFC4", NA)) + expect_equal(get_layer_data(p2b)$colour, c("#F8766D", "#00BFC4", NA)) + expect_equal(get_layer_data(p3b)$colour, c("#F8766D", "#00BFC4", NA)) }) # Ranges ------------------------------------------------------------------ @@ -52,7 +52,7 @@ test_that("discrete ranges also encompass continuous values", { base <- ggplot(df, aes(y = y)) + scale_x_discrete() x_range <- function(x) { - layer_scales(x)$x$dimension() + get_panel_scales(x)$x$dimension() } expect_equal(x_range(base + geom_point(aes(x1))), c(1, 3)) @@ -71,7 +71,7 @@ test_that("discrete scale shrinks to range when setting limits", { p <- ggplot(df, aes(x, y)) + geom_point() + scale_x_discrete(limits = c("a", "b")) - expect_equal(layer_scales(p)$x$dimension(c(0, 1)), c(0, 3)) + expect_equal(get_panel_scales(p)$x$dimension(c(0, 1)), c(0, 3)) }) test_that("discrete position scales can accept functional limits", { @@ -98,14 +98,14 @@ test_that("discrete scale defaults can be set globally", { ggplot2.discrete.colour = c("#FFFFFF", "#000000")), { # nlevels == ncodes two <- ggplot(df, aes(x, y, colour = two, fill = two)) + geom_point() - expect_equal(layer_data(two)$colour, rep(c("#FFFFFF", "#000000"), 2)) - expect_equal(layer_data(two)$fill, rep(c("#FFFFFF", "#000000"), 2)) + expect_equal(get_layer_data(two)$colour, rep(c("#FFFFFF", "#000000"), 2)) + expect_equal(get_layer_data(two)$fill, rep(c("#FFFFFF", "#000000"), 2)) # nlevels > ncodes (so should fallback to scale_fill_hue()) four_default <- ggplot(df, aes(x, y, colour = four, fill = four)) + geom_point() four_hue <- four_default + scale_fill_hue() - expect_equal(layer_data(four_default)$colour, layer_data(four_hue)$colour) + expect_equal(get_layer_data(four_default)$colour, get_layer_data(four_hue)$colour) } ) @@ -122,13 +122,13 @@ test_that("discrete scale defaults can be set globally", { ), { # nlevels == 2 two <- ggplot(df, aes(x, y, colour = two, fill = two)) + geom_point() - expect_equal(layer_data(two)$colour, rep(c("#FFFFFF", "#000000"), 2)) - expect_equal(layer_data(two)$fill, rep(c("#FFFFFF", "#000000"), 2)) + expect_equal(get_layer_data(two)$colour, rep(c("#FFFFFF", "#000000"), 2)) + expect_equal(get_layer_data(two)$fill, rep(c("#FFFFFF", "#000000"), 2)) # nlevels == 4 four <- ggplot(df, aes(x, y, colour = four, fill = four)) + geom_point() - expect_equal(layer_data(four)$colour, c("#FF0000", "#00FF00", "#0000FF", "#FF00FF")) - expect_equal(layer_data(four)$fill, c("#FF0000", "#00FF00", "#0000FF", "#FF00FF")) + expect_equal(get_layer_data(four)$colour, c("#FF0000", "#00FF00", "#0000FF", "#FF00FF")) + expect_equal(get_layer_data(four)$fill, c("#FF0000", "#00FF00", "#0000FF", "#FF00FF")) } ) }) @@ -175,7 +175,7 @@ test_that("palettes work for discrete scales", { scale_x_discrete(palette = function(x) values) # Check limits are translated to correct values - ld <- layer_data(p) + ld <- get_layer_data(p) expect_equal(ld$x, values, ignore_attr = TRUE) # Check discsrete expansion is applied diff --git a/tests/testthat/test-scale-gradient.R b/tests/testthat/test-scale-gradient.R index b6da7049bb..3b3a1944dd 100644 --- a/tests/testthat/test-scale-gradient.R +++ b/tests/testthat/test-scale-gradient.R @@ -7,7 +7,7 @@ test_that("points outside the limits are plotted as NA", { scale_fill_gradient2(limits = c(-1, 1), midpoint = 2, na.value = "orange") correct_fill <- c("#B26D65", "#DCB4AF", "orange") - expect_equal(layer_data(p)$fill, correct_fill) + expect_equal(get_layer_data(p)$fill, correct_fill) }) test_that("midpoints are transformed", { diff --git a/tests/testthat/test-scale-manual.R b/tests/testthat/test-scale-manual.R index 532e18b2f6..4e45b65557 100644 --- a/tests/testthat/test-scale-manual.R +++ b/tests/testthat/test-scale-manual.R @@ -47,7 +47,7 @@ test_that("missing values are replaced with na.value", { geom_point() + scale_colour_manual(values = c("black", "black"), na.value = "red") - expect_equal(layer_data(p)$colour, c("black", "black", "red")) + expect_equal(get_layer_data(p)$colour, c("black", "black", "red")) }) test_that("insufficient values raise an error", { @@ -80,7 +80,7 @@ test_that("generic scale can be used in place of aesthetic-specific scales", { scale_discrete_manual(aesthetics = "colour", values = c("red", "green", "blue")) + scale_discrete_manual(aesthetics = "alpha", values = c(0.2, 0.4, 0.6)) - expect_equal(layer_data(p1), layer_data(p2)) + expect_equal(get_layer_data(p1), get_layer_data(p2)) }) test_that("named values do not match with breaks in manual scales", { diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index 49f86136fc..d24e0ab638 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -246,7 +246,10 @@ test_that("continuous limits accepts functions", { p <- ggplot(mpg, aes(class, hwy)) + scale_y_continuous(limits = function(lims) (c(lims[1] - 10, lims[2] + 100))) - expect_equal(layer_scales(p)$y$get_limits(), c(range(mpg$hwy)[1] - 10, range(mpg$hwy)[2] + 100)) + expect_equal( + get_panel_scales(p)$y$get_limits(), + c(range(mpg$hwy)[1] - 10, range(mpg$hwy)[2] + 100) + ) }) test_that("equal length breaks and labels can be passed to ViewScales with limits", { diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 79bd27af22..4e104f9024 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -52,7 +52,7 @@ test_that("identity scale preserves input values", { scale_shape_identity() + scale_size_identity() + scale_alpha_identity() - d1 <- layer_data(p1) + d1 <- get_layer_data(p1) expect_equal(d1$colour, as.character(df$z)) expect_equal(d1$fill, as.character(df$z)) @@ -66,7 +66,7 @@ test_that("identity scale preserves input values", { geom_point() + scale_discrete_identity(aesthetics = c("colour", "fill", "shape")) + scale_continuous_identity(aesthetics = c("size", "alpha")) - d2 <- layer_data(p2) + d2 <- get_layer_data(p2) expect_equal(d1, d2) }) @@ -258,7 +258,7 @@ test_that("aesthetics can be set independently of scale name", { p <- ggplot(df, aes(x, y, fill = y)) + scale_colour_manual(values = c("red", "green", "blue"), aesthetics = "fill") - expect_equal(layer_data(p)$fill, c("red", "green", "blue")) + expect_equal(get_layer_data(p)$fill, c("red", "green", "blue")) }) test_that("multiple aesthetics can be set with one function call", { @@ -272,8 +272,8 @@ test_that("multiple aesthetics can be set with one function call", { aesthetics = c("colour", "fill") ) - expect_equal(layer_data(p)$colour, c("grey20", "grey40", "grey60")) - expect_equal(layer_data(p)$fill, c("red", "green", "blue")) + expect_equal(get_layer_data(p)$colour, c("grey20", "grey40", "grey60")) + expect_equal(get_layer_data(p)$fill, c("red", "green", "blue")) # color order is determined by data order, and breaks are combined where possible df <- data_frame( @@ -286,8 +286,8 @@ test_that("multiple aesthetics can be set with one function call", { aesthetics = c("fill", "colour") ) - expect_equal(layer_data(p)$colour, c("cyan", "red", "green")) - expect_equal(layer_data(p)$fill, c("red", "green", "blue")) + expect_equal(get_layer_data(p)$colour, c("cyan", "red", "green")) + expect_equal(get_layer_data(p)$fill, c("red", "green", "blue")) }) test_that("limits with NA are replaced with the min/max of the data for continuous scales", { @@ -459,7 +459,7 @@ test_that("staged aesthetics are backtransformed properly (#4155)", { scale_x_sqrt(limits = c(0, 16), breaks = c(2, 4, 8)) # x / 2 should be 16 / 2 = 8, thus the result should be sqrt(8) on scale_x_sqrt() - expect_equal(layer_data(p)$x, sqrt(8)) + expect_equal(get_layer_data(p)$x, sqrt(8)) }) test_that("numeric scale transforms can produce breaks", { diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index cd02fe5459..2b8fde0d94 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -25,7 +25,7 @@ test_that("dup_axis() works", { name = "Unit A", sec.axis = dup_axis() ) - scale <- layer_scales(p)$x + scale <- get_panel_scales(p)$x expect_equal(scale$sec_name(), scale$name) breaks <- scale$break_info() expect_equal(breaks$minor_source, breaks$sec.minor_source_user) @@ -45,7 +45,7 @@ test_that("sec_axis() works with subtraction", { scale_y_continuous( sec.axis = sec_axis(~1-.) ) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y expect_equal(scale$sec_name(), scale$name) breaks <- scale$break_info() expect_equal(breaks$minor_source, breaks$sec.minor_source_user) @@ -81,7 +81,7 @@ test_that("sec_axis() breaks work for log-transformed scales", { geom_point() + scale_y_log10(sec.axis = dup_axis()) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() # test value @@ -96,7 +96,7 @@ test_that("sec_axis() breaks work for log-transformed scales", { geom_point() + scale_y_log10(sec.axis = sec_axis(~ . * 100)) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() # test value @@ -113,7 +113,7 @@ test_that("sec_axis() breaks work for log-transformed scales", { geom_point() + scale_y_log10(breaks = custom_breaks, sec.axis = sec_axis(~ . * 100)) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() expect_equal(breaks$major_source, log(custom_breaks, base = 10)) @@ -131,7 +131,7 @@ test_that("custom breaks work", { breaks = custom_breaks ) ) - scale <- layer_scales(p)$x + scale <- get_panel_scales(p)$x breaks <- scale$break_info() expect_equal(custom_breaks, breaks$sec.major_source_user) }) @@ -175,7 +175,7 @@ test_that("sec axis works with tidy eval", { p <- f(t, x, y, z) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() # test transform @@ -194,7 +194,7 @@ test_that("sec_axis() handles secondary power transformations", { geom_point() + scale_y_continuous(sec.axis = sec_axis(transform = (~ 2^.))) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() expect_equal(round(breaks$major[4:6], 2), round(breaks$sec.major[c(1, 2, 4)], 2)) @@ -274,7 +274,7 @@ test_that("sec_axis works with date/time/datetime scales", { dt <- ggplot(df, aes(dx, price)) + geom_line() + scale_x_datetime(sec.axis = dup_axis()) - scale <- layer_scales(dt)$x + scale <- get_panel_scales(dt)$x breaks <- scale$break_info() expect_equal(breaks$major_source, breaks$sec.major_source_user) @@ -282,7 +282,7 @@ test_that("sec_axis works with date/time/datetime scales", { dt <- ggplot(df, aes(date, price)) + geom_line() + scale_x_date(sec.axis = dup_axis()) - scale <- layer_scales(dt)$x + scale <- get_panel_scales(dt)$x breaks <- scale$break_info() expect_equal(breaks$major_source, breaks$sec.major_source_user) @@ -295,7 +295,7 @@ test_that("sec_axis works with date/time/datetime scales", { name = "UTC+12" ) ) - scale <- layer_scales(dt)$x + scale <- get_panel_scales(dt)$x breaks <- scale$break_info() expect_equal( @@ -362,21 +362,21 @@ test_that("sec_axis() works for power transformations (monotonicity test doesn't p <- ggplot(data = testdat, aes(x = x, y = y)) + geom_point() + scale_y_continuous(sec.axis = sec_axis(transform = ~ .^0.5)) - scale <- layer_scales(p)$y + scale <- get_panel_scales(p)$y breaks <- scale$break_info() expect_equal(breaks$major, sqrt(breaks$sec.major), tolerance = .005) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = dup_axis()) - scale <- layer_scales(p)$x + scale <- get_panel_scales(p)$x breaks <- scale$break_info() expect_equal(breaks$major, breaks$sec.major, tolerance = .001) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = sec_axis(~ . * 100)) - scale <- layer_scales(p)$x + scale <- get_panel_scales(p)$x breaks <- scale$break_info() expect_equal(breaks$major, breaks$sec.major, tolerance = .001) }) diff --git a/tests/testthat/test-stat-align.R b/tests/testthat/test-stat-align.R index 87a69cbba7..4c418037b3 100644 --- a/tests/testthat/test-stat-align.R +++ b/tests/testthat/test-stat-align.R @@ -56,12 +56,12 @@ test_that("alignment adjusts per panel", { p <- ggplot(df, aes(x, y, group = g)) # Here, x-range is large, so adjustment should be larger - ld <- layer_data(p + geom_area(aes(fill = f))) + ld <- get_layer_data(p + geom_area(aes(fill = f))) expect_equal(diff(ld$x[1:2]), 1/6, tolerance = 1e-4) # Here, x-ranges are smaller, so adjustment should be smaller instead of # considering the data as a whole - ld <- layer_data(p + geom_area() + facet_wrap(vars(f), scales = "free_x")) + ld <- get_layer_data(p + geom_area() + facet_wrap(vars(f), scales = "free_x")) expect_equal(diff(ld$x[1:2]), 1e-3, tolerance = 1e-4) }) diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index 6ab5ec96b2..0974196cb2 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -10,11 +10,11 @@ test_that("stat_bin throws error when wrong combination of aesthetic is present" test_that("stat_bin works in both directions", { p <- ggplot(mpg, aes(hwy)) + stat_bin(bins = 30) - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(mpg, aes(y = hwy)) + stat_bin(bins = 30) - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -25,7 +25,7 @@ test_that("stat_bin works in both directions", { test_that("bins specifies the number of bins", { df <- data_frame(x = 1:10) out <- function(x, ...) { - layer_data(ggplot(df, aes(x)) + geom_histogram(...)) + get_layer_data(ggplot(df, aes(x)) + geom_histogram(...)) } expect_equal(nrow(out(bins = 2)), 2) @@ -34,28 +34,28 @@ test_that("bins specifies the number of bins", { test_that("binwidth computes widths for function input", { df <- data_frame(x = 1:100) - out <- layer_data(ggplot(df, aes(x)) + geom_histogram(binwidth = function(x) 5)) + out <- get_layer_data(ggplot(df, aes(x)) + geom_histogram(binwidth = function(x) 5)) expect_equal(nrow(out), 21) }) test_that("geom_histogram defaults to pad = FALSE", { df <- data_frame(x = 1:3) - out <- layer_data(ggplot(df, aes(x)) + geom_histogram(binwidth = 1)) + out <- get_layer_data(ggplot(df, aes(x)) + geom_histogram(binwidth = 1)) expect_equal(out$count, c(1, 1, 1)) }) test_that("geom_freqpoly defaults to pad = TRUE", { df <- data_frame(x = 1:3) - out <- layer_data(ggplot(df, aes(x)) + geom_freqpoly(binwidth = 1)) + out <- get_layer_data(ggplot(df, aes(x)) + geom_freqpoly(binwidth = 1)) expect_equal(out$count, c(0, 1, 1, 1, 0)) }) test_that("can use breaks argument", { df <- data_frame(x = 1:3) - out <- layer_data(ggplot(df, aes(x)) + geom_histogram(breaks = c(0, 1.5, 5))) + out <- get_layer_data(ggplot(df, aes(x)) + geom_histogram(breaks = c(0, 1.5, 5))) expect_equal(out$count, c(1, 2)) }) @@ -65,7 +65,7 @@ test_that("fuzzy breaks are used when cutting", { p <- ggplot(df, aes(x)) + geom_histogram(binwidth = 0.1, boundary = 0.1, closed = "left") - bins <- layer_data(p) %>% subset(count > 0) %>% .[1:5] + bins <- get_layer_data(p) %>% subset(count > 0) %>% .[1:5] expect_equal(bins$count, c(1, 1, 1, 1)) }) @@ -73,15 +73,15 @@ test_that("breaks are transformed by the scale", { df <- data_frame(x = rep(1:4, 1:4)) base <- ggplot(df, aes(x)) + geom_histogram(breaks = c(1, 2.5, 4)) - out1 <- layer_data(base) - out2 <- layer_data(base + scale_x_sqrt()) + out1 <- get_layer_data(base) + out2 <- get_layer_data(base + scale_x_sqrt()) expect_equal(out1$xmin, c(1, 2.5)) expect_equal(out2$xmin, sqrt(c(1, 2.5))) }) test_that("geom_histogram() can be drawn over a 0-width range (#3043)", { df <- data_frame(x = rep(1, 100)) - out <- layer_data(ggplot(df, aes(x)) + geom_histogram(bins = 30)) + out <- get_layer_data(ggplot(df, aes(x)) + geom_histogram(bins = 30)) expect_equal(nrow(out), 1) expect_equal(out$xmin, 0.95) @@ -103,7 +103,7 @@ test_that("stat_bin() provides width (#3522)", { geom = "rect", binwidth = binwidth ) - out <- layer_data(p) + out <- get_layer_data(p) expect_equal(nrow(out), 10) # (x + width / 2) - (x - width / 2) = width @@ -121,7 +121,7 @@ test_that("bins() computes fuzz with non-finite breaks", { comp_bin <- function(df, ...) { plot <- ggplot(df, aes(x = x)) + stat_bin(...) - layer_data(plot) + get_layer_data(plot) } test_that("inputs to binning are checked", { @@ -178,7 +178,7 @@ test_that("setting boundary and center", { test_that("weights are added", { df <- data_frame(x = 1:10, y = 1:10) p <- ggplot(df, aes(x = x, weight = y)) + geom_histogram(binwidth = 1) - out <- layer_data(p) + out <- get_layer_data(p) expect_equal(out$count, df$y) }) diff --git a/tests/testthat/test-stat-bin2d.R b/tests/testthat/test-stat-bin2d.R index 5a30466bff..31e9c819c6 100644 --- a/tests/testthat/test-stat-bin2d.R +++ b/tests/testthat/test-stat-bin2d.R @@ -3,7 +3,7 @@ test_that("binwidth is respected", { base <- ggplot(df, aes(x, y)) + stat_bin_2d(geom = "tile", binwidth = 0.25) - out <- layer_data(base) + out <- get_layer_data(base) expect_equal(nrow(out), 2) # Adjust tolerance to account for fuzzy breaks adjustment expect_equal(out$xmin, c(1, 1.75), tolerance = 1e-7) @@ -31,7 +31,7 @@ test_that("breaks override binwidth", { binwidth = c(0.5, 0.5) ) - out <- layer_data(base) + out <- get_layer_data(base) expect_equal(out$xbin, cut(df$x, adjust_breaks(integer_breaks), include.lowest = TRUE, labels = FALSE)) expect_equal(out$ybin, cut(df$y, adjust_breaks(half_breaks), include.lowest = TRUE, labels = FALSE)) }) @@ -42,8 +42,8 @@ test_that("breaks are transformed by the scale", { stat_bin_2d( breaks = list(x = c(5, 50, 500), y = c(0.5, 1.5, 2.5))) - out1 <- layer_data(base) - out2 <- layer_data(base + scale_x_log10()) + out1 <- get_layer_data(base) + out2 <- get_layer_data(base + scale_x_log10()) expect_equal(out1$x, c(27.5, 275)) expect_equal(out2$x, c(1.19897, 2.19897)) }) diff --git a/tests/testthat/test-stat-contour.R b/tests/testthat/test-stat-contour.R index 0711fae3fc..bab39b7b6d 100644 --- a/tests/testthat/test-stat-contour.R +++ b/tests/testthat/test-stat-contour.R @@ -26,7 +26,7 @@ test_that("contouring irregularly spaced data works", { # we're testing for set equality here because contour lines are not # guaranteed to start and end at the same point on all architectures - d <- layer_data(p) + d <- get_layer_data(p) d4 <- d[d$level == 4,] expect_equal(nrow(d4), 7) expect_setequal(d4$x, c(4, 10, 100, 700)) @@ -53,14 +53,14 @@ test_that("geom_contour_filled() and stat_contour_filled() result in identical l p <- ggplot(faithfuld, aes(waiting, eruptions, z = density)) p1 <- p + stat_contour_filled() p2 <- p + geom_contour_filled() - expect_identical(layer_data(p1), layer_data(p2)) + expect_identical(get_layer_data(p1), get_layer_data(p2)) }) test_that("geom_contour() and stat_contour() result in identical layer data", { p <- ggplot(faithfuld, aes(waiting, eruptions, z = density)) p1 <- p + stat_contour() p2 <- p + geom_contour() - expect_identical(layer_data(p1), layer_data(p2)) + expect_identical(get_layer_data(p1), get_layer_data(p2)) }) test_that("basic stat_contour() plot builds", { diff --git a/tests/testthat/test-stat-count.R b/tests/testthat/test-stat-count.R index 7483becf94..b014fc672e 100644 --- a/tests/testthat/test-stat-count.R +++ b/tests/testthat/test-stat-count.R @@ -10,7 +10,7 @@ test_that("stat_count() respects uniqueness of `x`", { # if they are retained df <- data_frame0(x = c(1, 2, 1, 2) + rep(c(0, 1.01 * .Machine$double.eps), each = 2)) p <- ggplot(df, aes(x)) + stat_count(position = "identity") - data <- layer_data(p) + data <- get_layer_data(p) expect_length(vec_unique(df$x), 4) expect_equal(data$y, rep(1, 4)) diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 8a772b8873..5f2ec3adb8 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -5,7 +5,7 @@ test_that("stat_density actually computes density", { expected_density_fun <- stats::approxfun(data.frame(x = dens$x, y = dens$y)) plot <- ggplot(mtcars, aes(mpg)) + stat_density() - actual_density_fun <- stats::approxfun(layer_data(plot)[, c("x", "y")]) + actual_density_fun <- stats::approxfun(get_layer_data(plot)[, c("x", "y")]) test_sample <- unique(mtcars$mpg) expect_equal( @@ -25,7 +25,7 @@ test_that("stat_density can make weighted density estimation", { ) expected_density_fun <- stats::approxfun(data.frame(x = dens$x, y = dens$y)) - plot <- layer_data(ggplot(df, aes(mpg, weight = weight)) + stat_density()) + plot <- get_layer_data(ggplot(df, aes(mpg, weight = weight)) + stat_density()) actual_density_fun <- stats::approxfun(plot[, c("x", "y")]) test_sample <- unique(df$mpg) @@ -54,7 +54,7 @@ test_that("stat_density uses `bounds`", { ) bounded_plot <- ggplot(mtcars, aes(mpg)) + stat_density(bounds = bounds) - bounded_data <- layer_data(bounded_plot)[, c("x", "y")] + bounded_data <- get_layer_data(bounded_plot)[, c("x", "y")] plot_density <- stats::approxfun(bounded_data, yleft = 0, yright = 0) test_sample <- seq(mpg_min, mpg_max, by = 0.1) @@ -81,7 +81,7 @@ test_that("stat_density handles data outside of `bounds`", { # Both `x` and `weight` should be filtered out for out of `bounds` points expect_warning( - data_actual <- layer_data( + data_actual <- get_layer_data( ggplot(mtcars, aes(mpg, weight = cyl)) + stat_density(bounds = c(cutoff, Inf)) ), @@ -89,7 +89,7 @@ test_that("stat_density handles data outside of `bounds`", { ) mtcars_filtered <- mtcars[mtcars$mpg >= cutoff, ] - data_expected <- layer_data( + data_expected <- get_layer_data( ggplot(mtcars_filtered, aes(mpg, weight = cyl)) + stat_density(bounds = c(cutoff, Inf)) ) @@ -104,11 +104,11 @@ test_that("compute_density succeeds when variance is zero", { test_that("stat_density works in both directions", { p <- ggplot(mpg, aes(hwy)) + stat_density() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(mpg, aes(y = hwy)) + stat_density() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL diff --git a/tests/testthat/test-stat-density2d.R b/tests/testthat/test-stat-density2d.R index 59445805c2..2ecd50a8cb 100644 --- a/tests/testthat/test-stat-density2d.R +++ b/tests/testthat/test-stat-density2d.R @@ -4,7 +4,7 @@ test_that("uses scale limits, not data limits", { scale_x_continuous(limits = c(1, 6)) + scale_y_continuous(limits = c(5, 40)) - ret <- layer_data(base) + ret <- get_layer_data(base) # Check that the contour data goes beyond data range. # The specific values below are sort of arbitrary; but they go beyond the range # of the data @@ -21,17 +21,17 @@ test_that("stat_density2d can produce contour and raster data", { p_contour_bands <- p + stat_density_2d_filled() p_raster <- p + stat_density_2d(contour = FALSE) - d_lines <- layer_data(p_contour_lines) + d_lines <- get_layer_data(p_contour_lines) expect_true("level" %in% names(d_lines)) expect_false("level_low" %in% names(d_lines)) expect_true(is.numeric(d_lines$level)) - d_bands <- layer_data(p_contour_bands) + d_bands <- get_layer_data(p_contour_bands) expect_true("level" %in% names(d_bands)) expect_true("level_low" %in% names(d_bands)) expect_true(is.ordered(d_bands$level)) - d_raster <- layer_data(p_raster) + d_raster <- get_layer_data(p_raster) expect_true("density" %in% names(d_raster)) expect_true("ndensity" %in% names(d_raster)) expect_true("count" %in% names(d_raster)) @@ -41,7 +41,7 @@ test_that("stat_density2d can produce contour and raster data", { # stat_density_2d() and stat_density_2d_filled() produce identical # density output with `contour = FALSE` # (`fill` and `colour` will differ due to different default aesthetic mappings) - d_raster2 <- layer_data(p + stat_density_2d_filled(contour = FALSE)) + d_raster2 <- get_layer_data(p + stat_density_2d_filled(contour = FALSE)) expect_identical(d_raster$x, d_raster2$x) expect_identical(d_raster$y, d_raster2$y) expect_identical(d_raster$density, d_raster2$density) @@ -50,7 +50,7 @@ test_that("stat_density2d can produce contour and raster data", { # stat_density_2d() with contouring is the same as stat_contour() on calculated density p_lines2 <- ggplot(d_raster, aes(x, y, z = density)) + stat_contour() - d_lines2 <- layer_data(p_lines2) + d_lines2 <- get_layer_data(p_lines2) expect_identical(d_lines$x, d_lines2$x) expect_identical(d_lines$y, d_lines2$y) expect_identical(d_lines$piece, d_lines2$piece) @@ -59,7 +59,7 @@ test_that("stat_density2d can produce contour and raster data", { # same for stat_density_2d_filled() p_bands2 <- ggplot(d_raster, aes(x, y, z = density)) + stat_contour_filled() - d_bands2 <- layer_data(p_bands2) + d_bands2 <- get_layer_data(p_bands2) expect_identical(d_bands$x, d_bands2$x) expect_identical(d_bands$y, d_bands2$y) expect_identical(d_bands$piece, d_bands2$piece) @@ -69,9 +69,9 @@ test_that("stat_density2d can produce contour and raster data", { # and for contour_var = "ndensity" p_contour_lines <- p + stat_density_2d(contour_var = "ndensity") - d_lines <- layer_data(p_contour_lines) + d_lines <- get_layer_data(p_contour_lines) p_lines2 <- ggplot(d_raster, aes(x, y, z = ndensity)) + stat_contour() - d_lines2 <- layer_data(p_lines2) + d_lines2 <- get_layer_data(p_lines2) expect_identical(d_lines$x, d_lines2$x) expect_identical(d_lines$y, d_lines2$y) expect_identical(d_lines$piece, d_lines2$piece) @@ -80,9 +80,9 @@ test_that("stat_density2d can produce contour and raster data", { # and for contour_var = "count" p_contour_bands <- p + stat_density_2d_filled(contour_var = "count") - d_bands <- layer_data(p_contour_bands) + d_bands <- get_layer_data(p_contour_bands) p_bands2 <- ggplot(d_raster, aes(x, y, z = count)) + stat_contour_filled() - d_bands2 <- layer_data(p_bands2) + d_bands2 <- get_layer_data(p_bands2) expect_identical(d_bands$x, d_bands2$x) expect_identical(d_bands$y, d_bands2$y) expect_identical(d_bands$piece, d_bands2$piece) diff --git a/tests/testthat/test-stat-ecdf.R b/tests/testthat/test-stat-ecdf.R index 399dfbebb0..ce839bb3c4 100644 --- a/tests/testthat/test-stat-ecdf.R +++ b/tests/testthat/test-stat-ecdf.R @@ -1,10 +1,10 @@ test_that("stat_ecdf works in both directions", { p <- ggplot(mpg, aes(hwy)) + stat_ecdf() - x <- layer_data(p) + x <- get_layer_data(p) expect_false(x$flipped_aes[1]) p <- ggplot(mpg, aes(y = hwy)) + stat_ecdf() - y <- layer_data(p) + y <- get_layer_data(p) expect_true(y$flipped_aes[1]) x$flipped_aes <- NULL @@ -69,9 +69,9 @@ test_that("stat_ecdf responds to axis transformations", { answer <- c(seq(0, 1, length.out = n + 1), 1) p <- ggplot(data_frame0(x = seq_len(n)), aes(x)) + stat_ecdf() - ld <- layer_data(p) + ld <- get_layer_data(p) expect_equal(ld$y, answer) - ld <- layer_data(p + scale_y_sqrt()) + ld <- get_layer_data(p + scale_y_sqrt()) expect_equal(ld$y, sqrt(answer)) }) diff --git a/tests/testthat/test-stat-ellipsis.R b/tests/testthat/test-stat-ellipsis.R index 95a5df9ad7..0c4406f95c 100644 --- a/tests/testthat/test-stat-ellipsis.R +++ b/tests/testthat/test-stat-ellipsis.R @@ -4,7 +4,7 @@ test_that("stat_ellipsis returns correct data format", { p <- ggplot(d, aes(x = x, y = y, group = id)) + geom_point() + stat_ellipse(segments = n_seg) - out <- layer_data(p, 2) + out <- get_layer_data(p, 2) expect_equal(nrow(out), (n_seg + 1) * 2) expect_equal(unique(out$group), c(1, 2)) }) diff --git a/tests/testthat/test-stat-function.R b/tests/testthat/test-stat-function.R index 497c18ef41..4025dcca96 100644 --- a/tests/testthat/test-stat-function.R +++ b/tests/testthat/test-stat-function.R @@ -8,12 +8,12 @@ test_that("uses scale limits, not data limits", { full <- base + scale_x_continuous(limits = c(0.1, 100)) + scale_y_continuous() - ret <- layer_data(full) + ret <- get_layer_data(full) full_log <- base + scale_x_log10(limits = c(0.1, 100)) + scale_y_continuous() - ret_log <- layer_data(full_log) + ret_log <- get_layer_data(full_log) expect_equal(ret$y[c(1, 101)], ret_log$y[c(1, 101)]) expect_equal(range(ret$x), c(0.1, 100)) @@ -27,19 +27,19 @@ test_that("works in plots without any data", { # default limits, 0 to 1 base <- ggplot() + geom_function(fun = f, n = 6) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 1, length.out = 6)) expect_identical(ret$y, 2*ret$x) # manually set limits with xlim() base <- ggplot() + xlim(0, 2) + geom_function(fun = f, n = 6) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 2, length.out = 6)) expect_identical(ret$y, 2*ret$x) # manually set limits with xlim argument base <- ggplot() + geom_function(fun = f, n = 6, xlim = c(0, 2)) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 2, length.out = 6)) expect_identical(ret$y, 2*ret$x) @@ -47,7 +47,7 @@ test_that("works in plots without any data", { base <- ggplot() + geom_function(aes(color = "fun"), fun = f, n = 6) + scale_color_manual(values = c(fun = "#D55E00")) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 1, length.out = 6)) expect_identical(ret$y, 2*ret$x) expect_identical(ret$colour, rep("#D55E00", 6)) @@ -58,7 +58,7 @@ test_that("works with discrete x", { base <- ggplot(dat, aes(x, group = 1)) + stat_function(fun = as.numeric, geom = "point", n = 2) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_equal(ret$x, mapped_discrete(1:2)) expect_equal(ret$y, 1:2) @@ -71,22 +71,22 @@ test_that("works with transformed scales", { base <- ggplot(dat, aes(x, group = 1)) + stat_function(fun = ~ .x^2, n = 5) - ret <- layer_data(base) + ret <- get_layer_data(base) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(1, 10, length.out = 5)) expect_equal(ret$y, ret$x^2) - ret <- layer_data(base + scale_x_log10()) + ret <- get_layer_data(base + scale_x_log10()) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(0, 1, length.out = 5)) expect_equal(ret$y, (10^ret$x)^2) - ret <- layer_data(base + scale_y_log10()) + ret <- get_layer_data(base + scale_y_log10()) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(1, 10, length.out = 5)) expect_equal(10^ret$y, ret$x^2) - ret <- layer_data(base + scale_x_log10() + scale_y_log10()) + ret <- get_layer_data(base + scale_x_log10() + scale_y_log10()) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(0, 1, length.out = 5)) expect_equal(10^ret$y, (10^ret$x)^2) @@ -95,22 +95,22 @@ test_that("works with transformed scales", { base <- ggplot(dat, aes(x, y)) + geom_point() + stat_function(fun = ~ .x^2, n = 5) - ret <- layer_data(base, 2) + ret <- get_layer_data(base, 2) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(1, 10, length.out = 5)) expect_equal(ret$y, ret$x^2) - ret <- layer_data(base + scale_x_log10(), 2) + ret <- get_layer_data(base + scale_x_log10(), 2) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(0, 1, length.out = 5)) expect_equal(ret$y, (10^ret$x)^2) - ret <- layer_data(base + scale_y_log10(), 2) + ret <- get_layer_data(base + scale_y_log10(), 2) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(1, 10, length.out = 5)) expect_equal(10^ret$y, ret$x^2) - ret <- layer_data(base + scale_x_log10() + scale_y_log10(), 2) + ret <- get_layer_data(base + scale_x_log10() + scale_y_log10(), 2) expect_equal(nrow(ret), 5) expect_equal(ret$x, seq(0, 1, length.out = 5)) expect_equal(10^ret$y, (10^ret$x)^2) @@ -123,7 +123,7 @@ test_that("works with formula syntax", { base <- ggplot(dat, aes(x, group = 1)) + stat_function(fun = ~ .x^2, geom = "point", n = 5) + scale_x_continuous(limits = c(0, 10)) - ret <- layer_data(base) + ret <- get_layer_data(base) s <- seq(0, 10, length.out = 5) expect_equal(ret$x, s) @@ -143,7 +143,7 @@ test_that("Line style can be changed via provided data", { base <- ggplot(df) + geom_function(aes(color = fun), fun = identity, n = 6) + scale_color_identity() - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 1, length.out = 6)) expect_identical(ret$y, ret$x) expect_identical(ret$colour, rep("#D55E00", 6)) @@ -153,7 +153,7 @@ test_that("Line style can be changed via provided data", { data = df, aes(color = fun), fun = identity, n = 6 ) + scale_color_identity() - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 1, length.out = 6)) expect_identical(ret$y, ret$x) expect_identical(ret$colour, rep("#D55E00", 6)) @@ -163,7 +163,7 @@ test_that("Line style can be changed via provided data", { data = df, aes(color = fun), fun = identity, n = 6 ) + scale_color_identity() - ret <- layer_data(base) + ret <- get_layer_data(base) expect_identical(ret$x, seq(0, 1, length.out = 6)) expect_identical(ret$y, ret$x) expect_identical(ret$colour, rep("#D55E00", 6)) diff --git a/tests/testthat/test-stat-hex.R b/tests/testthat/test-stat-hex.R index 1bb2904f3d..c0355acc6b 100644 --- a/tests/testthat/test-stat-hex.R +++ b/tests/testthat/test-stat-hex.R @@ -3,5 +3,5 @@ test_that("can use length 1 binwidth", { df <- data_frame(x = c(1, 1, 2), y = c(1, 1, 2)) p <- ggplot(df, aes(x, y)) + stat_binhex(binwidth = 1) - expect_equal(nrow(layer_data(p)), 2) + expect_equal(nrow(get_layer_data(p)), 2) }) diff --git a/tests/testthat/test-stat-sf-coordinates.R b/tests/testthat/test-stat-sf-coordinates.R index 80307cfa3a..c6e3a21920 100644 --- a/tests/testthat/test-stat-sf-coordinates.R +++ b/tests/testthat/test-stat-sf-coordinates.R @@ -1,6 +1,6 @@ comp_sf_coord <- function(df, ...) { plot <- ggplot(df) + stat_sf_coordinates(...) - layer_data(plot) + get_layer_data(plot) } test_that("stat_sf_coordinates() retrieves coordinates from sf objects", { diff --git a/tests/testthat/test-stat-sum.R b/tests/testthat/test-stat-sum.R index 350665d561..b4fe14b79f 100644 --- a/tests/testthat/test-stat-sum.R +++ b/tests/testthat/test-stat-sum.R @@ -4,37 +4,37 @@ test_that("handles grouping correctly", { base <- ggplot(d, aes(cut, clarity)) - ret <- layer_data(base + stat_sum()) + ret <- get_layer_data(base + stat_sum()) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_true(all_ones(ret$prop)) - ret <- layer_data(base + stat_sum(aes(group = 1))) + ret <- get_layer_data(base + stat_sum(aes(group = 1))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_equal(sum(ret$prop), 1) - ret <- layer_data(base + stat_sum(aes(group = cut))) + ret <- get_layer_data(base + stat_sum(aes(group = cut))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_true(all_ones(tapply(ret$prop, ret$x, FUN = sum))) - ret <- layer_data(base + stat_sum(aes(group = cut, colour = cut))) + ret <- get_layer_data(base + stat_sum(aes(group = cut, colour = cut))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_true(all_ones(tapply(ret$prop, ret$x, FUN = sum))) - ret <- layer_data(base + stat_sum(aes(group = clarity))) + ret <- get_layer_data(base + stat_sum(aes(group = clarity))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_true(all_ones(tapply(ret$prop, ret$y, FUN = sum))) - ret <- layer_data(base + stat_sum(aes(group = clarity, colour = cut))) + ret <- get_layer_data(base + stat_sum(aes(group = clarity, colour = cut))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), nrow(d)) expect_true(all_ones(tapply(ret$prop, ret$y, FUN = sum))) - ret <- layer_data(base + stat_sum(aes(group = 1, weight = price))) + ret <- get_layer_data(base + stat_sum(aes(group = 1, weight = price))) expect_equal(nrow(ret), 38) expect_equal(sum(ret$n), sum(d$price)) expect_equal(sum(ret$prop), 1) diff --git a/tests/testthat/test-stat-summary.R b/tests/testthat/test-stat-summary.R index 925ba8d4b1..825efd981c 100644 --- a/tests/testthat/test-stat-summary.R +++ b/tests/testthat/test-stat-summary.R @@ -20,8 +20,8 @@ test_that("stat_summary(_bin) work with lambda expressions", { }) expect_equal( - layer_data(p1), - layer_data(p2) + get_layer_data(p1), + get_layer_data(p2) ) @@ -34,8 +34,8 @@ test_that("stat_summary(_bin) work with lambda expressions", { ) expect_equal( - layer_data(p1), - layer_data(p3) + get_layer_data(p1), + get_layer_data(p3) ) }) @@ -60,8 +60,8 @@ test_that("stat_summary_(2d|hex) work with lambda expressions", { stat_summary_2d(fun = ~ mean(.x)) expect_equal( - layer_data(p1), - layer_data(p2) + get_layer_data(p1), + get_layer_data(p2) ) @@ -76,8 +76,8 @@ test_that("stat_summary_(2d|hex) work with lambda expressions", { stat_summary_hex(fun = ~ mean(.x)) expect_equal( - layer_data(p1), - layer_data(p2) + get_layer_data(p1), + get_layer_data(p2) ) }) diff --git a/tests/testthat/test-stat-ydensity.R b/tests/testthat/test-stat-ydensity.R index 98138d2d21..d9f39b4708 100644 --- a/tests/testthat/test-stat-ydensity.R +++ b/tests/testthat/test-stat-ydensity.R @@ -14,13 +14,13 @@ test_that("`drop = FALSE` preserves groups with 1 observations", { p <- ggplot(df, mapping = aes(x, y, fill = g)) expect_warning( - ld <- layer_data(p + geom_violin(drop = TRUE)), + ld <- get_layer_data(p + geom_violin(drop = TRUE)), "Groups with fewer than two datapoints have been dropped" ) expect_equal(length(unique(ld$x)), 3) expect_warning( - ld <- layer_data(p + geom_violin(drop = FALSE)), + ld <- get_layer_data(p + geom_violin(drop = FALSE)), "Cannot compute density for groups with fewer than two datapoints" ) expect_equal(length(unique(ld$x)), 4) @@ -33,7 +33,7 @@ test_that("mapped_discrete class is preserved", { y = 1:6 ) - ld <- layer_data( + ld <- get_layer_data( ggplot(df, aes(x, y)) + geom_violin() + scale_x_discrete(drop = FALSE) ) diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 1200a56d99..4c1a24c369 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -287,7 +287,7 @@ test_that("incorrect theme specifications throw meaningful errors", { expect_snapshot_error(calc_element("line", theme(line = element_rect()))) register_theme_elements(element_tree = list(test = el_def("element_rect"))) expect_snapshot_error(calc_element("test", theme_gray() + theme(test = element_rect()))) - expect_snapshot_error(theme_set("foo")) + expect_snapshot_error(set_theme("foo")) }) test_that("element tree can be modified", { @@ -394,7 +394,7 @@ test_that("complete plot themes shouldn't inherit from default", { }) test_that("current theme can be updated with new elements", { - old <- theme_set(theme_grey()) + old <- set_theme(theme_grey()) b1 <- ggplot() + theme_grey() b2 <- ggplot() @@ -428,7 +428,7 @@ test_that("current theme can be updated with new elements", { expect_identical(e1, e2) reset_theme_settings() - theme_set(old) + set_theme(old) }) test_that("titleGrob() and margins() work correctly", { diff --git a/tests/testthat/test-viridis.R b/tests/testthat/test-viridis.R index 31dad3f3bb..7845063085 100644 --- a/tests/testthat/test-viridis.R +++ b/tests/testthat/test-viridis.R @@ -5,12 +5,12 @@ test_that("viridis scale changes point color", { geom_point() p2 <- p1 + scale_colour_viridis_d() - expect_false(layer_data(p1)$colour == layer_data(p2)$colour) - expect_equal(layer_data(p2)$colour, "#440154FF") + expect_false(get_layer_data(p1)$colour == get_layer_data(p2)$colour) + expect_equal(get_layer_data(p2)$colour, "#440154FF") }) test_that("viridis scale is used by default for ordered factors", { p <- ggplot(df, aes(x, y, colour = tier)) + geom_point() - expect_equal(layer_data(p)$colour, "#440154FF") + expect_equal(get_layer_data(p)$colour, "#440154FF") }) diff --git a/vignettes/articles/faq-customising.Rmd b/vignettes/articles/faq-customising.Rmd index 9268b8a0ff..5c8ed1b44f 100644 --- a/vignettes/articles/faq-customising.Rmd +++ b/vignettes/articles/faq-customising.Rmd @@ -367,11 +367,11 @@ ggplot(mpg, aes(x = hwy, y = cty, color = class)) + theme_gray(base_size = 18) ``` -If you would like all plots within a session/document to use a particular base size, you can set it with `theme_set()`. +If you would like all plots within a session/document to use a particular base size, you can set it with `set_theme()`. Run the following at the beginning of your session or include on top of your R Markdown document. ```{r eval = FALSE} -theme_set(theme_gray(base_size = 18)) +set_theme(theme_gray(base_size = 18)) ``` diff --git a/vignettes/ggplot2-in-packages.Rmd b/vignettes/ggplot2-in-packages.Rmd index 27196b1dea..691dac0298 100644 --- a/vignettes/ggplot2-in-packages.Rmd +++ b/vignettes/ggplot2-in-packages.Rmd @@ -204,7 +204,7 @@ mpg_drv_summary2 <- function() { ### Testing ggplot2 output -We suggest testing the output of ggplot2 in using the [vdiffr](https://cran.r-project.org/package=vdiffr) package, which is a tool to manage visual test cases (this is one of the ways we test ggplot2). If changes in ggplot2 or your code introduce a change in the visual output of a ggplot, tests will fail when you run them locally or as part of a Continuous Integration setup. To use vdiffr, make sure you are using [testthat](https://testthat.r-lib.org/) (you can use `usethis::use_testthat()` to get started) and add vdiffr to `Suggests` in your `DESCRIPTION`. Then, use `vdiffr::expect_doppleganger(, )` to make a test that fails if there are visual changes in ``. However, you should consider whether visual testing is the best strategy because it adds a dependency on how ggplot2 performs its rendering which may change between versions. If extracting the layer data using `layer_data()` and testing the values directly is possible it is far better as it more directly test the behaviour of your own code. +We suggest testing the output of ggplot2 in using the [vdiffr](https://cran.r-project.org/package=vdiffr) package, which is a tool to manage visual test cases (this is one of the ways we test ggplot2). If changes in ggplot2 or your code introduce a change in the visual output of a ggplot, tests will fail when you run them locally or as part of a Continuous Integration setup. To use vdiffr, make sure you are using [testthat](https://testthat.r-lib.org/) (you can use `usethis::use_testthat()` to get started) and add vdiffr to `Suggests` in your `DESCRIPTION`. Then, use `vdiffr::expect_doppleganger(, )` to make a test that fails if there are visual changes in ``. However, you should consider whether visual testing is the best strategy because it adds a dependency on how ggplot2 performs its rendering which may change between versions. If extracting the layer data using `get_layer_data()` and testing the values directly is possible it is far better as it more directly test the behaviour of your own code. ```r test_that("output of ggplot() is stable", { From e8cb599b7d9b9e00eb5f89ccc51f1f41d0b6a8ca Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 14:56:43 +0200 Subject: [PATCH 038/264] Add `ggplot_build()` method for class (#5803) * Add `ggplot_build.ggplot_built` method * small simplification in `get_guide_data()` * add news bullet --- NAMESPACE | 1 + NEWS.md | 2 ++ R/guides-.R | 4 +--- R/plot-build.R | 6 ++++++ 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 74fc47431f..104fd87e31 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -67,6 +67,7 @@ S3method(ggplot_add,list) S3method(ggplot_add,theme) S3method(ggplot_add,uneval) S3method(ggplot_build,ggplot) +S3method(ggplot_build,ggplot_built) S3method(ggplot_gtable,ggplot_built) S3method(grid.draw,absoluteGrob) S3method(grid.draw,ggplot) diff --git a/NEWS.md b/NEWS.md index df77db8c95..9f20de2a2e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -71,6 +71,8 @@ alignment is not necessary (#5788). * `position_stack()` skips computation when all `x` values are unique and therefore stacking is not necessary (#5788). +* A new `ggplot_build()` S3 method for classes was added, which + returns input unaltered (@teunbrand, #5800). # ggplot2 3.5.1 diff --git a/R/guides-.R b/R/guides-.R index 8a7396fab0..fc9d6e2b3c 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -792,9 +792,7 @@ get_guide_data <- function(plot = get_last_plot(), aesthetic, panel = 1L) { check_string(aesthetic, allow_empty = FALSE) aesthetic <- standardise_aes_names(aesthetic) - if (!inherits(plot, "ggplot_built")) { - plot <- ggplot_build(plot) - } + plot <- ggplot_build(plot) if (!aesthetic %in% c("x", "y", "x.sec", "y.sec", "theta", "r")) { # Non position guides: check if aesthetic in colnames of key diff --git a/R/plot-build.R b/R/plot-build.R index e2cc519823..7b90d9cf26 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -30,6 +30,12 @@ ggplot_build <- function(plot) { UseMethod('ggplot_build') } +#' @export +ggplot_build.ggplot_built <- function(plot) { + # This is a no-op + plot +} + #' @export ggplot_build.ggplot <- function(plot) { plot <- plot_clone(plot) From ecf5f40a38f24845ae45c8264eb4cb7e14a3bf33 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:15:35 +0200 Subject: [PATCH 039/264] Function for completing themes (#5804) * exported wrapper for `plot_theme()` * document * add test * add news bullet * Allow for unclassed list themes * fix failing test --- NAMESPACE | 1 + NEWS.md | 2 ++ R/theme.R | 36 ++++++++++++++++++++++++++++++++++++ man/complete_theme.Rd | 28 ++++++++++++++++++++++++++++ tests/testthat/test-theme.R | 24 ++++++++++++++++++++++++ 5 files changed, 91 insertions(+) create mode 100644 man/complete_theme.Rd diff --git a/NAMESPACE b/NAMESPACE index 104fd87e31..2d8b1f2015 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -305,6 +305,7 @@ export(borders) export(calc_element) export(check_device) export(combine_vars) +export(complete_theme) export(continuous_scale) export(coord_cartesian) export(coord_equal) diff --git a/NEWS.md b/NEWS.md index 9f20de2a2e..bb2730a82b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* New function `complete_theme()` to replicate how themes are handled during + plot building (#5801). * Special getter and setter functions have been renamed for consistency, allowing for better tab-completion with `get_*`- and `set_*`-prefixes. The old names remain available for backward compatibility (@teunbrand, #5568). diff --git a/R/theme.R b/R/theme.R index 28d9cf1008..4b7e543e06 100644 --- a/R/theme.R +++ b/R/theme.R @@ -560,6 +560,42 @@ validate_theme <- function(theme, tree = get_element_tree(), call = caller_env() ) } +#' Complete a theme +#' +#' This function takes a theme and completes it so that it can be used +#' downstream to render theme elements. Missing elements are filled in and +#' every item is validated to the specifications of the element tree. +#' +#' @param theme An incomplete [theme][theme()] object to complete, or `NULL` +#' to complete the default theme. +#' @param default A complete [theme][theme()] to fill in missing pieces. +#' Defaults to the global theme settings. +#' +#' @keywords internal +#' @return A [theme][theme()] object. +#' @export +#' +#' @examples +#' my_theme <- theme(line = element_line(colour = "red")) +#' complete_theme(my_theme) +complete_theme <- function(theme = NULL, default = theme_get()) { + if (!is_bare_list(theme)) { + check_object(theme, is.theme, "a {.cls theme} object", allow_null = TRUE) + } + check_object(default, is.theme, "a {.cls theme} object") + theme <- plot_theme(list(theme = theme), default = default) + + # Using `theme(!!!theme)` drops `NULL` entries, so strip most attributes and + # construct a new theme + attributes(theme) <- list(names = attr(theme, "names")) + structure( + theme, + class = c("theme", "gg"), + complete = TRUE, # This theme is complete and has no missing elements + validate = FALSE # Settings have already been validated + ) +} + # Combine plot defaults with current theme to get complete theme for a plot plot_theme <- function(x, default = get_theme()) { theme <- x$theme diff --git a/man/complete_theme.Rd b/man/complete_theme.Rd new file mode 100644 index 0000000000..b90e6abc9b --- /dev/null +++ b/man/complete_theme.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/theme.R +\name{complete_theme} +\alias{complete_theme} +\title{Complete a theme} +\usage{ +complete_theme(theme = NULL, default = theme_get()) +} +\arguments{ +\item{theme}{An incomplete \link[=theme]{theme} object to complete, or \code{NULL} +to complete the default theme.} + +\item{default}{A complete \link[=theme]{theme} to fill in missing pieces. +Defaults to the global theme settings.} +} +\value{ +A \link[=theme]{theme} object. +} +\description{ +This function takes a theme and completes it so that it can be used +downstream to render theme elements. Missing elements are filled in and +every item is validated to the specifications of the element tree. +} +\examples{ +my_theme <- theme(line = element_line(colour = "red")) +complete_theme(my_theme) +} +\keyword{internal} diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 4c1a24c369..b201602963 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -583,6 +583,30 @@ test_that("Minor tick length supports biparental inheritance", { ) }) +test_that("complete_theme completes a theme", { + # `NULL` should match default + gray <- theme_gray() + new <- complete_theme(NULL, default = gray) + expect_equal(new, gray, ignore_attr = "validate") + + # Elements are propagated + new <- complete_theme(theme(axis.line = element_line("red")), gray) + expect_equal(new$axis.line$colour, "red") + + # Missing elements are filled in if default theme is incomplete + new <- complete_theme(default = theme()) + expect_s3_class(new$axis.line, "element_blank") + + # Registered elements are included + register_theme_elements( + test = element_text(), + element_tree = list(test = el_def("element_text", "text")) + ) + new <- complete_theme(default = gray) + expect_s3_class(new$test, "element_text") + reset_theme_settings() +}) + # Visual tests ------------------------------------------------------------ test_that("aspect ratio is honored", { From be3ae5ac1015a41d816e9e264c5a1decf59dd1d5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:15:57 +0200 Subject: [PATCH 040/264] Add section about width/height (#5814) --- R/aes-position.R | 12 ++++++++++++ man/aes_position.Rd | 12 ++++++++++++ 2 files changed, 24 insertions(+) diff --git a/R/aes-position.R b/R/aes-position.R index 45590cc809..40b0089200 100644 --- a/R/aes-position.R +++ b/R/aes-position.R @@ -18,6 +18,18 @@ #' `xmiddle`, `middle`, `xupper`, `upper`, `x0` and `y0`. Many of these are used #' and automatically computed in [`geom_boxplot()`]. #' +#' ## Relation to `width` and `height` +#' +#' The position aesthetics mentioned above like `x` and `y` are all location +#' based. The `width` and `height` aesthetics are closely related length +#' based aesthetics, but are not position aesthetics. Consequently, `x` and `y` +#' aesthetics respond to scale transformations, whereas the length based +#' `width` and `height` aesthetics are not transformed by scales. For example, +#' if we have the pair `x = 10, width = 2`, that gets translated to the +#' locations `xmin = 9, xmax = 11` when using the default identity scales. +#' However, the same pair becomes `xmin = 1, xmax = 100` when using log10 scales, +#' as `width = 2` in log10-space spans a 100-fold change. +#' #' @name aes_position #' @aliases x y xmin xmax ymin ymax xend yend #' diff --git a/man/aes_position.Rd b/man/aes_position.Rd index 6777676b90..4f1cf4bbae 100644 --- a/man/aes_position.Rd +++ b/man/aes_position.Rd @@ -30,6 +30,18 @@ geometry that they're used in. These are \code{xintercept}, \code{yintercept}, \code{xmin_final}, \code{ymin_final}, \code{xmax_final}, \code{ymax_final}, \code{xlower}, \code{lower}, \code{xmiddle}, \code{middle}, \code{xupper}, \code{upper}, \code{x0} and \code{y0}. Many of these are used and automatically computed in \code{\link[=geom_boxplot]{geom_boxplot()}}. +\subsection{Relation to \code{width} and \code{height}}{ + +The position aesthetics mentioned above like \code{x} and \code{y} are all location +based. The \code{width} and \code{height} aesthetics are closely related length +based aesthetics, but are not position aesthetics. Consequently, \code{x} and \code{y} +aesthetics respond to scale transformations, whereas the length based +\code{width} and \code{height} aesthetics are not transformed by scales. For example, +if we have the pair \verb{x = 10, width = 2}, that gets translated to the +locations \verb{xmin = 9, xmax = 11} when using the default identity scales. +However, the same pair becomes \verb{xmin = 1, xmax = 100} when using log10 scales, +as \code{width = 2} in log10-space spans a 100-fold change. +} } \examples{ From 9c4ac3492fbe9eb61a40e74f6c70b2dd4bcb10c7 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:24:42 +0200 Subject: [PATCH 041/264] Set `width` as aesthetic in `geom_col()`/`geom_bar()`. (#5807) * replace hack with aesthetic * remove `width` as parameter * regenerate docs * add news bullet --- NEWS.md | 2 ++ R/geom-bar.R | 17 ++--------------- R/geom-col.R | 2 -- R/stat-count.R | 2 -- man/geom_bar.Rd | 8 ++------ 5 files changed, 6 insertions(+), 25 deletions(-) diff --git a/NEWS.md b/NEWS.md index bb2730a82b..0850e98fd5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -75,6 +75,8 @@ therefore stacking is not necessary (#5788). * A new `ggplot_build()` S3 method for classes was added, which returns input unaltered (@teunbrand, #5800). +* `width` is implemented as aesthetic instead of parameter in `geom_col()` and + `geom_bar()` (#3142). # ggplot2 3.5.1 diff --git a/R/geom-bar.R b/R/geom-bar.R index e4611fbabb..de7490bfc4 100644 --- a/R/geom-bar.R +++ b/R/geom-bar.R @@ -45,8 +45,6 @@ #' columns to the left/right of axis breaks. Note that this argument may have #' unintended behaviour when used with alternative positions, e.g. #' `position_dodge()`. -#' @param width Bar width. By default, set to 90% of the [resolution()] of the -#' data. #' @param geom,stat Override the default connection between `geom_bar()` and #' `stat_count()`. For more information about overriding these connections, #' see how the [stat][layer_stats] and [geom][layer_geoms] arguments work. @@ -98,7 +96,6 @@ geom_bar <- function(mapping = NULL, data = NULL, stat = "count", position = "stack", ..., just = 0.5, - width = NULL, na.rm = FALSE, orientation = NA, show.legend = NA, @@ -113,7 +110,6 @@ geom_bar <- function(mapping = NULL, data = NULL, inherit.aes = inherit.aes, params = list2( just = just, - width = width, na.rm = na.rm, orientation = orientation, ... @@ -134,6 +130,8 @@ GeomBar <- ggproto("GeomBar", GeomRect, # limits, not just those for which x and y are outside the limits non_missing_aes = c("xmin", "xmax", "ymin", "ymax"), + default_aes = aes(!!!GeomRect$default_aes, width = NULL), + setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params) params @@ -158,16 +156,5 @@ GeomBar <- ggproto("GeomBar", GeomRect, flip_data(data, params$flipped_aes) }, - draw_panel = function(self, data, panel_params, coord, lineend = "butt", - linejoin = "mitre", width = NULL, flipped_aes = FALSE) { - # Hack to ensure that width is detected as a parameter - ggproto_parent(GeomRect, self)$draw_panel( - data, - panel_params, - coord, - lineend = lineend, - linejoin = linejoin - ) - }, rename_size = TRUE ) diff --git a/R/geom-col.R b/R/geom-col.R index 2dc07f12da..77c756f573 100644 --- a/R/geom-col.R +++ b/R/geom-col.R @@ -4,7 +4,6 @@ geom_col <- function(mapping = NULL, data = NULL, position = "stack", ..., just = 0.5, - width = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { @@ -19,7 +18,6 @@ geom_col <- function(mapping = NULL, data = NULL, inherit.aes = inherit.aes, params = list2( just = just, - width = width, na.rm = na.rm, ... ) diff --git a/R/stat-count.R b/R/stat-count.R index 18dc1ebaa6..fd78d1beaa 100644 --- a/R/stat-count.R +++ b/R/stat-count.R @@ -13,7 +13,6 @@ stat_count <- function(mapping = NULL, data = NULL, geom = "bar", position = "stack", ..., - width = NULL, na.rm = FALSE, orientation = NA, show.legend = NA, @@ -22,7 +21,6 @@ stat_count <- function(mapping = NULL, data = NULL, params <- list2( na.rm = na.rm, orientation = orientation, - width = width, ... ) diff --git a/man/geom_bar.Rd b/man/geom_bar.Rd index a974f9824e..4f8196b4c1 100644 --- a/man/geom_bar.Rd +++ b/man/geom_bar.Rd @@ -13,7 +13,6 @@ geom_bar( position = "stack", ..., just = 0.5, - width = NULL, na.rm = FALSE, orientation = NA, show.legend = NA, @@ -26,7 +25,6 @@ geom_col( position = "stack", ..., just = 0.5, - width = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE @@ -38,7 +36,6 @@ stat_count( geom = "bar", position = "stack", ..., - width = NULL, na.rm = FALSE, orientation = NA, show.legend = NA, @@ -113,9 +110,6 @@ columns to the left/right of axis breaks. Note that this argument may have unintended behaviour when used with alternative positions, e.g. \code{position_dodge()}.} -\item{width}{Bar width. By default, set to 90\% of the \code{\link[=resolution]{resolution()}} of the -data.} - \item{na.rm}{If \code{FALSE}, the default, missing values are removed with a warning. If \code{TRUE}, missing values are silently removed.} @@ -182,6 +176,7 @@ This geom treats each axis differently and, thus, can thus have two orientations \item \code{\link[=aes_group_order]{group}} \item \code{\link[=aes_linetype_size_shape]{linetype}} \item \code{\link[=aes_linetype_size_shape]{linewidth}} +\item \code{width} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. @@ -196,6 +191,7 @@ Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. \item \code{\link[=aes_group_order]{group}} \item \code{\link[=aes_linetype_size_shape]{linetype}} \item \code{\link[=aes_linetype_size_shape]{linewidth}} +\item \code{width} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. From 89b829dfdb8a6db30c11de81432a76924235cc5b Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:40:44 +0200 Subject: [PATCH 042/264] Fix `linewidth` of `draw_key_polygon()` (#5815) * `draw_key_polygon()` uses actual linewidth * add news bullet --- NEWS.md | 2 ++ R/legend-draw.R | 10 ++++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0850e98fd5..4b10da1543 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* The size of the `draw_key_polygon()` glyph now reflects the `linewidth` + aesthetic (#4852). * New function `complete_theme()` to replicate how themes are handled during plot building (#5801). * Special getter and setter functions have been renamed for consistency, allowing diff --git a/R/legend-draw.R b/R/legend-draw.R index ce16f7a6ab..8e7e8b9ae4 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -71,9 +71,9 @@ draw_key_polygon <- function(data, params, size) { data$linewidth <- 0.5 } - lwd <- min(data$linewidth, min(size) / 4) + lwd <- data$linewidth - rectGrob( + grob <- rectGrob( width = unit(1, "npc") - unit(lwd, "mm"), height = unit(1, "npc") - unit(lwd, "mm"), gp = ggpar( @@ -84,6 +84,12 @@ draw_key_polygon <- function(data, params, size) { linejoin = params$linejoin %||% "mitre", lineend = params$lineend %||% "butt" )) + + # Magic number is 5 because we convert mm to cm (divide by 10) but we + # draw two lines in each direction (times 2) + attr(grob, "width") <- lwd / 5 + attr(grob, "height") <- lwd / 5 + grob } #' @export From 6f6076604351ad93ffc2506722173094c75d99c6 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:46:27 +0200 Subject: [PATCH 043/264] include center as option (#5871) --- R/theme.R | 4 ++-- man/theme.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/theme.R b/R/theme.R index 4b7e543e06..7e8a794a11 100644 --- a/R/theme.R +++ b/R/theme.R @@ -116,8 +116,8 @@ #' @param legend.box arrangement of multiple legends ("horizontal" or #' "vertical") #' @param legend.box.just justification of each legend within the overall -#' bounding box, when there are multiple legends ("top", "bottom", "left", or -#' "right") +#' bounding box, when there are multiple legends ("top", "bottom", "left", +#' "right", "center" or "centre") #' @param legend.box.margin margins around the full legend area, as specified #' using [margin()]; inherits from `margins`. #' @param legend.box.background background of legend area ([element_rect()]; diff --git a/man/theme.Rd b/man/theme.Rd index 5635049b5c..1f12df3ba9 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -272,8 +272,8 @@ string. Can be \code{"panel"} (default) to align legends to the panels or "vertical")} \item{legend.box.just}{justification of each legend within the overall -bounding box, when there are multiple legends ("top", "bottom", "left", or -"right")} +bounding box, when there are multiple legends ("top", "bottom", "left", +"right", "center" or "centre")} \item{legend.box.margin}{margins around the full legend area, as specified using \code{\link[=margin]{margin()}}; inherits from \code{margins}.} From 49b45c11f97977e2f69202092f8dc2bbac051b75 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 15:53:18 +0200 Subject: [PATCH 044/264] Apply jitter in `position_jitterdodge()` once (#5819) * Follow #4403 * add test * add news bullet --- NEWS.md | 2 ++ R/position-jitterdodge.R | 13 ++++++++++++- tests/testthat/test-position-jitterdodge.R | 12 ++++++++++++ 3 files changed, 26 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 4b10da1543..212b44326e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -79,6 +79,8 @@ returns input unaltered (@teunbrand, #5800). * `width` is implemented as aesthetic instead of parameter in `geom_col()` and `geom_bar()` (#3142). +* Fix a bug in `position_jitterdodge()` where different jitters would be applied + to different position aesthetics of the same axis (@teunbrand, #5818). # ggplot2 3.5.1 diff --git a/R/position-jitterdodge.R b/R/position-jitterdodge.R index 291f03f263..fba28a47fa 100644 --- a/R/position-jitterdodge.R +++ b/R/position-jitterdodge.R @@ -76,7 +76,18 @@ PositionJitterdodge <- ggproto("PositionJitterdodge", Position, trans_x <- if (params$jitter.width > 0) function(x) jitter(x, amount = params$jitter.width) trans_y <- if (params$jitter.height > 0) function(x) jitter(x, amount = params$jitter.height) - data <- with_seed_null(params$seed, transform_position(data, trans_x, trans_y)) + x_aes <- intersect(ggplot_global$x_aes, names(data)) + y_aes <- intersect(ggplot_global$y_aes, names(data)) + + x <- if (length(x_aes) == 0) 0 else data[[x_aes[1]]] + y <- if (length(y_aes) == 0) 0 else data[[y_aes[1]]] + dummy_data <- data_frame0(x = x, y = y, .size = nrow(data)) + + fixed_jitter <- with_seed_null(params$seed, transform_position(dummy_data, trans_x, trans_y)) + x_jit <- fixed_jitter$x - x + y_jit <- fixed_jitter$y - y + + data <- transform_position(data, function(x) x + x_jit, function(x) x + y_jit) flip_data(data, params$flipped_aes) } ) diff --git a/tests/testthat/test-position-jitterdodge.R b/tests/testthat/test-position-jitterdodge.R index 8f6b9227eb..49e8378666 100644 --- a/tests/testthat/test-position-jitterdodge.R +++ b/tests/testthat/test-position-jitterdodge.R @@ -2,3 +2,15 @@ test_that("position_jitterdodge() fails with meaningful error", { p <- ggplot(mtcars) + geom_point(aes(disp, mpg), position = 'jitterdodge') expect_snapshot_error(ggplot_build(p)) }) + +test_that("position_jitterdodge preserves widths", { + ld <- layer_data( + ggplot(mtcars, aes(factor(cyl), fill = factor(am))) + + geom_bar(position = position_jitterdodge()) + ) + + expect_equal( + as.numeric(ld$xmax - ld$xmin), + rep(0.45, nrow(ld)) + ) +}) From 3b83eeaa11cac5dcb6f641cb384281118ce84a11 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 16:02:43 +0200 Subject: [PATCH 045/264] Binned guides discard out-of-bound breaks (#5873) * oob breaks are discarded * add test * add news bullet --- NEWS.md | 2 ++ R/guide-bins.R | 1 + tests/testthat/test-guides.R | 8 ++++++++ 3 files changed, 11 insertions(+) diff --git a/NEWS.md b/NEWS.md index 212b44326e..87f1c93c50 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug where binned guides would keep out-of-bounds breaks + (@teunbrand, #5870). * The size of the `draw_key_polygon()` glyph now reflects the `linewidth` aesthetic (#4852). * New function `complete_theme()` to replicate how themes are handled during diff --git a/R/guide-bins.R b/R/guide-bins.R index 571a461d4b..e2bd0db428 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -339,6 +339,7 @@ parse_binned_breaks = function(scale, breaks = scale$get_breaks()) { if (!is.numeric(scale$breaks)) { breaks <- breaks[!breaks %in% limits] } + breaks <- oob_discard(breaks, limits) all_breaks <- unique0(c(limits[1], breaks, limits[2])) bin_at <- all_breaks[-1] - diff(all_breaks) / 2 } else { diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 4930188025..8d677dc1bf 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -300,6 +300,14 @@ test_that("guide_coloursteps and guide_bins return ordered breaks", { g <- guide_bins() key <- g$train(scale = scale, aesthetics = "colour")$key expect_true(all(diff(key$.value) > 0)) + + # Out of bound breaks are removed + scale <- scale_colour_viridis_c(breaks = c(10, 20, 30, 40, 50), na.value = "grey50") + scale$train(c(15, 45)) + + g <- guide_colorsteps() + key <- g$train(scale = scale, aesthetic = "colour")$key + expect_equal(sum(key$colour == "grey50"), 0) }) test_that("guide_coloursteps can parse (un)even steps from discrete scales", { From c9a2d6a306f4dd90263457639b41fd4ae4c4a5a8 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 20 May 2024 18:40:54 +0200 Subject: [PATCH 046/264] Adhere more strictly to `bins` argument in `stat_bin()` (#5891) * try respecting `bins` better * fix #5890 * add test * add news bullet --- NEWS.md | 2 ++ R/bin.R | 4 ++++ tests/testthat/test-stat-bin.R | 24 ++++++++++++++++++++++++ 3 files changed, 30 insertions(+) diff --git a/NEWS.md b/NEWS.md index 87f1c93c50..54bbcdd7b6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -83,6 +83,8 @@ `geom_bar()` (#3142). * Fix a bug in `position_jitterdodge()` where different jitters would be applied to different position aesthetics of the same axis (@teunbrand, #5818). +* In `stat_bin()`, the default `boundary` is now chosen to better adhere to + the `nbin` argument (@teunbrand, #5882, #5036) # ggplot2 3.5.1 diff --git a/R/bin.R b/R/bin.R index 8ca4bff921..856568f08c 100644 --- a/R/bin.R +++ b/R/bin.R @@ -117,8 +117,12 @@ bin_breaks_bins <- function(x_range, bins = 30, center = NULL, } else if (bins == 1) { width <- diff(x_range) boundary <- x_range[1] + center <- NULL } else { width <- (x_range[2] - x_range[1]) / (bins - 1) + if (is.null(center)) { + boundary <- boundary %||% x_range[1] - width / 2 + } } bin_breaks_width(x_range, width, boundary = boundary, center = center, diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index 0974196cb2..af0ae467f3 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -119,6 +119,30 @@ test_that("bins() computes fuzz with non-finite breaks", { expect_equal(difference[2], 1000 * .Machine$double.eps, tolerance = 0) }) +test_that("bins is strictly adhered to", { + + nbins <- c(1, 2, 3, 4, 5, 10, 20, 30, 40, 50) + + # Default case + nbreaks <- vapply(nbins, function(bins) { + length(bin_breaks_bins(c(0, 10), bins)$breaks) + }, numeric(1)) + expect_equal(nbreaks, nbins + 1) + + # Center is provided + nbreaks <- vapply(nbins, function(bins) { + length(bin_breaks_bins(c(0, 10), bins, center = 0)$breaks) + }, numeric(1)) + expect_equal(nbreaks, nbins + 1) + + # Boundary is provided + nbreaks <- vapply(nbins, function(bins) { + length(bin_breaks_bins(c(0, 10), bins, boundary = 0)$breaks) + }, numeric(1)) + expect_equal(nbreaks, nbins + 1) + +}) + comp_bin <- function(df, ...) { plot <- ggplot(df, aes(x = x)) + stat_bin(...) get_layer_data(plot) From 341e8fce31a15d574739cfd5f686f01600f353b0 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 21 May 2024 13:54:04 +0200 Subject: [PATCH 047/264] Additional `arrow.fill` parameters for line-based functions. (#5768) * add `arrow.fill` to `element_line()` * add `arrow.fill` to other line geoms * propagate `arrow.fill` in `geom_sf()` * Add news bullet * include `geom_step()` --- NEWS.md | 3 +++ R/geom-function.R | 4 ++-- R/geom-path.R | 16 ++++++++++++---- R/geom-sf.R | 7 ++++--- R/theme-elements.R | 33 ++++++++++++++++++++++----------- man/element.Rd | 3 +++ man/geom_path.Rd | 4 ++++ 7 files changed, 50 insertions(+), 20 deletions(-) diff --git a/NEWS.md b/NEWS.md index 54bbcdd7b6..6ba924fb1c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* The `arrow.fill` parameter is now applied to more line-based functions: + `geom_path()`, `geom_line()`, `geom_step()` `geom_function()`, line + geometries in `geom_sf()` and `element_line()`. * Fixed bug where binned guides would keep out-of-bounds breaks (@teunbrand, #5870). * The size of the `draw_key_polygon()` glyph now reflects the `linewidth` diff --git a/R/geom-function.R b/R/geom-function.R index 47ce54a627..c566731996 100644 --- a/R/geom-function.R +++ b/R/geom-function.R @@ -90,7 +90,7 @@ geom_function <- function(mapping = NULL, data = NULL, stat = "function", #' @export #' @include geom-path.R GeomFunction <- ggproto("GeomFunction", GeomPath, - draw_panel = function(self, data, panel_params, coord, arrow = NULL, + draw_panel = function(self, data, panel_params, coord, arrow = NULL, arrow.fill = NULL, lineend = "butt", linejoin = "round", linemitre = 10, na.rm = FALSE) { groups <- unique0(data$group) @@ -102,7 +102,7 @@ GeomFunction <- ggproto("GeomFunction", GeomPath, } ggproto_parent(GeomPath, self)$draw_panel( - data, panel_params, coord, arrow, lineend, linejoin, linemitre, na.rm + data, panel_params, coord, arrow, arrow.fill, lineend, linejoin, linemitre, na.rm ) } ) diff --git a/R/geom-path.R b/R/geom-path.R index b705162b9f..9db4c80ca9 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -18,6 +18,8 @@ #' @param linejoin Line join style (round, mitre, bevel). #' @param linemitre Line mitre limit (number greater than 1). #' @param arrow Arrow specification, as created by [grid::arrow()]. +#' @param arrow.fill fill colour to use for the arrow head (if closed). `NULL` +#' means use `colour` aesthetic. #' @seealso #' [geom_polygon()]: Filled paths (polygons); #' [geom_segment()]: Line segments @@ -101,6 +103,7 @@ geom_path <- function(mapping = NULL, data = NULL, linejoin = "round", linemitre = 10, arrow = NULL, + arrow.fill = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { @@ -117,6 +120,7 @@ geom_path <- function(mapping = NULL, data = NULL, linejoin = linejoin, linemitre = linemitre, arrow = arrow, + arrow.fill = arrow.fill, na.rm = na.rm, ... ) @@ -152,7 +156,7 @@ GeomPath <- ggproto("GeomPath", Geom, data }, - draw_panel = function(self, data, panel_params, coord, arrow = NULL, + draw_panel = function(self, data, panel_params, coord, arrow = NULL, arrow.fill = NULL, lineend = "butt", linejoin = "round", linemitre = 10, na.rm = FALSE) { data <- check_linewidth(data, snake_class(self)) @@ -193,6 +197,8 @@ GeomPath <- ggproto("GeomPath", Geom, start <- c(TRUE, group_diff) end <- c(group_diff, TRUE) + munched$fill <- arrow.fill %||% munched$colour + if (!constant) { arrow <- repair_segment_arrow(arrow, munched$group) @@ -202,7 +208,7 @@ GeomPath <- ggproto("GeomPath", Geom, default.units = "native", arrow = arrow, gp = ggpar( col = alpha(munched$colour, munched$alpha)[!end], - fill = alpha(munched$colour, munched$alpha)[!end], + fill = alpha(munched$fill, munched$alpha)[!end], lwd = munched$linewidth[!end], lty = munched$linetype[!end], lineend = lineend, @@ -217,7 +223,7 @@ GeomPath <- ggproto("GeomPath", Geom, default.units = "native", arrow = arrow, gp = ggpar( col = alpha(munched$colour, munched$alpha)[start], - fill = alpha(munched$colour, munched$alpha)[start], + fill = alpha(munched$fill, munched$alpha)[start], lwd = munched$linewidth[start], lty = munched$linetype[start], lineend = lineend, @@ -324,11 +330,13 @@ geom_step <- function(mapping = NULL, data = NULL, stat = "identity", GeomStep <- ggproto("GeomStep", GeomPath, draw_panel = function(data, panel_params, coord, lineend = "butt", linejoin = "round", linemitre = 10, + arrow = NULL, arrow.fill = NULL, direction = "hv") { data <- dapply(data, "group", stairstep, direction = direction) GeomPath$draw_panel( data, panel_params, coord, - lineend = lineend, linejoin = linejoin, linemitre = linemitre + lineend = lineend, linejoin = linejoin, linemitre = linemitre, + arrow = arrow, arrow.fill = arrow.fill ) } ) diff --git a/R/geom-sf.R b/R/geom-sf.R index cdcadb1140..c0541cf369 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -190,7 +190,7 @@ GeomSf <- ggproto("GeomSf", Geom, draw_panel = function(self, data, panel_params, coord, legend = NULL, lineend = "butt", linejoin = "round", linemitre = 10, - arrow = NULL, na.rm = TRUE) { + arrow = NULL, arrow.fill = NULL, na.rm = TRUE) { if (!inherits(coord, "CoordSf")) { cli::cli_abort("{.fn {snake_class(self)}} can only be used with {.fn coord_sf}.") } @@ -198,7 +198,7 @@ GeomSf <- ggproto("GeomSf", Geom, # Need to refactor this to generate one grob per geometry type coord <- coord$transform(data, panel_params) sf_grob(coord, lineend = lineend, linejoin = linejoin, linemitre = linemitre, - arrow = arrow, na.rm = na.rm) + arrow = arrow, arrow.fill = arrow.fill, na.rm = na.rm) }, draw_key = function(data, params, size) { @@ -224,7 +224,7 @@ default_aesthetics <- function(type) { } sf_grob <- function(x, lineend = "butt", linejoin = "round", linemitre = 10, - arrow = NULL, na.rm = TRUE) { + arrow = NULL, arrow.fill = NULL, na.rm = TRUE) { type <- sf_types[sf::st_geometry_type(x$geometry)] is_point <- type == "point" is_line <- type == "line" @@ -249,6 +249,7 @@ sf_grob <- function(x, lineend = "butt", linejoin = "round", linemitre = 10, alpha <- x$alpha %||% NA fill <- fill_alpha(x$fill %||% NA, alpha) + fill[is_line] <- arrow.fill %||% fill[is_line] col <- x$colour %||% NA col[is_point | is_line] <- alpha(col[is_point | is_line], alpha[is_point | is_line]) diff --git a/R/theme-elements.R b/R/theme-elements.R index 23bf79bd6e..378ef3a7d9 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -16,6 +16,7 @@ #' @param colour,color Line/border colour. Color is an alias for colour. #' @param linewidth Line/border size in mm. #' @param size text size in pts. +#' @param arrow.fill Fill colour for arrows. #' @param inherit.blank Should this element inherit the existence of an #' `element_blank` among its parents? If `TRUE` the existence of #' a blank element among its parents will cause this element to be blank as @@ -87,18 +88,21 @@ element_rect <- function(fill = NULL, colour = NULL, linewidth = NULL, #' @param lineend Line end Line end style (round, butt, square) #' @param arrow Arrow specification, as created by [grid::arrow()] element_line <- function(colour = NULL, linewidth = NULL, linetype = NULL, - lineend = NULL, color = NULL, arrow = NULL, inherit.blank = FALSE, size = deprecated()) { + lineend = NULL, color = NULL, arrow = NULL, arrow.fill = NULL, + inherit.blank = FALSE, size = deprecated()) { if (lifecycle::is_present(size)) { deprecate_soft0("3.4.0", "element_line(size)", "element_line(linewidth)") linewidth <- size } - if (!is.null(color)) colour <- color - if (is.null(arrow)) arrow <- FALSE + colour <- color %||% colour + arrow.fill <- arrow.fill %||% colour + arrow <- arrow %||% FALSE + structure( list(colour = colour, linewidth = linewidth, linetype = linetype, lineend = lineend, - arrow = arrow, inherit.blank = inherit.blank), + arrow = arrow, arrow.fill = arrow.fill, inherit.blank = inherit.blank), class = c("element_line", "element") ) } @@ -253,6 +257,7 @@ element_grob.element_text <- function(element, label = "", x = NULL, y = NULL, #' @export element_grob.element_line <- function(element, x = 0:1, y = 0:1, colour = NULL, linewidth = NULL, linetype = NULL, lineend = NULL, + arrow.fill = NULL, default.units = "npc", id.lengths = NULL, ..., size = deprecated()) { if (lifecycle::is_present(size)) { @@ -260,21 +265,27 @@ element_grob.element_line <- function(element, x = 0:1, y = 0:1, linewidth <- size } + arrow <- if (is.logical(element$arrow) && !element$arrow) { + NULL + } else { + element$arrow + } + if (is.null(arrow)) { + arrow.fill <- colour + element$arrow.fill <- element$colour + } + # The gp settings can override element_gp gp <- ggpar( - col = colour, fill = colour, + col = colour, fill = arrow.fill %||% colour, lwd = linewidth, lty = linetype, lineend = lineend ) element_gp <- ggpar( - col = element$colour, fill = element$colour, + col = element$colour, fill = element$arrow.fill %||% element$colour, lwd = element$linewidth, lty = element$linetype, lineend = element$lineend ) - arrow <- if (is.logical(element$arrow) && !element$arrow) { - NULL - } else { - element$arrow - } + polylineGrob( x, y, default.units = default.units, gp = modify_list(element_gp, gp), diff --git a/man/element.Rd b/man/element.Rd index a3c27a259c..2a4f68e2eb 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -28,6 +28,7 @@ element_line( lineend = NULL, color = NULL, arrow = NULL, + arrow.fill = NULL, inherit.blank = FALSE, size = deprecated() ) @@ -75,6 +76,8 @@ calculating final element state.} \item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}} +\item{arrow.fill}{Fill colour for arrows.} + \item{family}{Font family} \item{face}{Font face ("plain", "italic", "bold", "bold.italic")} diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 4a59e4a081..00a3ef8e5a 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -16,6 +16,7 @@ geom_path( linejoin = "round", linemitre = 10, arrow = NULL, + arrow.fill = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE @@ -128,6 +129,9 @@ lists which parameters it can accept. \item{arrow}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.} +\item{arrow.fill}{fill colour to use for the arrow head (if closed). \code{NULL} +means use \code{colour} aesthetic.} + \item{na.rm}{If \code{FALSE}, the default, missing values are removed with a warning. If \code{TRUE}, missing values are silently removed.} From 5199cee62f90c2484b0d34888910663d3eac8d5d Mon Sep 17 00:00:00 2001 From: Johannes Johow Date: Tue, 21 May 2024 13:54:46 +0200 Subject: [PATCH 048/264] Update guide-legend.R (#5806) * Update guide-legend.R typo * document --------- Co-authored-by: Teun van den Brand --- R/guide-legend.R | 2 +- man/guide_bins.Rd | 2 +- man/guide_legend.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/guide-legend.R b/R/guide-legend.R index 157018dc48..7dd8e9128c 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -19,7 +19,7 @@ #' @param position A character string indicating where the legend should be #' placed relative to the plot panels. #' @param direction A character string indicating the direction of the guide. -#' One of "horizontal" or "vertical." +#' One of "horizontal" or "vertical". #' @param override.aes A list specifying aesthetic parameters of legend key. #' See details and examples. #' @param nrow,ncol The desired number of rows and column of legends diff --git a/man/guide_bins.Rd b/man/guide_bins.Rd index 8633915f2d..ead7b8a099 100644 --- a/man/guide_bins.Rd +++ b/man/guide_bins.Rd @@ -30,7 +30,7 @@ guide overrides, and is combined with, the plot's theme.} placed relative to the plot panels.} \item{direction}{A character string indicating the direction of the guide. -One of "horizontal" or "vertical."} +One of "horizontal" or "vertical".} \item{override.aes}{A list specifying aesthetic parameters of legend key. See details and examples.} diff --git a/man/guide_legend.Rd b/man/guide_legend.Rd index d2db3b2da4..67465c9877 100644 --- a/man/guide_legend.Rd +++ b/man/guide_legend.Rd @@ -31,7 +31,7 @@ guide overrides, and is combined with, the plot's theme.} placed relative to the plot panels.} \item{direction}{A character string indicating the direction of the guide. -One of "horizontal" or "vertical."} +One of "horizontal" or "vertical".} \item{override.aes}{A list specifying aesthetic parameters of legend key. See details and examples.} From 0d0dc62c03c7e431082ee664a02f139572c65cb3 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 22 May 2024 19:23:46 +0200 Subject: [PATCH 049/264] `after_*()` length checks (#5902) * throw warnings * simplify `try_fetch()` block in legend * add tests * add news bullet * nicer pluralisation --- NEWS.md | 2 ++ R/geom-.R | 3 +++ R/guide-legend.R | 12 +----------- R/layer.R | 16 ++++++++++++++++ tests/testthat/test-aes-calculated.R | 22 ++++++++++++++++++++++ 5 files changed, 44 insertions(+), 11 deletions(-) diff --git a/NEWS.md b/NEWS.md index 6ba924fb1c..c469b5255c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -88,6 +88,8 @@ to different position aesthetics of the same axis (@teunbrand, #5818). * In `stat_bin()`, the default `boundary` is now chosen to better adhere to the `nbin` argument (@teunbrand, #5882, #5036) +* `after_stat()` and `after_scale()` throw warnings when the computed aesthetics + are not of the correct length (#5901). # ggplot2 3.5.1 diff --git a/R/geom-.R b/R/geom-.R index ab4e1ed1b7..f538cf0bb6 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -167,6 +167,9 @@ Geom <- ggproto("Geom", } names(modified_aes) <- names(rename_aes(modifiers)) + + modified_aes <- cleanup_mismatched_data(modified_aes, nrow(data), "after_scale") + modified_aes <- data_frame0(!!!compact(modified_aes)) data <- cunion(modified_aes, data) diff --git a/R/guide-legend.R b/R/guide-legend.R index 7dd8e9128c..2ef01fbae9 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -238,17 +238,7 @@ GuideLegend <- ggproto( is_modified <- is_scaled_aes(aesthetics) | is_staged_aes(aesthetics) modifiers <- aesthetics[is_modified] - data <- try_fetch( - layer$geom$use_defaults(params$key[matched_aes], - layer_params, modifiers), - error = function(cnd) { - cli::cli_warn( - "Failed to apply {.fn after_scale} modifications to legend", - parent = cnd - ) - layer$geom$use_defaults(params$key[matched_aes], layer_params, list()) - } - ) + data <- layer$geom$use_defaults(params$key[matched_aes], layer_params, modifiers) data$.draw <- keep_key_data(params$key, df, matched_aes, layer$show.legend) } else { reps <- rep(1, nrow(params$key)) diff --git a/R/layer.R b/R/layer.R index 7df5119aae..88b6a9b026 100644 --- a/R/layer.R +++ b/R/layer.R @@ -412,6 +412,7 @@ Layer <- ggproto("Layer", NULL, if (self$stat$retransform) { stat_data <- plot$scales$transform_df(stat_data) } + stat_data <- cleanup_mismatched_data(stat_data, nrow(data), "after_stat") cunion(stat_data, data) }, @@ -498,3 +499,18 @@ set_draw_key <- function(geom, draw_key = NULL) { ggproto("", geom, draw_key = draw_key) } +cleanup_mismatched_data <- function(data, n, fun) { + failed <- !lengths(data) %in% c(0, 1, n) + if (!any(failed)) { + return(data) + } + + failed <- names(data)[failed] + cli::cli_warn( + "Failed to apply {.fn {fun}} for the following \\ + aesthetic{?s}: {.field {failed}}." + ) + + data[failed] <- NULL + data +} diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index 256a246f83..62d25697d3 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -70,6 +70,28 @@ test_that("staged aesthetics warn appropriately for duplicated names", { expect_snapshot_warning(ggplot_build(p)) }) +test_that("calculated aesthetics throw warnings when lengths mismatch", { + + df <- data.frame(x = 1:2) + + p <- ggplot(df, aes(x, x)) + + expect_warning( + ggplot_build( + p + geom_point(aes(colour = after_stat(c("A", "B", "C")))) + ), + "Failed to apply" + ) + + expect_warning( + ggplot_build( + p + geom_point(aes(colour = after_scale(c("red", "green", "blue")))) + ), + "Failed to apply" + ) + +}) + test_that("A deprecated warning is issued when stat(var) or ..var.. is used", { p1 <- ggplot(NULL, aes(stat(foo))) expect_snapshot_warning(b1 <- ggplot_build(p1)) From e3a4dafa50c67d9ce5d7567b92cb8192f5a6c81f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 24 May 2024 08:55:53 +0200 Subject: [PATCH 050/264] Rename `ggpar()` to `gg_par()` (#5899) * rename `ggpar()` to `gparam()` * rename to `gg_par()` --- NAMESPACE | 2 +- NEWS.md | 2 +- R/annotation-logticks.R | 8 ++++---- R/annotation-map.R | 2 +- R/coord-radial.R | 2 +- R/coord-sf.R | 2 +- R/geom-curve.R | 2 +- R/geom-dotplot.R | 8 ++++---- R/geom-hex.R | 2 +- R/geom-label.R | 8 ++++---- R/geom-map.R | 2 +- R/geom-path.R | 4 ++-- R/geom-point.R | 2 +- R/geom-polygon.R | 4 ++-- R/geom-rect.R | 2 +- R/geom-ribbon.R | 4 ++-- R/geom-rug.R | 2 +- R/geom-segment.R | 2 +- R/geom-text.R | 2 +- R/guide-colorbar.R | 4 ++-- R/guide-colorsteps.R | 2 +- R/legend-draw.R | 30 +++++++++++++++--------------- R/margins.R | 10 +++++----- R/theme-elements.R | 12 ++++++------ R/utilities-grid.R | 2 +- man/{ggpar.Rd => gg_par.Rd} | 6 +++--- 26 files changed, 64 insertions(+), 64 deletions(-) rename man/{ggpar.Rd => gg_par.Rd} (88%) diff --git a/NAMESPACE b/NAMESPACE index 2d8b1f2015..9068973de0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -429,7 +429,7 @@ export(get_layer_grob) export(get_panel_scales) export(get_theme) export(gg_dep) -export(ggpar) +export(gg_par) export(ggplot) export(ggplotGrob) export(ggplot_add) diff --git a/NEWS.md b/NEWS.md index c469b5255c..de3e87cee3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -61,7 +61,7 @@ (@teunbrand, #5756). * Fixed bug in `guide_custom()` that would throw error with `theme_void()` (@teunbrand, #5856). -* New helper function `ggpar()` to translate ggplot2's interpretation of +* New helper function `gg_par()` to translate ggplot2's interpretation of graphical parameters to {grid}'s interpretation (@teunbrand, #5866). * `scale_{x/y}_discrete()` can now accept a `sec.axis`. It is recommended to only use `dup_axis()` to set custom breaks or labels, as discrete variables diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R index 1d25332a91..33f0a952a4 100644 --- a/R/annotation-logticks.R +++ b/R/annotation-logticks.R @@ -175,14 +175,14 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, ticks$x_b <- with(data, segmentsGrob( x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"), y0 = unit(xticks$start, "cm"), y1 = unit(xticks$end, "cm"), - gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) + gp = gg_par(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } if (grepl("t", sides) && nrow(xticks) > 0) { ticks$x_t <- with(data, segmentsGrob( x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"), y0 = unit(1, "npc") - unit(xticks$start, "cm"), y1 = unit(1, "npc") - unit(xticks$end, "cm"), - gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) + gp = gg_par(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } } @@ -213,14 +213,14 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, ticks$y_l <- with(data, segmentsGrob( y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"), x0 = unit(yticks$start, "cm"), x1 = unit(yticks$end, "cm"), - gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) + gp = gg_par(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } if (grepl("r", sides) && nrow(yticks) > 0) { ticks$y_r <- with(data, segmentsGrob( y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"), x0 = unit(1, "npc") - unit(yticks$start, "cm"), x1 = unit(1, "npc") - unit(yticks$end, "cm"), - gp = ggpar(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) + gp = gg_par(col = alpha(colour, alpha), lty = linetype, lwd = linewidth) )) } } diff --git a/R/annotation-map.R b/R/annotation-map.R index 2e53b3b9c2..c6888f2add 100644 --- a/R/annotation-map.R +++ b/R/annotation-map.R @@ -95,7 +95,7 @@ GeomAnnotationMap <- ggproto("GeomAnnotationMap", GeomMap, polygonGrob(coords$x, coords$y, default.units = "native", id = grob_id, - gp = ggpar( + gp = gg_par( col = data$colour, fill = alpha(data$fill, data$alpha), lwd = data$linewidth) ) diff --git a/R/coord-radial.R b/R/coord-radial.R index b5ad621beb..b426bc27a8 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -326,7 +326,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, y = c(Inf, -Inf, -Inf, Inf) ) background <- coord_munch(self, background, panel_params, is_closed = TRUE) - bg_gp <- ggpar( + bg_gp <- gg_par( lwd = bg_element$linewidth, col = bg_element$colour, fill = bg_element$fill, lty = bg_element$linetype diff --git a/R/coord-sf.R b/R/coord-sf.R index bb408b4126..f861ae2d28 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -335,7 +335,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, if (inherits(el, "element_blank")) { grobs <- list(element_render(theme, "panel.background")) } else { - line_gp <- ggpar( + line_gp <- gg_par( col = el$colour, lwd = el$linewidth, lty = el$linetype diff --git a/R/geom-curve.R b/R/geom-curve.R index 079bf636df..4c5b60e2c5 100644 --- a/R/geom-curve.R +++ b/R/geom-curve.R @@ -62,7 +62,7 @@ GeomCurve <- ggproto("GeomCurve", GeomSegment, default.units = "native", curvature = curvature, angle = angle, ncp = ncp, square = FALSE, squareShape = 1, inflect = FALSE, open = TRUE, - gp = ggpar( + gp = gg_par( col = alpha(trans$colour, trans$alpha), fill = alpha(arrow.fill, trans$alpha), lwd = trans$linewidth, diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index cdbc137fe7..e163fb272b 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -293,10 +293,10 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y, dotdia = dotdianpc, stackposition = tdata$stackpos, stackdir = stackdir, stackratio = stackratio, default.units = "npc", - gp = ggpar(col = alpha(tdata$colour, tdata$alpha), - fill = fill_alpha(tdata$fill, tdata$alpha), - lwd = tdata$stroke / .pt, lty = tdata$linetype, - lineend = lineend)) + gp = gg_par(col = alpha(tdata$colour, tdata$alpha), + fill = fill_alpha(tdata$fill, tdata$alpha), + lwd = tdata$stroke / .pt, lty = tdata$linetype, + lineend = lineend)) ) }, diff --git a/R/geom-hex.R b/R/geom-hex.R index 19076138dc..8573d6d8ba 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -89,7 +89,7 @@ GeomHex <- ggproto("GeomHex", Geom, ggname("geom_hex", polygonGrob( coords$x, coords$y, - gp = ggpar( + gp = gg_par( col = data$colour, fill = fill_alpha(data$fill, data$alpha), lwd = data$linewidth, diff --git a/R/geom-label.R b/R/geom-label.R index 30ee6aa388..e8a4605b54 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -90,14 +90,14 @@ GeomLabel <- ggproto("GeomLabel", Geom, padding = label.padding, r = label.r, angle = row$angle, - text.gp = ggpar( + text.gp = gg_par( col = row$colour, fontsize = row$size * size.unit, fontfamily = row$family, fontface = row$fontface, lineheight = row$lineheight ), - rect.gp = ggpar( + rect.gp = gg_par( col = if (isTRUE(all.equal(label.size, 0))) NA else row$colour, fill = fill_alpha(row$fill, row$alpha), lwd = label.size @@ -115,7 +115,7 @@ GeomLabel <- ggproto("GeomLabel", Geom, labelGrob <- function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "center", padding = unit(0.25, "lines"), r = unit(0.1, "snpc"), angle = NULL, default.units = "npc", name = NULL, - text.gp = gpar(), rect.gp = ggpar(fill = "white"), vp = NULL) { + text.gp = gpar(), rect.gp = gg_par(fill = "white"), vp = NULL) { if (length(label) != 1) { cli::cli_abort("{.arg label} must be of length 1.") @@ -130,7 +130,7 @@ labelGrob <- function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), vp <- viewport( angle = angle, x = x, y = y, width = unit(0, "cm"), height = unit(0, "cm"), - gp = ggpar(fontsize = text.gp$fontsize) + gp = gg_par(fontsize = text.gp$fontsize) ) x <- unit(rep(0.5, length(x)), "npc") y <- unit(rep(0.5, length(y)), "npc") diff --git a/R/geom-map.R b/R/geom-map.R index 8086db6209..7f4b860378 100644 --- a/R/geom-map.R +++ b/R/geom-map.R @@ -144,7 +144,7 @@ GeomMap <- ggproto("GeomMap", GeomPolygon, data <- data[data_rows, , drop = FALSE] polygonGrob(coords$x, coords$y, default.units = "native", id = grob_id, - gp = ggpar( + gp = gg_par( col = data$colour, fill = fill_alpha(data$fill, data$alpha), lwd = data$linewidth, diff --git a/R/geom-path.R b/R/geom-path.R index 9db4c80ca9..fe4359fb08 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -206,7 +206,7 @@ GeomPath <- ggproto("GeomPath", Geom, segmentsGrob( munched$x[!end], munched$y[!end], munched$x[!start], munched$y[!start], default.units = "native", arrow = arrow, - gp = ggpar( + gp = gg_par( col = alpha(munched$colour, munched$alpha)[!end], fill = alpha(munched$fill, munched$alpha)[!end], lwd = munched$linewidth[!end], @@ -221,7 +221,7 @@ GeomPath <- ggproto("GeomPath", Geom, polylineGrob( munched$x, munched$y, id = id, default.units = "native", arrow = arrow, - gp = ggpar( + gp = gg_par( col = alpha(munched$colour, munched$alpha)[start], fill = alpha(munched$fill, munched$alpha)[start], lwd = munched$linewidth[start], diff --git a/R/geom-point.R b/R/geom-point.R index 990b2778c3..26e6705398 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -149,7 +149,7 @@ GeomPoint <- ggproto("GeomPoint", Geom, pointsGrob( coords$x, coords$y, pch = coords$shape, - gp = ggpar( + gp = gg_par( col = alpha(coords$colour, coords$alpha), fill = fill_alpha(coords$fill, coords$alpha), pointsize = coords$size, diff --git a/R/geom-polygon.R b/R/geom-polygon.R index 3cdce9b53e..8e812e2737 100644 --- a/R/geom-polygon.R +++ b/R/geom-polygon.R @@ -130,7 +130,7 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, polygonGrob( munched$x, munched$y, default.units = "native", id = munched$group, - gp = ggpar( + gp = gg_par( col = first_rows$colour, fill = fill_alpha(first_rows$fill, first_rows$alpha), lwd = first_rows$linewidth, @@ -161,7 +161,7 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, munched$x, munched$y, default.units = "native", id = id, pathId = munched$group, rule = rule, - gp = ggpar( + gp = gg_par( col = first_rows$colour, fill = fill_alpha(first_rows$fill, first_rows$alpha), lwd = first_rows$linewidth, diff --git a/R/geom-rect.R b/R/geom-rect.R index cfd39dab4a..f5eee4d4c5 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -57,7 +57,7 @@ GeomRect <- ggproto("GeomRect", Geom, height = coords$ymax - coords$ymin, default.units = "native", just = c("left", "top"), - gp = ggpar( + gp = gg_par( col = coords$colour, fill = fill_alpha(coords$fill, coords$alpha), lwd = coords$linewidth, diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 4170d87d21..549320deb9 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -215,7 +215,7 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, g_poly <- polygonGrob( munched_poly$x, munched_poly$y, id = munched_poly$id, default.units = "native", - gp = ggpar( + gp = gg_par( fill = fill_alpha(aes$fill, aes$alpha), col = if (is_full_outline) aes$colour else NA, lwd = if (is_full_outline) aes$linewidth else 0, @@ -246,7 +246,7 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, g_lines <- polylineGrob( munched_lines$x, munched_lines$y, id = munched_lines$id, default.units = "native", - gp = ggpar( + gp = gg_par( col = aes$colour, lwd = aes$linewidth, lty = aes$linetype, diff --git a/R/geom-rug.R b/R/geom-rug.R index cda6a01bc4..f41ea44fa8 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -108,7 +108,7 @@ GeomRug <- ggproto("GeomRug", Geom, list(min = -1 * length, max = unit(1, "npc") + length) } - gp <- ggpar( + gp <- gg_par( col = alpha(data$colour, data$alpha), lty = data$linetype, lwd = data$linewidth, diff --git a/R/geom-segment.R b/R/geom-segment.R index 9a4de4dbb3..be3492bb56 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -122,7 +122,7 @@ GeomSegment <- ggproto("GeomSegment", Geom, arrow.fill <- arrow.fill %||% coord$colour return(segmentsGrob(coord$x, coord$y, coord$xend, coord$yend, default.units = "native", - gp = ggpar( + gp = gg_par( col = alpha(coord$colour, coord$alpha), fill = alpha(arrow.fill, coord$alpha), lwd = coord$linewidth, diff --git a/R/geom-text.R b/R/geom-text.R index ea996cb040..d0f33a12ff 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -239,7 +239,7 @@ GeomText <- ggproto("GeomText", Geom, data$x, data$y, default.units = "native", hjust = data$hjust, vjust = data$vjust, rot = data$angle, - gp = ggpar( + gp = gg_par( col = alpha(data$colour, data$alpha), fontsize = data$size * size.unit, fontfamily = data$family, diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index 6d90f13a82..ca63f29b54 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -379,7 +379,7 @@ GuideColourbar <- ggproto( vjust = 0, hjust = 0, width = width, height = height, default.units = "npc", - gp = ggpar(col = NA, fill = decor$colour) + gp = gg_par(col = NA, fill = decor$colour) ) } else if (params$display == "gradient") { check_device("gradients", call = expr(guide_colourbar())) @@ -394,7 +394,7 @@ GuideColourbar <- ggproto( vertical = list(x1 = unit(0.5, "npc"), x2 = unit(0.5, "npc")) ) gradient <- inject(linearGradient(decor$colour, value, !!!position)) - grob <- rectGrob(gp = ggpar(fill = gradient, col = NA)) + grob <- rectGrob(gp = gg_par(fill = gradient, col = NA)) } frame <- element_grob(elements$frame, fill = NA) diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index cd21dce6a4..de10b51a04 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -204,7 +204,7 @@ GuideColoursteps <- ggproto( size <- abs(decor$max - decor$min) just <- as.numeric(decor$min > decor$max) - gp <- ggpar(col = NA, fill = decor$colour) + gp <- gg_par(col = NA, fill = decor$colour) if (params$direction == "vertical") { grob <- rectGrob( x = 0, y = decor$min, diff --git a/R/legend-draw.R b/R/legend-draw.R index 8e7e8b9ae4..9bfd1d9d93 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -33,7 +33,7 @@ draw_key_point <- function(data, params, size) { # NULL means the default stroke size, and NA means no stroke. pointsGrob(0.5, 0.5, pch = data$shape, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% "black", data$alpha), fill = fill_alpha(data$fill %||% "black", data$alpha), pointsize = data$size %||% 1.5, @@ -46,7 +46,7 @@ draw_key_point <- function(data, params, size) { #' @rdname draw_key draw_key_abline <- function(data, params, size) { segmentsGrob(0, 0, 1, 1, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, @@ -58,7 +58,7 @@ draw_key_abline <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_rect <- function(data, params, size) { - rectGrob(gp = ggpar( + rectGrob(gp = gg_par( col = NA, fill = fill_alpha(data$fill %||% data$colour %||% "grey20", data$alpha), lty = data$linetype %||% 1 @@ -76,7 +76,7 @@ draw_key_polygon <- function(data, params, size) { grob <- rectGrob( width = unit(1, "npc") - unit(lwd, "mm"), height = unit(1, "npc") - unit(lwd, "mm"), - gp = ggpar( + gp = gg_par( col = data$colour %||% NA, fill = fill_alpha(data$fill %||% "grey20", data$alpha), lty = data$linetype %||% 1, @@ -101,7 +101,7 @@ draw_key_blank <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_boxplot <- function(data, params, size) { - gp <- ggpar( + gp <- gg_par( col = data$colour %||% "grey20", fill = fill_alpha(data$fill %||% "white", data$alpha), lwd = data$linewidth %||% 0.5, @@ -132,7 +132,7 @@ draw_key_boxplot <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_crossbar <- function(data, params, size) { - gp <- ggpar( + gp <- gg_par( col = data$colour %||% "grey20", fill = fill_alpha(data$fill %||% "white", data$alpha), lwd = data$linewidth %||% 0.5, @@ -164,7 +164,7 @@ draw_key_path <- function(data, params, size) { data$linetype[is.na(data$linetype)] <- 0 } grob <- segmentsGrob(0.1, 0.5, 0.9, 0.5, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), fill = alpha(params$arrow.fill %||% data$colour %||% data$fill %||% "black", data$alpha), @@ -187,7 +187,7 @@ draw_key_path <- function(data, params, size) { #' @rdname draw_key draw_key_vpath <- function(data, params, size) { grob <- segmentsGrob(0.5, 0.1, 0.5, 0.9, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, @@ -209,7 +209,7 @@ draw_key_vpath <- function(data, params, size) { draw_key_dotplot <- function(data, params, size) { pointsGrob(0.5, 0.5, size = unit(.5, "npc"), pch = 21, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% "black", data$alpha), fill = fill_alpha(data$fill %||% "black", data$alpha), lty = data$linetype %||% 1, @@ -250,7 +250,7 @@ draw_key_smooth <- function(data, params, size) { path <- draw_key_path(data, params, size) grob <- grobTree( - if (isTRUE(params$se)) rectGrob(gp = ggpar(col = NA, fill = data$fill)), + if (isTRUE(params$se)) rectGrob(gp = gg_par(col = NA, fill = data$fill)), path ) attr(grob, "width") <- attr(path, "width") @@ -271,7 +271,7 @@ draw_key_text <- function(data, params, size) { angle = data$angle, hjust = hjust, vjust = vjust, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), fontfamily = data$family %||% "", fontface = data$fontface %||% 1, @@ -307,13 +307,13 @@ draw_key_label <- function(data, params, size) { just = c(hjust, vjust), padding = padding, r = params$label.r %||% unit(0.15, "lines"), - text.gp = ggpar( + text.gp = gg_par( col = data$colour %||% "black", fontfamily = data$family %||% "", fontface = data$fontface %||% 1, fontsize = (data$size %||% 3.88) * .pt ), - rect.gp = ggpar( + rect.gp = gg_par( col = if (isTRUE(all.equal(params$label.size, 0))) NA else data$colour, fill = alpha(data$fill %||% "white", data$alpha), lwd = params$label.size @@ -334,7 +334,7 @@ draw_key_label <- function(data, params, size) { #' @rdname draw_key draw_key_vline <- function(data, params, size) { segmentsGrob(0.5, 0, 0.5, 1, - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, @@ -355,7 +355,7 @@ draw_key_timeseries <- function(data, params, size) { grid::linesGrob( x = c(0, 0.4, 0.6, 1), y = c(0.1, 0.6, 0.4, 0.9), - gp = ggpar( + gp = gg_par( col = alpha(data$colour %||% data$fill %||% "black", data$alpha), lwd = data$linewidth %||% 0.5, lty = data$linetype %||% 1, diff --git a/R/margins.R b/R/margins.R index c1ad607a21..0fee3ca0ab 100644 --- a/R/margins.R +++ b/R/margins.R @@ -124,9 +124,9 @@ titleGrob <- function(label, x, y, hjust, vjust, angle = 0, gp = gpar(), rectGrob( x = x, y = y, width = width, height = height, hjust = just$hjust, vjust = just$vjust, - gp = ggpar(fill = "cornsilk", col = NA) + gp = gg_par(fill = "cornsilk", col = NA) ), - pointsGrob(x, y, pch = 20, gp = ggpar(col = "gold")), + pointsGrob(x, y, pch = 20, gp = gg_par(col = "gold")), grob ) } else { @@ -193,7 +193,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, if (isTRUE(debug)) { children <- gList( - rectGrob(gp = ggpar(fill = "lightcyan", col = NA)), + rectGrob(gp = gg_par(fill = "lightcyan", col = NA)), grobs ) } @@ -219,7 +219,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, #cat("E - hjust, vjust:", c(hjust, vjust), "\n") grobTree( result_grob, - pointsGrob(x, y, pch = 20, gp = ggpar(col = "mediumturquoise")) + pointsGrob(x, y, pch = 20, gp = gg_par(col = "mediumturquoise")) ) } else { result_grob @@ -307,7 +307,7 @@ font_descent <- function(family = "", face = "plain", size = 12, cex = 1) { if (is.null(descent)) { descent <- convertHeight(grobDescent(textGrob( label = "gjpqyQ", - gp = ggpar( + gp = gg_par( fontsize = size, cex = cex, fontfamily = family, diff --git a/R/theme-elements.R b/R/theme-elements.R index 378ef3a7d9..6aa27dd5f8 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -216,8 +216,8 @@ element_grob.element_rect <- function(element, x = 0.5, y = 0.5, } # The gp settings can override element_gp - gp <- ggpar(lwd = linewidth, col = colour, fill = fill, lty = linetype) - element_gp <- ggpar(lwd = element$linewidth, col = element$colour, + gp <- gg_par(lwd = linewidth, col = colour, fill = fill, lty = linetype) + element_gp <- gg_par(lwd = element$linewidth, col = element$colour, fill = element$fill, lty = element$linetype) rectGrob(x, y, width, height, gp = modify_list(element_gp, gp), ...) @@ -240,10 +240,10 @@ element_grob.element_text <- function(element, label = "", x = NULL, y = NULL, angle <- angle %||% element$angle %||% 0 # The gp settings can override element_gp - gp <- ggpar(fontsize = size, col = colour, + gp <- gg_par(fontsize = size, col = colour, fontfamily = family, fontface = face, lineheight = lineheight) - element_gp <- ggpar(fontsize = element$size, col = element$colour, + element_gp <- gg_par(fontsize = element$size, col = element$colour, fontfamily = element$family, fontface = element$face, lineheight = element$lineheight) @@ -276,11 +276,11 @@ element_grob.element_line <- function(element, x = 0:1, y = 0:1, } # The gp settings can override element_gp - gp <- ggpar( + gp <- gg_par( col = colour, fill = arrow.fill %||% colour, lwd = linewidth, lty = linetype, lineend = lineend ) - element_gp <- ggpar( + element_gp <- gg_par( col = element$colour, fill = element$arrow.fill %||% element$colour, lwd = element$linewidth, lty = element$linetype, lineend = element$lineend diff --git a/R/utilities-grid.R b/R/utilities-grid.R index 8efdee4d02..c231f0b279 100644 --- a/R/utilities-grid.R +++ b/R/utilities-grid.R @@ -25,7 +25,7 @@ ggname <- function(prefix, grob) { #' @return An object of class 'gpar'. #' @keywords internal #' @export -ggpar <- function(..., stroke = NULL, pointsize = NULL) { +gg_par <- function(..., stroke = NULL, pointsize = NULL) { args <- list2(...) args <- args[lengths(args) > 0] diff --git a/man/ggpar.Rd b/man/gg_par.Rd similarity index 88% rename from man/ggpar.Rd rename to man/gg_par.Rd index 3186597d02..90594cdb3e 100644 --- a/man/ggpar.Rd +++ b/man/gg_par.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/utilities-grid.R -\name{ggpar} -\alias{ggpar} +\name{gg_par} +\alias{gg_par} \title{Interpreter for graphical parameters} \usage{ -ggpar(..., stroke = NULL, pointsize = NULL) +gg_par(..., stroke = NULL, pointsize = NULL) } \arguments{ \item{...}{Named arguments passed on to \code{gpar()}.} From 28aec3a90d2798382c7da384fece6227e12092f8 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 24 May 2024 08:56:43 +0200 Subject: [PATCH 051/264] Add midpoint example (#5896) --- R/scale-gradient.R | 8 ++++++++ man/scale_gradient.Rd | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/R/scale-gradient.R b/R/scale-gradient.R index f0b2771154..788ee3e9f0 100644 --- a/R/scale-gradient.R +++ b/R/scale-gradient.R @@ -54,6 +54,14 @@ #' geom_point(aes(colour = z1)) + #' scale_colour_gradientn(colours = terrain.colors(10)) #' +#' # The gradientn scale can be centered by using a rescaler +#' ggplot(df, aes(x, y)) + +#' geom_point(aes(colour = z1)) + +#' scale_colour_gradientn( +#' colours = c("blue", "dodgerblue", "white", "orange", "red"), +#' rescaler = ~ scales::rescale_mid(.x, mid = 0) +#' ) +#' #' # Equivalent fill scales do the same job for the fill aesthetic #' ggplot(faithfuld, aes(waiting, eruptions)) + #' geom_raster(aes(fill = density)) + diff --git a/man/scale_gradient.Rd b/man/scale_gradient.Rd index 368ef16509..f861378c0c 100644 --- a/man/scale_gradient.Rd +++ b/man/scale_gradient.Rd @@ -260,6 +260,14 @@ ggplot(df, aes(x, y)) + geom_point(aes(colour = z1)) + scale_colour_gradientn(colours = terrain.colors(10)) +# The gradientn scale can be centered by using a rescaler +ggplot(df, aes(x, y)) + + geom_point(aes(colour = z1)) + + scale_colour_gradientn( + colours = c("blue", "dodgerblue", "white", "orange", "red"), + rescaler = ~ scales::rescale_mid(.x, mid = 0) + ) + # Equivalent fill scales do the same job for the fill aesthetic ggplot(faithfuld, aes(waiting, eruptions)) + geom_raster(aes(fill = density)) + From 6c975e86cf2446f08267cf25d3cb6abfbd4610ae Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 4 Jun 2024 12:19:45 +0200 Subject: [PATCH 052/264] Let `Layer$compute_geom_2()` handle legend defaults (#5903) * use ellipses in `use_defaults()`/`compute_geom_2()` * return empty keys as-is * let `compute_geom_2()` handle populating defaults * ensure legends can be rendered for unrelated geoms * add visual tests for geom_sf legend types * simplify sf legend type detection * geom_sf can compute defaults for legend * remove vestigial `default_aesthetics()` --- R/geom-.R | 2 +- R/geom-sf.R | 34 ++++---- R/guide-legend.R | 33 ++++---- R/layer-sf.R | 44 ++++------ R/layer.R | 4 +- .../_snaps/geom-sf/geom-sf-line-legend.svg | 82 +++++++++++++++++++ .../_snaps/geom-sf/geom-sf-point-legend.svg | 78 ++++++++++++++++++ .../_snaps/geom-sf/geom-sf-polygon-legend.svg | 82 +++++++++++++++++++ tests/testthat/test-geom-sf.R | 50 +++++++++-- tests/testthat/test-guides.R | 19 +++++ 10 files changed, 357 insertions(+), 71 deletions(-) create mode 100644 tests/testthat/_snaps/geom-sf/geom-sf-line-legend.svg create mode 100644 tests/testthat/_snaps/geom-sf/geom-sf-point-legend.svg create mode 100644 tests/testthat/_snaps/geom-sf/geom-sf-polygon-legend.svg diff --git a/R/geom-.R b/R/geom-.R index f538cf0bb6..c3da9be244 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -114,7 +114,7 @@ Geom <- ggproto("Geom", setup_data = function(data, params) data, # Combine data with defaults and set aesthetics from parameters - use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL) { + use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL, ...) { default_aes <- default_aes %||% self$default_aes # Inherit size as linewidth if no linewidth aesthetic and param exist diff --git a/R/geom-sf.R b/R/geom-sf.R index c0541cf369..ba559c1243 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -131,15 +131,21 @@ GeomSf <- ggproto("GeomSf", Geom, stroke = 0.5 ), - use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL) { + use_defaults = function(self, data, params = list(), modifiers = aes(), + default_aes = NULL, ...) { data <- ggproto_parent(Geom, self)$use_defaults(data, params, modifiers, default_aes) - # Early exit for e.g. legend data that don't have geometry columns if (!"geometry" %in% names(data)) { return(data) } + # geometry column is a character if we're populating legend keys + type <- if (is.character(data$geometry)) { + data$geometry + } else { + sf_types[sf::st_geometry_type(data$geometry)] + } + # Devise splitting index for geometry types - type <- sf_types[sf::st_geometry_type(data$geometry)] type <- factor(type, c("point", "line", "other", "collection")) index <- split(seq_len(nrow(data)), type) @@ -202,27 +208,15 @@ GeomSf <- ggproto("GeomSf", Geom, }, draw_key = function(data, params, size) { - data <- modify_list(default_aesthetics(params$legend), data) - if (params$legend == "point") { - draw_key_point(data, params, size) - } else if (params$legend == "line") { - draw_key_path(data, params, size) - } else { + switch( + params$legend %||% "other", + point = draw_key_point(data, params, size), + line = draw_key_path(data, params, size), draw_key_polygon(data, params, size) - } + ) } ) -default_aesthetics <- function(type) { - if (type == "point") { - GeomPoint$default_aes - } else if (type == "line") { - GeomLine$default_aes - } else { - modify_list(GeomPolygon$default_aes, list(fill = "grey90", colour = "grey35")) - } -} - sf_grob <- function(x, lineend = "butt", linejoin = "round", linemitre = 10, arrow = NULL, arrow.fill = NULL, na.rm = TRUE) { type <- sf_types[sf::st_geometry_type(x$geometry)] diff --git a/R/guide-legend.R b/R/guide-legend.R index 2ef01fbae9..95dba1cfa0 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -225,31 +225,36 @@ GuideLegend <- ggproto( get_layer_key = function(params, layers, data) { + # Return empty guides as-is + if (nrow(params$key) < 1) { + return(params) + } + decor <- Map(layer = layers, df = data, f = function(layer, df) { + # Subset key to the column with aesthetic matching the layer matched_aes <- matched_aes(layer, params) + key <- params$key[matched_aes] + key$.id <- seq_len(nrow(key)) - if (length(matched_aes) > 0) { - # Filter out aesthetics that can't be applied to the legend - n <- lengths(layer$aes_params, use.names = FALSE) - layer_params <- layer$aes_params[n == 1] + # Filter static aesthetics to those with single values + single_params <- lengths(layer$aes_params) == 1L + single_params <- layer$aes_params[single_params] - aesthetics <- layer$computed_mapping - is_modified <- is_scaled_aes(aesthetics) | is_staged_aes(aesthetics) - modifiers <- aesthetics[is_modified] + # Use layer to populate defaults + key <- layer$compute_geom_2(key, single_params) - data <- layer$geom$use_defaults(params$key[matched_aes], layer_params, modifiers) - data$.draw <- keep_key_data(params$key, df, matched_aes, layer$show.legend) - } else { - reps <- rep(1, nrow(params$key)) - data <- layer$geom$use_defaults(NULL, layer$aes_params)[reps, ] + # Filter non-existing levels + if (length(matched_aes) > 0) { + key$.draw <- keep_key_data(params$key, df, matched_aes, layer$show.legend) } - data <- modify_list(data, params$override.aes) + # Apply overrides + key <- modify_list(key, params$override.aes) list( draw_key = layer$geom$draw_key, - data = data, + data = key, params = c(layer$computed_geom_params, layer$computed_stat_params) ) }) diff --git a/R/layer-sf.R b/R/layer-sf.R index 4a1b8e6512..437ecef3df 100644 --- a/R/layer-sf.R +++ b/R/layer-sf.R @@ -38,10 +38,6 @@ layer_sf <- function(geom = NULL, stat = NULL, LayerSf <- ggproto("LayerSf", Layer, legend_key_type = NULL, - # This field carry state throughout rendering but will always be - # calculated before use - computed_legend_key_type = NULL, - setup_layer = function(self, data, plot) { # process generic layer setup first data <- ggproto_parent(Layer, self)$setup_layer(data, plot) @@ -56,35 +52,28 @@ LayerSf <- ggproto("LayerSf", Layer, self$computed_mapping$geometry <- sym(geometry_col) } } - - # automatically determine the legend type - if (is.null(self$legend_key_type)) { - # first, set default value in case downstream tests fail - self$computed_legend_key_type <- "polygon" - - # now check if the type should not be polygon - if (!is.null(self$computed_mapping$geometry) && quo_is_symbol(self$computed_mapping$geometry)) { - geometry_column <- as_name(self$computed_mapping$geometry) - if (inherits(data[[geometry_column]], "sfc")) { - sf_type <- detect_sf_type(data[[geometry_column]]) - if (sf_type == "point") { - self$computed_legend_key_type <- "point" - } else if (sf_type == "line") { - self$computed_legend_key_type <- "line" - } - } - } - } else { - self$computed_legend_key_type <- self$legend_key_type - } data }, compute_geom_1 = function(self, data) { data <- ggproto_parent(Layer, self)$compute_geom_1(data) + # Determine the legend type + legend_type <- self$legend_key_type + if (is.null(legend_type)) { + legend_type <- switch( + detect_sf_type(data$geometry), + point = "point", line = "line", "other" + ) + } + # Add legend type after computed_geom_params has been calculated - self$computed_geom_params$legend <- self$computed_legend_key_type + self$computed_geom_params$legend <- legend_type data + }, + + compute_geom_2 = function(self, data, params = self$aes_params, ...) { + data$geometry <- data$geometry %||% self$computed_geom_params$legend + ggproto_parent(Layer, self)$compute_geom_2(data, params, ...) } ) @@ -113,6 +102,9 @@ scale_type.sfc <- function(x) "identity" # helper function to determine the geometry type of sf object detect_sf_type <- function(sf) { + if (is.null(sf)) { + return("other") + } geometry_type <- unique0(as.character(sf::st_geometry_type(sf))) if (length(geometry_type) != 1) geometry_type <- "GEOMETRY" sf_types[geometry_type] diff --git a/R/layer.R b/R/layer.R index 88b6a9b026..8b4621bde2 100644 --- a/R/layer.R +++ b/R/layer.R @@ -438,14 +438,14 @@ Layer <- ggproto("Layer", NULL, self$position$compute_layer(data, params, layout) }, - compute_geom_2 = function(self, data) { + compute_geom_2 = function(self, data, params = self$aes_params, ...) { # Combine aesthetics, defaults, & params if (empty(data)) return(data) aesthetics <- self$computed_mapping modifiers <- aesthetics[is_scaled_aes(aesthetics) | is_staged_aes(aesthetics)] - self$geom$use_defaults(data, self$aes_params, modifiers) + self$geom$use_defaults(data, params, modifiers, ...) }, finish_statistics = function(self, data) { diff --git a/tests/testthat/_snaps/geom-sf/geom-sf-line-legend.svg b/tests/testthat/_snaps/geom-sf/geom-sf-line-legend.svg new file mode 100644 index 0000000000..642a061bab --- /dev/null +++ b/tests/testthat/_snaps/geom-sf/geom-sf-line-legend.svg @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3.0 +3.5 +4.0 +4.5 +5.0 +5.5 +6.0 + + + + + + + + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +3.5 +4.0 + +col + + + + +bar +foo +geom_sf line legend + + diff --git a/tests/testthat/_snaps/geom-sf/geom-sf-point-legend.svg b/tests/testthat/_snaps/geom-sf/geom-sf-point-legend.svg new file mode 100644 index 0000000000..e92ba98f8e --- /dev/null +++ b/tests/testthat/_snaps/geom-sf/geom-sf-point-legend.svg @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3.0 +3.2 +3.4 +3.6 +3.8 +4.0 + + + + + + + + + + + + +1.0 +1.2 +1.4 +1.6 +1.8 +2.0 + +col + + + + +bar +foo +geom_sf point legend + + diff --git a/tests/testthat/_snaps/geom-sf/geom-sf-polygon-legend.svg b/tests/testthat/_snaps/geom-sf/geom-sf-polygon-legend.svg new file mode 100644 index 0000000000..6eb5d587a8 --- /dev/null +++ b/tests/testthat/_snaps/geom-sf/geom-sf-polygon-legend.svg @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3.0 +3.5 +4.0 +4.5 +5.0 +5.5 +6.0 + + + + + + + + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +3.5 +4.0 + +col + + + + +bar +foo +geom_sf polygon legend + + diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index d79146ff73..666c9799ea 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -37,7 +37,7 @@ test_that("geom_sf() determines the legend type automatically", { expect_identical(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "line") expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$show.legend, TRUE) - expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "polygon") + expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "other") # test that automatic choice can be overridden manually expect_identical(fun_geom_sf(mp, "point")$plot$layers[[1]]$show.legend, TRUE) @@ -74,13 +74,6 @@ test_that("geom_sf() determines the legend type from mapped geometry column", { ggplot(d_sf) + geom_sf(aes(geometry = g_line, colour = "a")) ) expect_identical(p$plot$layers[[1]]$computed_geom_params$legend, "line") - - # If `geometry` is not a symbol, `LayerSf$setup_layer()` gives up guessing - # the legend type, and falls back to "polygon" - p <- ggplot_build( - ggplot(d_sf) + geom_sf(aes(geometry = identity(g_point), colour = "a")) - ) - expect_identical(p$plot$layers[[1]]$computed_geom_params$legend, "polygon") }) test_that("geom_sf() removes rows containing missing aes", { @@ -196,6 +189,47 @@ test_that("geom_sf draws correctly", { ) }) +test_that("geom_sf data type renders appropriate legends", { + skip_if_not_installed("sf") + p <- ggplot() + geom_sf(aes(colour = col)) + + # Point data + data <- sf::st_as_sf( + data.frame(lon = c(1, 2), lat = c(3, 4), col = c("foo", "bar")), + coords = c("lon", "lat") + ) + expect_doppelganger( + "geom_sf point legend", + p %+% data + ) + + # Line data + data <- sf::st_as_sf( + sf::st_sfc( + sf::st_linestring(x = cbind(1:2, 3:4)), + sf::st_linestring(x = cbind(3:4, 5:6)) + ), + col = c("foo", "bar") + ) + expect_doppelganger( + "geom_sf line legend", + p %+% data + ) + + # Polygon data + data <- sf::st_as_sf( + sf::st_sfc( + sf::st_polygon(list(cbind(c(1, 2, 2, 1), c(3, 3, 4, 3)))), + sf::st_polygon(list(cbind(c(3, 3, 4, 3), c(5, 6, 6, 5)))) + ), + col = c("foo", "bar") + ) + expect_doppelganger( + "geom_sf polygon legend", + p %+% data + ) +}) + test_that("geom_sf uses combinations of geometry correctly", { skip_if_not_installed("sf") diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 8d677dc1bf..a2e5ae918d 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -552,6 +552,25 @@ test_that("bins can be parsed by guides for all scale types", { ) }) +test_that("legends can be forced to display unrelated geoms", { + + df <- data.frame(x = 1:2) + + p <- ggplot(df, aes(x, x)) + + geom_tile(fill = "red", show.legend = TRUE) + + scale_colour_discrete( + limits = c("A", "B") + ) + + b <- ggplot_build(p) + legend <- b$plot$guides$params[[1]] + + expect_equal( + legend$decor[[1]]$data$fill, + c("red", "red") + ) +}) + # Visual tests ------------------------------------------------------------ test_that("axis guides are drawn correctly", { From 8f3a4baafc5db39fdcbcdbb3b5062d08a03845f4 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 4 Jun 2024 12:36:51 +0200 Subject: [PATCH 053/264] Fallback for `dir = 'h'/'v'` (#5907) * internally deprecate `dir = "h"/"v"` * add test * amend message --- NEWS.md | 3 ++- R/facet-wrap.R | 15 +++++++++++++++ tests/testthat/test-facet-.R | 12 ++++++++++++ 3 files changed, 29 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index de3e87cee3..71d565db9a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -44,7 +44,8 @@ * (Internal) Applying defaults in `geom_sf()` has moved from the internal `sf_grob()` to `GeomSf$use_defaults()` (@teunbrand). * `facet_wrap()` has new options for the `dir` argument to more precisely - control panel directions (@teunbrand, #5212) + control panel directions. Internally `dir = "h"` or `dir = "v"` is deprecated + (@teunbrand, #5212). * Prevented `facet_wrap(..., drop = FALSE)` from throwing spurious errors when a character facetting variable contained `NA`s (@teunbrand, #5485). * When facets coerce the faceting variables to factors, the 'ordered' class diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 720e2e8e37..dfe487a3f8 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -586,6 +586,21 @@ wrap_layout <- function(id, dims, dir) { as.table <- TRUE n <- attr(id, "n") + if (nchar(dir) != 2) { + # Should only occur when `as.table` was not incorporated into `dir` + dir <- switch(dir, h = "lt", v = "tl") + deprecate_soft0( + "3.5.2", + what = I("Internal use of `dir = \"h\"` and `dir = \"v\"` in `facet_wrap()`"), + details = I(c( + "The `dir` argument should incorporate the `as.table` argument.", + paste0("Falling back to `dir = \"", dir, "\"`.") + )) + ) + } + + dir <- arg_match0(dir, c("lt", "tl", "lb", "bl", "rt", "tr", "rb", "br")) + ROW <- switch( dir, lt = , rt = (id - 1L) %/% dims[2] + 1L, diff --git a/tests/testthat/test-facet-.R b/tests/testthat/test-facet-.R index 8573ef80d5..9e536798a8 100644 --- a/tests/testthat/test-facet-.R +++ b/tests/testthat/test-facet-.R @@ -325,6 +325,18 @@ test_that("facet_wrap `axes` can draw inner axes.", { expect_equal(sum(vapply(left, inherits, logical(1), "absoluteGrob")), 2) }) +test_that("facet_wrap throws deprecation messages", { + withr::local_options(lifecycle_verbosity = "warning") + + facet <- facet_wrap(vars(year)) + facet$params$dir <- "h" + + lifecycle::expect_deprecated( + ggplot_build(ggplot(mpg, aes(displ, hwy)) + geom_point() + facet), + "Internal use of" + ) +}) + # Variable combinations --------------------------------------------------- test_that("zero-length vars in combine_vars() generates zero combinations", { From 79b6e1c3d13b421ab594cf2d8a69d9e78b36e565 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 4 Jun 2024 12:52:31 +0200 Subject: [PATCH 054/264] Use `group` to dodge in `position_jitterdodge()` (#5922) * dodge by max number of groups per panel/position * fill missing defaults * `position_jitterdodge()` doesn't fail this test-case anymore * add news bullet * Copy faster approach from #5928 --- NEWS.md | 1 + R/position-jitterdodge.R | 19 ++++++------------- tests/testthat/_snaps/position-jitterdodge.md | 8 -------- tests/testthat/test-position-jitterdodge.R | 5 ----- 4 files changed, 7 insertions(+), 26 deletions(-) delete mode 100644 tests/testthat/_snaps/position-jitterdodge.md diff --git a/NEWS.md b/NEWS.md index 71d565db9a..d31e6b4a45 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* `position_jitterdodge()` now dodges by `group` (@teunbrand, #3656) * The `arrow.fill` parameter is now applied to more line-based functions: `geom_path()`, `geom_line()`, `geom_step()` `geom_function()`, line geometries in `geom_sf()` and `element_line()`. diff --git a/R/position-jitterdodge.R b/R/position-jitterdodge.R index fba28a47fa..768f3d8385 100644 --- a/R/position-jitterdodge.R +++ b/R/position-jitterdodge.R @@ -47,21 +47,14 @@ PositionJitterdodge <- ggproto("PositionJitterdodge", Position, flipped_aes <- has_flipped_aes(data) data <- flip_data(data, flipped_aes) width <- self$jitter.width %||% (resolution(data$x, zero = FALSE, TRUE) * 0.4) - # Adjust the x transformation based on the number of 'dodge' variables - possible_dodge <- c("fill", "colour", "linetype", "shape", "size", "alpha") - dodgecols <- intersect(possible_dodge, colnames(data)) - if (length(dodgecols) == 0) { - cli::cli_abort(c( - "{.fn position_jitterdodge} requires at least one aesthetic to dodge by.", - i = "Use one of {.or {.val {possible_dodge}}} aesthetics." - )) - } - ndodge <- lapply(data[dodgecols], levels) # returns NULL for numeric, i.e. non-dodge layers - ndodge <- vec_unique_count(unlist(ndodge)) + + ndodge <- vec_unique(data[c("group", "PANEL", "x")]) + ndodge <- vec_group_id(ndodge[c("PANEL", "x")]) + ndodge <- max(tabulate(ndodge, attr(ndodge, "n"))) list( - dodge.width = self$dodge.width, - jitter.height = self$jitter.height, + dodge.width = self$dodge.width %||% 0.75, + jitter.height = self$jitter.height %||% 0, jitter.width = width / (ndodge + 2), seed = self$seed, flipped_aes = flipped_aes diff --git a/tests/testthat/_snaps/position-jitterdodge.md b/tests/testthat/_snaps/position-jitterdodge.md deleted file mode 100644 index 1a387e880e..0000000000 --- a/tests/testthat/_snaps/position-jitterdodge.md +++ /dev/null @@ -1,8 +0,0 @@ -# position_jitterdodge() fails with meaningful error - - Problem while computing position. - i Error occurred in the 1st layer. - Caused by error in `setup_params()`: - ! `position_jitterdodge()` requires at least one aesthetic to dodge by. - i Use one of "fill", "colour", "linetype", "shape", "size", or "alpha" aesthetics. - diff --git a/tests/testthat/test-position-jitterdodge.R b/tests/testthat/test-position-jitterdodge.R index 49e8378666..fb3274e61a 100644 --- a/tests/testthat/test-position-jitterdodge.R +++ b/tests/testthat/test-position-jitterdodge.R @@ -1,8 +1,3 @@ -test_that("position_jitterdodge() fails with meaningful error", { - p <- ggplot(mtcars) + geom_point(aes(disp, mpg), position = 'jitterdodge') - expect_snapshot_error(ggplot_build(p)) -}) - test_that("position_jitterdodge preserves widths", { ld <- layer_data( ggplot(mtcars, aes(factor(cyl), fill = factor(am))) + From 78660a98076b15e987dbce4f9068e7ae54ffc129 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 4 Jun 2024 13:29:59 +0200 Subject: [PATCH 055/264] Robust `position_dodge(preserve = "single")` (#5928) * count groups per position instead of position per group * add news bullet --- NEWS.md | 2 ++ R/position-dodge.R | 6 +++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index d31e6b4a45..583017fc33 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `position_dodge(preserve = "single")` now handles multi-row geoms better, + such as `geom_violin()` (@teunbrand based on @clauswilke's work, #2801). * `position_jitterdodge()` now dodges by `group` (@teunbrand, #3656) * The `arrow.fill` parameter is now applied to more line-based functions: `geom_path()`, `geom_line()`, `geom_step()` `geom_function()`, line diff --git a/R/position-dodge.R b/R/position-dodge.R index 17bd607324..c2d0dc1eca 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -111,9 +111,9 @@ PositionDodge <- ggproto("PositionDodge", Position, if (identical(self$preserve, "total")) { n <- NULL } else { - panels <- unname(split(data, data$PANEL)) - ns <- vapply(panels, function(panel) max(table(panel$xmin)), double(1)) - n <- max(ns) + n <- vec_unique(data[c("group", "PANEL", "xmin")]) + n <- vec_group_id(n[c("PANEL", "xmin")]) + n <- max(tabulate(n, attr(n, "n"))) } list( From e6352628d3dbafe9acd702f40a267c7cb9ba45d4 Mon Sep 17 00:00:00 2001 From: Paul Newell <153114211+pn317@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:00:45 +0100 Subject: [PATCH 056/264] 'geom_rug()' prints a warning when 'na.rm = FALSE' (#5906) * 'geom_rug()' prints a warning when 'na.rm = FALSE' Fixes issue #5905. When presented with missing values, 'geom_rug()' was not printing a warning message, contrary to the documentation. A warning message is now printed when 'na.rm = FALSE' ad suppressed when 'na.rm = TRUE', as expected. * Impement local changes in 'handle_na()' Make local changes in 'handle_na() instead of global changes to 'GeomRug' * Test for 'geom_rug()' warning about missing values Also added the issue number to NEWS * Handle rugs in orthogonal directions better When plotting rugs in both the 'x' and 'y' direction simultaneously, values of 'x' were being dropped when 'y' was missing, and vice versa. A warning will be given for each axis ('x' or 'y') that contains missing values, if 'na.rm = FALSE'. * Remove dependence on 'dplyr' Use 'vctrs::vec_set_union()' instead of 'dplyr::union()' * Update 'testthat' version to 3.1.5 * Add github handle to NEWS bullet --- DESCRIPTION | 2 +- NEWS.md | 1 + R/geom-rug.R | 41 +++++++++++++++++++++++++++++++++- tests/testthat/test-geom-rug.R | 18 +++++++++++++++ 4 files changed, 60 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f3b9ee7208..dcaf992c7f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -67,7 +67,7 @@ Suggests: rpart, sf (>= 0.7-3), svglite (>= 2.1.2), - testthat (>= 3.1.2), + testthat (>= 3.1.5), vdiffr (>= 1.0.6), xml2 Enhances: diff --git a/NEWS.md b/NEWS.md index 583017fc33..67c07b0b05 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* `geom_rug()` prints a warning when `na.rm = FALSE`, as per documentation (@pn317, #5905) * `position_dodge(preserve = "single")` now handles multi-row geoms better, such as `geom_violin()` (@teunbrand based on @clauswilke's work, #2801). * `position_jitterdodge()` now dodges by `group` (@teunbrand, #3656) diff --git a/R/geom-rug.R b/R/geom-rug.R index f41ea44fa8..a1273e3e08 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -157,5 +157,44 @@ GeomRug <- ggproto("GeomRug", Geom, draw_key = draw_key_path, - rename_size = TRUE + rename_size = TRUE, + + handle_na = function(self, data, params) { + sides_aes <- character() + + if (grepl("b|t", params$sides)) { + sides_aes <- c(sides_aes, "x") + } + + if (grepl("l|r", params$sides)) { + sides_aes <- c(sides_aes, "y") + } + + if (length(sides_aes) > 0) { + df_list <- lapply( + sides_aes, + function(axis) { + remove_missing( + data, params$na.rm, + c(axis, self$required_aes, self$non_missing_aes), + snake_class(self) + ) + } + ) + data <- switch( + paste0(sides_aes, collapse = ""), + "x" = , + "y" = df_list[[1]], + "xy" = vctrs::vec_set_union(df_list[[1]], df_list[[2]]) + ) + } else { + data <- remove_missing( + data, params$na.rm, + c(self$required_aes, self$non_missing_aes), + snake_class(self) + ) + } + + data + } ) diff --git a/tests/testthat/test-geom-rug.R b/tests/testthat/test-geom-rug.R index a613e58f0d..28aa17efcb 100644 --- a/tests/testthat/test-geom-rug.R +++ b/tests/testthat/test-geom-rug.R @@ -40,3 +40,21 @@ test_that("Rug lengths are correct", { }) +test_that( + "geom_rug() warns about missing values when na.rm = FALSE", + { + df2 <- df + n_missing <- 2 + df2$x[sample(nrow(df2), size = n_missing)] <- NA + + p1 <- ggplot(df2, aes(x = x)) + geom_rug() + p2 <- ggplot(df2, aes(x = x)) + geom_rug(na.rm = TRUE) + + expect_warning( + ggplotGrob(p1), + paste0("Removed ", n_missing, " rows containing missing values or values outside the scale range") + ) + + expect_no_warning(ggplotGrob(p2)) + } +) From ba0b18ab7bcc37e86b971e382710ce2cac6ed60e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 18 Jun 2024 11:22:06 +0200 Subject: [PATCH 057/264] margins can be units (#5932) --- R/theme-elements.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/R/theme-elements.R b/R/theme-elements.R index 6aa27dd5f8..bf3c693f3b 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -431,7 +431,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { text = el_def("element_text"), title = el_def("element_text", "text"), spacing = el_def("unit"), - margins = el_def("margin"), + margins = el_def(c("margin", "unit")), axis.line = el_def("element_line", "line"), axis.text = el_def("element_text", "text"), @@ -517,7 +517,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { ), legend.background = el_def("element_rect", "rect"), - legend.margin = el_def(c("margin", "rel"), "margins"), + legend.margin = el_def(c("margin", "unit", "rel"), "margins"), legend.spacing = el_def(c("unit", "rel"), "spacing"), legend.spacing.x = el_def(c("unit", "rel"), "legend.spacing"), legend.spacing.y = el_def(c("unit", "rel"), "legend.spacing"), @@ -566,7 +566,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { legend.box = el_def("character"), legend.box.just = el_def("character"), - legend.box.margin = el_def(c("margin", "rel"), "margins"), + legend.box.margin = el_def(c("margin", "unit", "rel"), "margins"), legend.box.background = el_def("element_rect", "rect"), legend.box.spacing = el_def(c("unit", "rel"), "spacing"), @@ -606,7 +606,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { plot.tag = el_def("element_text", "title"), plot.tag.position = el_def(c("character", "numeric", "integer")), # Need to also accept numbers plot.tag.location = el_def("character"), - plot.margin = el_def(c("margin", "rel"), "margins"), + plot.margin = el_def(c("margin", "unit", "rel"), "margins"), aspect.ratio = el_def(c("numeric", "integer")) ) From af8e236e25be06b2a4f49b8a148c4dd5fbd193b1 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 24 Jun 2024 10:22:12 +0200 Subject: [PATCH 058/264] Refactor facet panel drawing code (#5917) * isolate wrap panel initialisation * isolate wrap axis attachment * isolate wrap strip attachment * isolate grid panel initialisation * isolate grid axis attachment * isolate grid strip attachment * eliminate need for strips to know about axis size * make formals consistent * include all cases of grid strip/axis interactions in tests * use `seam_table()` helper * fix bug * remove duplicate test from #4669 * share init_gtable method * share majority of `draw_panels()` * add news bullet * Update snapshots for cli 3.6.3 * fix note --- NEWS.md | 1 + R/facet-.R | 86 +++++- R/facet-grid-.R | 263 ++++++++-------- R/facet-wrap.R | 368 +++++++++++------------ R/stat-ecdf.R | 2 +- tests/testthat/_snaps/coord-cartesian.md | 2 +- tests/testthat/_snaps/coord-flip.md | 2 +- tests/testthat/_snaps/coord-map.md | 2 +- tests/testthat/_snaps/coord-transform.md | 2 +- tests/testthat/_snaps/coord_sf.md | 2 +- tests/testthat/_snaps/facet-layout.md | 2 +- tests/testthat/test-facet-strips.R | 48 ++- 12 files changed, 415 insertions(+), 365 deletions(-) diff --git a/NEWS.md b/NEWS.md index 67c07b0b05..80d4dd7d02 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). * `geom_rug()` prints a warning when `na.rm = FALSE`, as per documentation (@pn317, #5905) * `position_dodge(preserve = "single")` now handles multi-row geoms better, such as `geom_violin()` (@teunbrand based on @clauswilke's work, #2801). diff --git a/R/facet-.R b/R/facet-.R index abdd373d05..f985d84afc 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -133,8 +133,32 @@ Facet <- ggproto("Facet", NULL, draw_front = function(data, layout, x_scales, y_scales, theme, params) { rep(list(zeroGrob()), vec_unique_count(layout$PANEL)) }, - draw_panels = function(panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) { - cli::cli_abort("Not implemented.") + draw_panels = function(self, panels, layout, x_scales = NULL, y_scales = NULL, + ranges, coord, data = NULL, theme, params) { + + free <- params$free %||% list(x = FALSE, y = FALSE) + space <- params$space_free %||% list(x = FALSE, y = FALSE) + + if ((free$x || free$y) && !coord$is_free()) { + cli::cli_abort( + "{.fn {snake_class(self)}} can't use free scales with \\ + {.fn {snake_class(coord)}}." + ) + } + + aspect_ratio <- theme$aspect.ratio + if (!is.null(aspect_ratio) && (space$x || space$y)) { + cli::cli_abort("Free scales cannot be mixed with a fixed aspect ratio.") + } + + table <- self$init_gtable( + panels, layout, theme, ranges, params, + aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]), + clip = coord$clip + ) + + table <- self$attach_axes(table, layout, ranges, coord, theme, params) + self$attach_strips(table, layout, params, theme) }, draw_labels = function(panels, layout, x_scales, y_scales, ranges, coord, data, theme, labels, params) { panel_dim <- find_panel(panels) @@ -173,6 +197,64 @@ Facet <- ggproto("Facet", NULL, finish_data = function(data, layout, x_scales, y_scales, params) { data }, + init_gtable = function(panels, layout, theme, ranges, params, + aspect_ratio = NULL, clip = "on") { + + # Initialise matrix of panels + dim <- c(max(layout$ROW), max(layout$COL)) + table <- matrix(list(zeroGrob()), dim[1], dim[2]) + table[cbind(layout$ROW, layout$COL)] <- panels + + # Set initial sizes + widths <- unit(rep(1, dim[2]), "null") + heights <- unit(rep(1 * abs(aspect_ratio %||% 1), dim[1]), "null") + + # When space are free, let panel parameter limits determine size of panel + space <- params$space_free %||% list(x = FALSE, y = FALSE) + if (space$x) { + idx <- layout$PANEL[layout$ROW == 1] + widths <- vapply(idx, function(i) diff(ranges[[i]]$x.range), numeric(1)) + widths <- unit(widths, "null") + } + + if (space$y) { + idx <- layout$PANEL[layout$COL == 1] + heights <- vapply(idx, function(i) diff(ranges[[i]]$y.range), numeric(1)) + heights <- unit(heights, "null") + } + + # Build gtable + table <- gtable_matrix( + "layout", table, + widths = widths, heights = heights, + respect = !is.null(aspect_ratio), + clip = clip, z = matrix(1, dim[1], dim[2]) + ) + + # Set panel names + table$layout$name <- paste( + "panel", + rep(seq_len(dim[2]), dim[1]), + rep(seq_len(dim[1]), each = dim[2]), + sep = "-" + ) + + # Add spacing between panels + spacing <- lapply( + c(x = "panel.spacing.x", y = "panel.spacing.y"), + calc_element, theme = theme + ) + + table <- gtable_add_col_space(table, spacing$x) + table <- gtable_add_row_space(table, spacing$y) + table + }, + attach_axes = function(table, layout, ranges, coord, theme, params) { + table + }, + attach_strips = function(table, layout, params, theme) { + table + }, vars = function() { character(0) } diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 0854b5299b..4d4f12f345 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -335,175 +335,101 @@ FacetGrid <- ggproto("FacetGrid", Facet, } data }, - draw_panels = function(panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) { - if ((params$free$x || params$free$y) && !coord$is_free()) { - cli::cli_abort("{.fn {snake_class(coord)}} doesn't support free scales.") - } - # Fill missing parameters for backward compatibility - params$draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE) - params$axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE) + attach_axes = function(table, layout, ranges, coord, theme, params) { + + # Setup parameters + draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE) + axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE) - if (!params$axis_labels$x) { - cols <- seq_len(nrow(layout)) - x_axis_order <- as.integer(layout$PANEL[order(layout$ROW, layout$COL)]) + dim <- c(max(layout$ROW), max(layout$COL)) + if (!axis_labels$x) { + cols <- seq_len(nrow(layout)) + x_order <- as.integer(layout$PANEL[order(layout$ROW, layout$COL)]) } else { - cols <- which(layout$ROW == 1) - x_axis_order <- layout$COL + cols <- which(layout$ROW == 1) + x_order <- layout$COL } - if (!params$axis_labels$y) { - rows <- seq_len(nrow(layout)) - y_axis_order <- as.integer(layout$PANEL[order(layout$ROW, layout$COL)]) + if (!axis_labels$y) { + rows <- seq_len(nrow(layout)) + y_order <- as.integer(layout$PANEL[order(layout$ROW, layout$COL)]) } else { - rows <- which(layout$COL == 1) - y_axis_order <- layout$ROW + rows <- which(layout$COL == 1) + y_order <- layout$ROW } - ranges <- censor_labels(ranges, layout, params$axis_labels) - axes <- render_axes(ranges[cols], ranges[rows], coord, theme, transpose = TRUE) - - col_vars <- unique0(layout[names(params$cols)]) - row_vars <- unique0(layout[names(params$rows)]) - # Adding labels metadata, useful for labellers - attr(col_vars, "type") <- "cols" - attr(col_vars, "facet") <- "grid" - attr(row_vars, "type") <- "rows" - attr(row_vars, "facet") <- "grid" - strips <- render_strips(col_vars, row_vars, params$labeller, theme) + # Render individual axes + ranges <- censor_labels(ranges, layout, axis_labels) + axes <- render_axes(ranges[cols], ranges[rows], coord, theme, transpose = TRUE) + mtx <- function(x, o) matrix(x[o], dim[1], dim[2], byrow = TRUE) - aspect_ratio <- theme$aspect.ratio - if (!is.null(aspect_ratio) && (params$space_free$x || params$space_free$y)) { - cli::cli_abort("Free scales cannot be mixed with a fixed aspect ratio.") - } - aspect_ratio <- aspect_ratio %||% coord$aspect(ranges[[1]]) - if (is.null(aspect_ratio)) { - aspect_ratio <- 1 - respect <- FALSE - } else { - respect <- TRUE - } - ncol <- max(layout$COL) - nrow <- max(layout$ROW) - mtx <- function(x) matrix(x, nrow = nrow, ncol = ncol, byrow = TRUE) - panel_table <- mtx(panels) - - # @kohske - # Now size of each panel is calculated using PANEL$ranges, which is given by - # coord_train called by train_range. - # So here, "scale" need not to be referred. - # - # In general, panel has all information for building facet. - if (params$space_free$x) { - ps <- layout$PANEL[layout$ROW == 1] - widths <- vapply(ps, function(i) diff(ranges[[i]]$x.range), numeric(1)) - panel_widths <- unit(widths, "null") + if (draw_axes$x) { + table <- weave_axes(table, lapply(axes$x, mtx, o = x_order)) } else { - panel_widths <- rep(unit(1, "null"), ncol) + table <- seam_table(table, axes$x$top, side = "top", name = "axis-t", z = 3) + table <- seam_table(table, axes$x$bottom, side = "bottom", name = "axis-b", z = 3) } - if (params$space_free$y) { - ps <- layout$PANEL[layout$COL == 1] - heights <- vapply(ps, function(i) diff(ranges[[i]]$y.range), numeric(1)) - panel_heights <- unit(heights, "null") + + if (draw_axes$y) { + table <- weave_axes(table, lapply(axes$y, mtx, o = y_order)) } else { - panel_heights <- rep(unit(1 * abs(aspect_ratio), "null"), nrow) + table <- seam_table(table, axes$y$left, side = "left", name = "axis-l", z = 3) + table <- seam_table(table, axes$y$right, side = "right", name = "axis-r", z = 3) } - panel_table <- gtable_matrix("layout", panel_table, - panel_widths, panel_heights, respect = respect, clip = coord$clip, z = mtx(1)) - panel_table$layout$name <- paste0('panel-', rep(seq_len(nrow), ncol), '-', rep(seq_len(ncol), each = nrow)) + table + }, - spacing_x <- calc_element("panel.spacing.x", theme) - spacing_y <- calc_element("panel.spacing.y", theme) - panel_table <- gtable_add_col_space(panel_table, spacing_x) - panel_table <- gtable_add_row_space(panel_table, spacing_y) + attach_strips = function(table, layout, params, theme) { - # Add axes - if (params$draw_axes$x) { - axes$x <- lapply(axes$x, function(x) mtx(x[x_axis_order])) - panel_table <- weave_axes(panel_table, axes$x)$panels - } else { - panel_table <- gtable_add_rows(panel_table, max_height(axes$x$top), 0) - panel_table <- gtable_add_rows(panel_table, max_height(axes$x$bottom), -1) - panel_pos_col <- panel_cols(panel_table) - panel_table <- gtable_add_grob(panel_table, axes$x$top, 1, panel_pos_col$l, clip = "off", name = paste0("axis-t-", seq_along(axes$x$top)), z = 3) - panel_table <- gtable_add_grob(panel_table, axes$x$bottom, -1, panel_pos_col$l, clip = "off", name = paste0("axis-b-", seq_along(axes$x$bottom)), z = 3) - } + col_vars <- unique0(layout[names(params$cols)]) + row_vars <- unique0(layout[names(params$rows)]) + attr(col_vars, "type") <- "cols" + attr(row_vars, "type") <- "rows" + attr(col_vars, "facet") <- "grid" + attr(row_vars, "facet") <- "grid" - if (params$draw_axes$y) { - axes$y <- lapply(axes$y, function(y) mtx(y[y_axis_order])) - panel_table <- weave_axes(panel_table, axes$y)$panels - } else { - panel_table <- gtable_add_cols(panel_table, max_width(axes$y$left), 0) - panel_table <- gtable_add_cols(panel_table, max_width(axes$y$right), -1) - panel_pos_rows <- panel_rows(panel_table) - panel_table <- gtable_add_grob(panel_table, axes$y$left, panel_pos_rows$t, 1, clip = "off", name = paste0("axis-l-", seq_along(axes$y$left)), z = 3) - panel_table <- gtable_add_grob(panel_table, axes$y$right, panel_pos_rows$t, -1, clip = "off", name = paste0("axis-r-", seq_along(axes$y$right)), z= 3) - } + strips <- render_strips(col_vars, row_vars, params$labeller, theme) + padding <- convertUnit(calc_element("strip.switch.pad.grid", theme), "cm") - # Add strips switch_x <- !is.null(params$switch) && params$switch %in% c("both", "x") - switch_y <- !is.null(params$switch) && params$switch %in% c("both", "y") - inside_x <- (theme$strip.placement.x %||% theme$strip.placement %||% "inside") == "inside" - inside_y <- (theme$strip.placement.y %||% theme$strip.placement %||% "inside") == "inside" - strip_padding <- convertUnit(calc_element("strip.switch.pad.grid", theme), "cm") - panel_pos_col <- panel_cols(panel_table) + inside_x <- (calc_element("strip.placement.x", theme) %||% "inside") == "inside" + shift_x <- if (inside_x) 1 else 2 + if (switch_x) { - if (!is.null(strips$x$bottom)) { - if (inside_x) { - panel_table <- gtable_add_rows(panel_table, max_height(strips$x$bottom), -2) - panel_table <- gtable_add_grob(panel_table, strips$x$bottom, -2, panel_pos_col$l, clip = "on", name = paste0("strip-b-", seq_along(strips$x$bottom)), z = 2) - } else { - if (!all(vapply(axes$x$bottom, is.zero, logical(1)))) { - panel_table <- gtable_add_rows(panel_table, strip_padding, -1) - } - panel_table <- gtable_add_rows(panel_table, max_height(strips$x$bottom), -1) - panel_table <- gtable_add_grob(panel_table, strips$x$bottom, -1, panel_pos_col$l, clip = "on", name = paste0("strip-b-", seq_along(strips$x$bottom)), z = 2) - } - } + space <- if (!inside_x & table_has_grob(table, "axis-b")) padding + table <- seam_table( + table, strips$x$bottom, side = "bottom", name = "strip-b", + shift = shift_x, z = 2, clip = "on", spacing = space + ) } else { - if (!is.null(strips$x$top)) { - if (inside_x) { - panel_table <- gtable_add_rows(panel_table, max_height(strips$x$top), 1) - panel_table <- gtable_add_grob(panel_table, strips$x$top, 2, panel_pos_col$l, clip = "on", name = paste0("strip-t-", seq_along(strips$x$top)), z = 2) - } else { - if (!all(vapply(axes$x$top, is.zero, logical(1)))) { - panel_table <- gtable_add_rows(panel_table, strip_padding, 0) - } - panel_table <- gtable_add_rows(panel_table, max_height(strips$x$top), 0) - panel_table <- gtable_add_grob(panel_table, strips$x$top, 1, panel_pos_col$l, clip = "on", name = paste0("strip-t-", seq_along(strips$x$top)), z = 2) - } - } + space <- if (!inside_x & table_has_grob(table, "axis-t")) padding + table <- seam_table( + table, strips$x$top, side = "top", name = "strip-t", + shift = shift_x, z = 2, clip = "on", spacing = space + ) } - panel_pos_rows <- panel_rows(panel_table) + + switch_y <- !is.null(params$switch) && params$switch %in% c("both", "y") + inside_y <- (calc_element("strip.placement.y", theme) %||% "inside") == "inside" + shift_y <- if (inside_y) 1 else 2 + if (switch_y) { - if (!is.null(strips$y$left)) { - if (inside_y) { - panel_table <- gtable_add_cols(panel_table, max_width(strips$y$left), 1) - panel_table <- gtable_add_grob(panel_table, strips$y$left, panel_pos_rows$t, 2, clip = "on", name = paste0("strip-l-", seq_along(strips$y$left)), z = 2) - } else { - if (!all(vapply(axes$y$left, is.zero, logical(1)))) { - panel_table <- gtable_add_cols(panel_table, strip_padding, 0) - } - panel_table <- gtable_add_cols(panel_table, max_width(strips$y$left), 0) - panel_table <- gtable_add_grob(panel_table, strips$y$left, panel_pos_rows$t, 1, clip = "on", name = paste0("strip-l-", seq_along(strips$y$left)), z = 2) - } - } + space <- if (!inside_y & table_has_grob(table, "axis-l")) padding + table <- seam_table( + table, strips$y$left, side = "left", name = "strip-l", + shift = shift_y, z = 2, clip = "on", spacing = space + ) } else { - if (!is.null(strips$y$right)) { - if (inside_y) { - panel_table <- gtable_add_cols(panel_table, max_width(strips$y$right), -2) - panel_table <- gtable_add_grob(panel_table, strips$y$right, panel_pos_rows$t, -2, clip = "on", name = paste0("strip-r-", seq_along(strips$y$right)), z = 2) - } else { - if (!all(vapply(axes$y$right, is.zero, logical(1)))) { - panel_table <- gtable_add_cols(panel_table, strip_padding, -1) - } - panel_table <- gtable_add_cols(panel_table, max_width(strips$y$right), -1) - panel_table <- gtable_add_grob(panel_table, strips$y$right, panel_pos_rows$t, -1, clip = "on", name = paste0("strip-r-", seq_along(strips$y$right)), z = 2) - } - } + space <- if (!inside_y & table_has_grob(table, "axis-r")) padding + table <- seam_table( + table, strips$y$right, side = "right", name = "strip-r", + shift = shift_y, z = 2, clip = "on", spacing = space + ) } - panel_table + table }, + vars = function(self) { names(c(self$params$rows, self$params$cols)) } @@ -519,3 +445,52 @@ ulevels <- function(x, na.last = TRUE) { sort(unique0(x), na.last = na.last) } } + +table_has_grob <- function(table, pattern) { + grobs <- table$grobs[grep(pattern, table$layout$name)] + !all(vapply(grobs, is.zero, logical(1))) +} + +seam_table <- function(table, grobs = NULL, side, shift = 1, name, z = 1, + clip = "off", spacing = NULL) { + if (is.null(grobs)) { + return(table) + } + + panel_col <- panel_cols(table) + panel_row <- panel_rows(table) + + row <- switch( + side, + bottom = max(panel_row$b) + shift - 1L, + top = min(panel_row$t) - shift, + panel_row$t + ) + + col <- switch( + side, + right = max(panel_col$r) + shift - 1L, + left = min(panel_col$l) - shift, + panel_col$l + ) + + if (!is.null(spacing)) { + table <- switch( + side, + bottom = , top = gtable_add_rows(table, spacing, row), + left = , right = gtable_add_cols(table, spacing, col) + ) + row <- row + as.numeric(side == "bottom") + col <- col + as.numeric(side == "right") + } + + table <- switch( + side, + bottom = , top = gtable_add_rows(table, max_height(grobs), row), + left = , right = gtable_add_cols(table, max_width(grobs), col) + ) + name <- paste(name, seq_along(grobs), sep = "-") + row <- row + as.numeric(side %in% c("top", "bottom")) + col <- col + as.numeric(side %in% c("left", "right")) + gtable_add_grob(table, grobs, t = row, l = col, name = name, z = z, clip = clip) +} diff --git a/R/facet-wrap.R b/R/facet-wrap.R index dfe487a3f8..4f07736f7d 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -257,227 +257,203 @@ FacetWrap <- ggproto("FacetWrap", Facet, data$PANEL <- layout$PANEL[match(keys$x, keys$y)] data }, - draw_panels = function(self, panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) { - if ((params$free$x || params$free$y) && !coord$is_free()) { - cli::cli_abort("{.fn {snake_class(self)}} can't use free scales with {.fn {snake_class(coord)}}.") + + attach_axes = function(table, layout, ranges, coord, theme, params) { + + # Setup parameters + draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE) + axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE) + free <- params$free %||% list(x = FALSE, y = FALSE) + + # Render individual axes + ranges <- censor_labels(ranges, layout, axis_labels) + original <- render_axes(ranges, ranges, coord, theme, transpose = TRUE) + + # Sort axes + x_order <- if (axis_labels$x) layout$SCALE_X else seq_len(nrow(layout)) + y_order <- if (axis_labels$y) layout$SCALE_Y else seq_len(nrow(layout)) + original$x <- lapply(original$x, `[`, i = x_order) + original$y <- lapply(original$y, `[`, i = y_order) + + # Setup matrices for axes + dim <- c(max(layout$ROW), max(layout$COL)) + index <- convertInd(layout$ROW, layout$COL, dim[1]) + empty <- matrix(list(zeroGrob()), dim[1], dim[2]) + top <- bottom <- left <- right <- empty + + # Fill axis matrices + top[index] <- original$x$top + bottom[index] <- original$x$bottom + left[index] <- original$y$left + right[index] <- original$y$right + + # Suppress interior axes + if (!(free$x || draw_axes$x)) { + top[-1, ] <- list(zeroGrob()) + bottom[-dim[1], ] <- list(zeroGrob()) + } + if (!(free$y || draw_axes$y)) { + left[, -1] <- list(zeroGrob()) + right[, -dim[2]] <- list(zeroGrob()) } - if (inherits(coord, "CoordFlip")) { - if (params$free$x) { - layout$SCALE_X <- seq_len(nrow(layout)) - } else { - layout$SCALE_X <- 1L + # Check for empty panels and exit early if there are none + empty <- matrix(TRUE, dim[1], dim[2]) + empty[index] <- FALSE + if (!any(empty)) { + axes <- list(top = top, bottom = bottom, left = left, right = right) + return(weave_axes(table, axes, empty)) + } + + # Match empty table to layout + matched <- vec_match( + data_frame0(ROW = as.vector(row(empty)), COL = as.vector(col(empty))), + layout[, c("ROW", "COL")] + ) + + # Figure out where axes should be added back + empty_bottom <- which( apply(empty, 2, function(x) c(diff(x) == 1, FALSE))) + empty_top <- which( apply(empty, 2, function(x) c(FALSE, diff(x) == -1))) + empty_right <- which(t(apply(empty, 1, function(x) c(diff(x) == 1, FALSE)))) + empty_left <- which(t(apply(empty, 1, function(x) c(FALSE, diff(x) == -1)))) + + # Keep track of potential clashes between strips and axes + inside <- (theme$strip.placement %||% "inside") == "inside" + strip <- params$strip.position %||% "top" + clash <- c(top = FALSE, bottom = FALSE, left = FALSE, right = FALSE) + + # Go through every position and place back axes + if (length(empty_bottom) > 0) { + x_axes <- original$x$bottom[matched[empty_bottom]] + clash["bottom"] <- strip == "bottom" && !inside && !free$x && + !all(vapply(x_axes, is.zero, logical(1))) + if (!clash["bottom"]) { + bottom[empty_bottom] <- x_axes } - if (params$free$y) { - layout$SCALE_Y <- seq_len(nrow(layout)) - } else { - layout$SCALE_Y <- 1L + } + + if (length(empty_top) > 0) { + x_axes <- original$x$top[matched[empty_top]] + clash["top"] <- strip == "top" && !inside && !free$x && + !all(vapply(x_axes, is.zero, logical(1))) + if (!clash["top"]) { + top[empty_top] <- x_axes } } - ncol <- max(layout$COL) - nrow <- max(layout$ROW) - n <- nrow(layout) - panel_order <- order(layout$ROW, layout$COL) - layout <- layout[panel_order, ] - panels <- panels[panel_order] - panel_pos <- convertInd(layout$ROW, layout$COL, nrow) + if (length(empty_right) > 0) { + y_axes <- original$y$right[matched[empty_right]] + clash["right"] <- strip == "right" && !inside && !free$y && + !all(vapply(y_axes, is.zero, logical(1))) + if (!clash["right"]) { + right[empty_right] <- y_axes + } + } - # Fill missing parameters for backward compatibility - params$draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE) - params$axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE) + if (length(empty_left) > 0) { + y_axes <- original$y$left[matched[empty_left]] + clash["left"] <- strip == "left" && !inside && !free$y && + !all(vapply(y_axes, is.zero, logical(1))) + if (!clash["left"]) { + left[empty_left] <- y_axes + } + } - x_axis_order <- if (params$axis_labels$x) layout$SCALE_X else seq(n) - y_axis_order <- if (params$axis_labels$y) layout$SCALE_Y else seq(n) + if (any(clash)) { + cli::cli_warn( + "Suppressing axis rendering when \\ + {.code strip.position =\"{strip}\"} and \\ + {.code strip.placement = \"outside\".}" + ) + } + + axes <- list(top = top, bottom = bottom, left = left, right = right) + weave_axes(table, axes, empty) + }, - ranges <- censor_labels(ranges, layout, params$axis_labels) - axes <- render_axes(ranges, ranges, coord, theme, transpose = TRUE) + attach_strips = function(table, layout, params, theme) { + # Format labels if (length(params$facets) == 0) { - # Add a dummy label - labels_df <- data_frame0("(all)" = "(all)", .size = 1) + labels <- data_frame0("(all)" = "(all)", .size = 1) } else { - labels_df <- layout[names(params$facets)] + labels <- layout[names(params$facets)] } - attr(labels_df, "facet") <- "wrap" - strips <- render_strips( - structure(labels_df, type = "rows"), - structure(labels_df, type = "cols"), - params$labeller, theme) + attr(labels, "facet") <- "wrap" - # If user hasn't set aspect ratio, ask the coordinate system if - # it wants to specify one - aspect_ratio <- theme$aspect.ratio %||% coord$aspect(ranges[[1]]) + # Render individual strips + strips <- render_strips( + x = structure(labels, type = "rows"), + y = structure(labels, type = "cols"), + params$labeller, theme + ) - if (is.null(aspect_ratio)) { - aspect_ratio <- 1 - respect <- FALSE + # Set position invariant parameters + padding <- convertUnit(calc_element("strip.switch.pad.wrap", theme), "cm") + position <- params$strip.position %||% "top" + pos <- substr(position, 1, 1) + prefix <- paste0("strip-", pos) + + # Setup weaving table + dim <- c(max(layout$ROW), max(layout$COL)) + index <- convertInd(layout$ROW, layout$COL, dim[1]) + mat <- matrix(list(zeroGrob()), dim[1], dim[2]) + mat[index] <- unlist(unname(strips), recursive = FALSE)[[position]] + + # Setup orientation dependent parameters + if (position %in% c("top", "bottom")) { + inside <- "strip.placement.x" + size <- apply(mat, 1, max_height, value_only = TRUE) + weave <- weave_tables_row } else { - respect <- TRUE + inside <- "strip.placement.y" + size <- apply(mat, 2, max_width, value_only = TRUE) + weave <- weave_tables_col } - empty_table <- matrix(list(zeroGrob()), nrow = nrow, ncol = ncol) - panel_table <- empty_table - panel_table[panel_pos] <- panels - empties <- apply(panel_table, c(1,2), function(x) is.zero(x[[1]])) - panel_table <- gtable_matrix("layout", panel_table, - widths = unit(rep(1, ncol), "null"), - heights = unit(rep(abs(aspect_ratio), nrow), "null"), respect = respect, clip = coord$clip, z = matrix(1, ncol = ncol, nrow = nrow)) - panel_table$layout$name <- paste0('panel-', rep(seq_len(ncol), nrow), '-', rep(seq_len(nrow), each = ncol)) - - - panel_table <- gtable_add_col_space(panel_table, calc_element("panel.spacing.x", theme)) - panel_table <- gtable_add_row_space(panel_table, calc_element("panel.spacing.y", theme)) - - # Add axes - axis_mat_x_top <- empty_table - axis_mat_x_top[panel_pos] <- axes$x$top[x_axis_order] - axis_mat_x_bottom <- empty_table - axis_mat_x_bottom[panel_pos] <- axes$x$bottom[x_axis_order] - axis_mat_y_left <- empty_table - axis_mat_y_left[panel_pos] <- axes$y$left[y_axis_order] - axis_mat_y_right <- empty_table - axis_mat_y_right[panel_pos] <- axes$y$right[y_axis_order] - if (!(params$free$x || params$draw_axes$x)) { - axis_mat_x_top[-1,]<- list(zeroGrob()) - axis_mat_x_bottom[-nrow,]<- list(zeroGrob()) - } - if (!(params$free$y || params$draw_axes$y)) { - axis_mat_y_left[, -1] <- list(zeroGrob()) - axis_mat_y_right[, -ncol] <- list(zeroGrob()) + inside <- (calc_element(inside, theme) %||% "inside") == "inside" + shift <- switch(position, top = , left = c(-1, -2), c(0, 1)) + shift <- if (inside) shift[1] else shift[2] + size <- unit(size, "cm") + + table <- weave(table, mat, shift, size, name = prefix, z = 2, clip = "on") + + if (!inside) { + axes <- grepl(paste0("axis-", pos), table$layout$name) + has_axes <- !vapply(table$grobs[axes], is.zero, logical(1)) + has_axes <- split(has_axes, table$layout[[pos]][axes]) + has_axes <- vapply(has_axes, sum, numeric(1)) > 0 + padding <- rep(padding, length(has_axes)) + padding[!has_axes] <- unit(0, "cm") + table <- weave(table, , shift, padding) } + table + }, - # Add back missing axes - if (any(empties)) { - row_ind <- row(empties) - col_ind <- col(empties) - inside <- (theme$strip.placement %||% "inside") == "inside" - empty_bottom <- apply(empties, 2, function(x) c(diff(x) == 1, FALSE)) - if (any(empty_bottom)) { - pos <- which(empty_bottom) - panel_loc <- data_frame0( - ROW = row_ind[pos], - COL = col_ind[pos], - .size = length(pos) - ) - panels <- vec_match(panel_loc, layout[, c("ROW", "COL")]) - x_axes <- axes$x$bottom[x_axis_order[panels]] - if (params$strip.position == "bottom" && - !inside && - any(!vapply(x_axes, is.zero, logical(1))) && - !params$free$x) { - cli::cli_warn("Suppressing axis rendering when {.code strip.position = \"bottom\"} and {.code strip.placement == \"outside\"}") - } else { - axis_mat_x_bottom[pos] <- x_axes - } - } - empty_top <- apply(empties, 2, function(x) c(FALSE, diff(x) == -1)) - if (any(empty_top)) { - pos <- which(empty_top) - panel_loc <- data_frame0( - ROW = row_ind[pos], - COL = col_ind[pos], - .size = length(pos) - ) - panels <- vec_match(panel_loc, layout[, c("ROW", "COL")]) - x_axes <- axes$x$top[x_axis_order[panels]] - if (params$strip.position == "top" && - !inside && - any(!vapply(x_axes, is.zero, logical(1))) && - !params$free$x) { - cli::cli_warn("Suppressing axis rendering when {.code strip.position = \"top\"} and {.code strip.placement == \"outside\"}") - } else { - axis_mat_x_top[pos] <- x_axes - } - } - empty_right <- t(apply(empties, 1, function(x) c(diff(x) == 1, FALSE))) - if (any(empty_right)) { - pos <- which(empty_right) - panel_loc <- data_frame0( - ROW = row_ind[pos], - COL = col_ind[pos], - .size = length(pos) - ) - panels <- vec_match(panel_loc, layout[, c("ROW", "COL")]) - y_axes <- axes$y$right[y_axis_order[panels]] - if (params$strip.position == "right" && - !inside && - any(!vapply(y_axes, is.zero, logical(1))) && - !params$free$y) { - cli::cli_warn("Suppressing axis rendering when {.code strip.position = \"right\"} and {.code strip.placement == \"outside\"}") - } else { - axis_mat_y_right[pos] <- y_axes - } - } - empty_left <- t(apply(empties, 1, function(x) c(FALSE, diff(x) == -1))) - if (any(empty_left)) { - pos <- which(empty_left) - panel_loc <- data_frame0( - ROW = row_ind[pos], - COL = col_ind[pos], - .size = length(pos) - ) - panels <- vec_match(panel_loc, layout[, c("ROW", "COL")]) - y_axes <- axes$y$left[y_axis_order[panels]] - if (params$strip.position == "left" && - !inside && - any(!vapply(y_axes, is.zero, logical(1))) && - !params$free$y) { - cli::cli_warn("Suppressing axis rendering when {.code strip.position = \"left\"} and {.code strip.placement == \"outside\"}") - } else { - axis_mat_y_left[pos] <- y_axes - } - } - } - panel_table <- weave_axes( - panel_table, - axes = list( - top = axis_mat_x_top, bottom = axis_mat_x_bottom, - left = axis_mat_y_left, right = axis_mat_y_right - ), - empty = empties - ) - axis_size <- panel_table$sizes - panel_table <- panel_table$panels - - strip_padding <- convertUnit(calc_element("strip.switch.pad.wrap", theme), "cm") - strip_name <- paste0("strip-", substr(params$strip.position, 1, 1)) - strip_mat <- empty_table - strip_mat[panel_pos] <- unlist(unname(strips), recursive = FALSE)[[params$strip.position]] - if (params$strip.position %in% c("top", "bottom")) { - inside_x <- (theme$strip.placement.x %||% theme$strip.placement %||% "inside") == "inside" - if (params$strip.position == "top") { - placement <- if (inside_x) -1 else -2 - strip_pad <- axis_size$top + draw_panels = function(self, panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) { + if (inherits(coord, "CoordFlip")) { + if (params$free$x) { + layout$SCALE_X <- seq_len(nrow(layout)) } else { - placement <- if (inside_x) 0 else 1 - strip_pad <- axis_size$bottom - } - strip_height <- unit(apply(strip_mat, 1, max_height, value_only = TRUE), "cm") - panel_table <- weave_tables_row(panel_table, strip_mat, placement, strip_height, strip_name, 2, coord$clip) - if (!inside_x) { - strip_pad[as.numeric(strip_pad) != 0] <- strip_padding - panel_table <- weave_tables_row(panel_table, row_shift = placement, row_height = strip_pad) + layout$SCALE_X <- 1L } - } else { - inside_y <- (theme$strip.placement.y %||% theme$strip.placement %||% "inside") == "inside" - if (params$strip.position == "left") { - placement <- if (inside_y) -1 else -2 - strip_pad <- axis_size$left + if (params$free$y) { + layout$SCALE_Y <- seq_len(nrow(layout)) } else { - placement <- if (inside_y) 0 else 1 - strip_pad <- axis_size$right - } - strip_pad[as.numeric(strip_pad) != 0] <- strip_padding - strip_width <- unit(apply(strip_mat, 2, max_width, value_only = TRUE), "cm") - panel_table <- weave_tables_col(panel_table, strip_mat, placement, strip_width, strip_name, 2, coord$clip) - if (!inside_y) { - strip_pad[as.numeric(strip_pad) != 0] <- strip_padding - panel_table <- weave_tables_col(panel_table, col_shift = placement, col_width = strip_pad) + layout$SCALE_Y <- 1L } } - panel_table + + panel_order <- order(layout$ROW, layout$COL) + layout <- layout[panel_order, ] + panels <- panels[panel_order] + + ggproto_parent(Facet, self)$draw_panels( + panels = panels, layout = layout, + ranges = ranges, coord = coord, + theme = theme, params = params + ) }, vars = function(self) { names(self$params$facets) @@ -559,7 +535,7 @@ weave_axes <- function(panels, axes, empty = NULL, z = 3L) { for (i in seq_along(axes)) { panels <- weave[[i]](panels, axes[[i]], shift[i], sizes[[i]], names[i], z = z) } - list(panels = panels, sizes = sizes) + panels } # Measures the size of axes while ignoring those bordering empty panels diff --git a/R/stat-ecdf.R b/R/stat-ecdf.R index fc55dc2e04..85287b9130 100644 --- a/R/stat-ecdf.R +++ b/R/stat-ecdf.R @@ -183,7 +183,7 @@ wecdf <- function(x, weights = NULL) { ) # Like `ecdf(x)`, we return an approx function - approxfun( + stats::approxfun( vals, cumsum(agg_weights) / total, method = "constant", diff --git a/tests/testthat/_snaps/coord-cartesian.md b/tests/testthat/_snaps/coord-cartesian.md index 7da67ba9c9..e7ed10569a 100644 --- a/tests/testthat/_snaps/coord-cartesian.md +++ b/tests/testthat/_snaps/coord-cartesian.md @@ -1,6 +1,6 @@ # cartesian coords throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector of length 2, not a object. --- diff --git a/tests/testthat/_snaps/coord-flip.md b/tests/testthat/_snaps/coord-flip.md index b7717a7381..99806717ba 100644 --- a/tests/testthat/_snaps/coord-flip.md +++ b/tests/testthat/_snaps/coord-flip.md @@ -1,6 +1,6 @@ # flip coords throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector of length 2, not a object. --- diff --git a/tests/testthat/_snaps/coord-map.md b/tests/testthat/_snaps/coord-map.md index 372d54df39..011a6dd41f 100644 --- a/tests/testthat/_snaps/coord-map.md +++ b/tests/testthat/_snaps/coord-map.md @@ -1,6 +1,6 @@ # coord map throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector of length 2, not a object. --- diff --git a/tests/testthat/_snaps/coord-transform.md b/tests/testthat/_snaps/coord-transform.md index 14be4bd125..def35a0f27 100644 --- a/tests/testthat/_snaps/coord-transform.md +++ b/tests/testthat/_snaps/coord-transform.md @@ -1,6 +1,6 @@ # coord_trans() throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector of length 2, not a object. --- diff --git a/tests/testthat/_snaps/coord_sf.md b/tests/testthat/_snaps/coord_sf.md index 486763d781..bb43424d33 100644 --- a/tests/testthat/_snaps/coord_sf.md +++ b/tests/testthat/_snaps/coord_sf.md @@ -21,7 +21,7 @@ # coord_sf() throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector of length 2, not a object. --- diff --git a/tests/testthat/_snaps/facet-layout.md b/tests/testthat/_snaps/facet-layout.md index 03cdcbe8b3..142bde22fe 100644 --- a/tests/testthat/_snaps/facet-layout.md +++ b/tests/testthat/_snaps/facet-layout.md @@ -33,7 +33,7 @@ # facet_grid throws errors at bad layout specs - `coord_fixed()` doesn't support free scales. + `facet_grid()` can't use free scales with `coord_fixed()`. --- diff --git a/tests/testthat/test-facet-strips.R b/tests/testthat/test-facet-strips.R index 1ee8792e99..ece67935a4 100644 --- a/tests/testthat/test-facet-strips.R +++ b/tests/testthat/test-facet-strips.R @@ -135,38 +135,54 @@ test_that("strips can be removed", { expect_true(all(sapply(strip_grobs, inherits, 'zeroGrob'))) }) -test_that("strips can be removed", { - dat <- data_frame(a = rep(LETTERS[1:10], 10), x = rnorm(100), y = rnorm(100)) - g <- ggplot(dat, aes(x = x, y = y)) + - geom_point() + - facet_wrap(~a) + - theme(strip.background = element_blank(), strip.text = element_blank()) - g_grobs <- ggplotGrob(g) - strip_grobs <- g_grobs$grobs[grepl('strip-', g_grobs$layout$name)] - expect_true(all(sapply(strip_grobs, inherits, 'zeroGrob'))) -}) - test_that("padding is only added if axis is present", { p <- ggplot(data = mpg, aes(x = displ, y = hwy)) + - facet_grid(. ~ drv) + + facet_grid(year ~ drv) + theme( strip.placement = "outside", strip.switch.pad.grid = unit(10, "mm") ) pg <- ggplotGrob(p) - expect_equal(length(pg$heights), 17) + expect_equal(length(pg$heights), 19) + expect_equal(length(pg$widths), 18) - pg <- ggplotGrob(p + scale_x_continuous(position = "top")) - expect_equal(length(pg$heights), 18) + pg <- ggplotGrob( + p + scale_x_continuous(position = "top") + + scale_y_continuous(position = "right") + ) + expect_equal(length(pg$heights), 20) expect_equal(as.character(pg$heights[9]), "1cm") + expect_equal(length(pg$widths), 19) + expect_equal(as.character(pg$widths[13]), "1cm") # Also add padding with negative ticks and no text (#5251) pg <- ggplotGrob( p + scale_x_continuous(labels = NULL, position = "top") + theme(axis.ticks.length.x.top = unit(-2, "mm")) ) - expect_equal(length(pg$heights), 18) + expect_equal(length(pg$heights), 20) expect_equal(as.character(pg$heights[9]), "1cm") + + # Inverse should be true when strips are switched + p <- ggplot(data = mpg, aes(x = displ, y = hwy)) + + facet_grid(year ~ drv, switch = "both") + + theme( + strip.placement = "outside", + strip.switch.pad.grid = unit(10, "mm") + ) + + pg <- ggplotGrob(p) + expect_equal(length(pg$heights), 20) + expect_equal(as.character(pg$heights[13]), "1cm") + expect_equal(length(pg$widths), 19) + expect_equal(as.character(pg$widths[7]), "1cm") + + pg <- ggplotGrob( + p + scale_x_continuous(position = "top") + + scale_y_continuous(position = "right") + ) + expect_equal(length(pg$heights), 19) + expect_equal(length(pg$widths), 18) }) test_that("y strip labels are rotated when strips are switched", { From c95e0614b9fd82df48ca1d822266ae159fb2323a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 25 Jun 2024 15:51:24 +0200 Subject: [PATCH 059/264] Reduce panel parameter setup in facetted plots (#5431) * coords append information to layout * compute panel params/guides once per scale combination * Facets render axes once per x/y combination * anonymous function to `MoreArgs` * Sprinkle some comments * Add news bullet * add test * format bullet --- NEWS.md | 4 +++- R/coord-.R | 5 +++++ R/coord-flip.R | 1 + R/layout.R | 28 ++++++++++++++++++++-------- tests/testthat/test-coord-.R | 23 +++++++++++++++++++++++ 5 files changed, 52 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index 80d4dd7d02..e99235a3a0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,8 @@ # ggplot2 (development version) -* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). +* (internal) The plot's layout now has a coord parameter that is used to + prevent setting up identical panel parameters (#5427) +* (internal) rearranged the code of `Facet$draw_panels()` method (@teunbrand). * `geom_rug()` prints a warning when `na.rm = FALSE`, as per documentation (@pn317, #5905) * `position_dodge(preserve = "single")` now handles multi-row geoms better, such as `geom_violin()` (@teunbrand based on @clauswilke's work, #2801). diff --git a/R/coord-.R b/R/coord-.R index ced1257b42..6736059fbc 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -196,6 +196,11 @@ Coord <- ggproto("Coord", }, setup_layout = function(layout, params) { + # We're appending a COORD variable to the layout that determines the + # uniqueness of panel parameters. The layout uses this to prevent redundant + # setups of these parameters. + scales <- layout[c("SCALE_X", "SCALE_Y")] + layout$COORD <- vec_match(scales, unique0(scales)) layout }, diff --git a/R/coord-flip.R b/R/coord-flip.R index 7ff519d15c..eb46d12669 100644 --- a/R/coord-flip.R +++ b/R/coord-flip.R @@ -99,6 +99,7 @@ CoordFlip <- ggproto("CoordFlip", CoordCartesian, }, setup_layout = function(layout, params) { + layout <- Coord$setup_layout(layout, params) # Switch the scales layout[c("SCALE_X", "SCALE_Y")] <- layout[c("SCALE_Y", "SCALE_X")] layout diff --git a/R/layout.R b/R/layout.R index 41efa7e828..f6e04f9b9c 100644 --- a/R/layout.R +++ b/R/layout.R @@ -212,20 +212,32 @@ Layout <- ggproto("Layout", NULL, # scales is not elegant, but it is pragmatic self$coord$modify_scales(self$panel_scales_x, self$panel_scales_y) - scales_x <- self$panel_scales_x[self$layout$SCALE_X] - scales_y <- self$panel_scales_y[self$layout$SCALE_Y] + # We only need to setup panel params once for unique combinations of x/y + # scales. These will be repeated for duplicated combinations. + index <- vec_unique_loc(self$layout$COORD) + order <- vec_match(self$layout$COORD, self$layout$COORD[index]) - setup_panel_params <- function(scale_x, scale_y) { - self$coord$setup_panel_params(scale_x, scale_y, params = self$coord_params) - } - self$panel_params <- Map(setup_panel_params, scales_x, scales_y) + scales_x <- self$panel_scales_x[self$layout$SCALE_X[index]] + scales_y <- self$panel_scales_y[self$layout$SCALE_Y[index]] + + self$panel_params <- Map( + self$coord$setup_panel_params, + scales_x, scales_y, + MoreArgs = list(params = self$coord_params) + )[order] # `[order]` does the repeating invisible() }, setup_panel_guides = function(self, guides, layers) { + + # Like in `setup_panel_params`, we only need to setup guides for unique + # combinations of x/y scales. + index <- vec_unique_loc(self$layout$COORD) + order <- vec_match(self$layout$COORD, self$layout$COORD[index]) + self$panel_params <- lapply( - self$panel_params, + self$panel_params[index], self$coord$setup_panel_guides, guides, self$coord_params @@ -236,7 +248,7 @@ Layout <- ggproto("Layout", NULL, self$coord$train_panel_guides, layers, self$coord_params - ) + )[order] invisible() }, diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index ca7f62c06e..b372478981 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -53,3 +53,26 @@ test_that("check coord limits errors only on bad inputs", { # Should raise error if vector of wrong length is passed expect_error(check_coord_limits(1:3)) }) + +test_that("coords append a column to the layout correctly", { + layout <- data_frame0(SCALE_X = c(1, 1, 1), SCALE_Y = c(1, 1, 1)) + test <- Coord$setup_layout(layout) + expect_equal(test$COORD, c(1, 1, 1)) + + layout <- data_frame0(SCALE_X = c(1, 1, 1), SCALE_Y = c(1, 2, 2)) + test <- Coord$setup_layout(layout) + expect_equal(test$COORD, c(1, 2, 2)) + + layout <- data_frame0(SCALE_X = c(1, 2, 3), SCALE_Y = c(1, 1, 1)) + test <- Coord$setup_layout(layout) + expect_equal(test$COORD, c(1, 2, 3)) + + layout <- data_frame0(SCALE_X = c(1, 2, 3), SCALE_Y = c(1, 2, 3)) + test <- Coord$setup_layout(layout) + expect_equal(test$COORD, c(1, 2, 3)) + + layout <- data_frame0(SCALE_X = c(1, 1, 1), SCALE_Y = c(1, 2, 1)) + test <- Coord$setup_layout(layout) + expect_equal(test$COORD, c(1, 2, 1)) +}) + From 2610840f7478af027294db0793df839199b8cb6b Mon Sep 17 00:00:00 2001 From: "Alexander I. Jordan" Date: Fri, 28 Jun 2024 19:25:34 +0200 Subject: [PATCH 060/264] `stat_bin()` accepts functions for argument `breaks` (#5963) * `stat_bin()` accepts functions for argument `breaks` * add news bullet --- NEWS.md | 1 + R/stat-bin.R | 5 ++++- man/geom_histogram.Rd | 2 +- tests/testthat/test-stat-bin.R | 8 ++++++++ 4 files changed, 14 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index e99235a3a0..d553c7f924 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* `stat_bin()` now accepts functions for argument `breaks` (@aijordan, #4561) * (internal) The plot's layout now has a coord parameter that is used to prevent setting up identical panel parameters (#5427) * (internal) rearranged the code of `Facet$draw_panels()` method (@teunbrand). diff --git a/R/stat-bin.R b/R/stat-bin.R index 4f35d83a84..4c00b2e3ab 100644 --- a/R/stat-bin.R +++ b/R/stat-bin.R @@ -22,7 +22,7 @@ #' outside the range of the data. #' @param breaks Alternatively, you can supply a numeric vector giving #' the bin boundaries. Overrides `binwidth`, `bins`, `center`, -#' and `boundary`. +#' and `boundary`. Can also be a function that takes group-wise values as input and returns bin boundaries. #' @param closed One of `"right"` or `"left"` indicating whether right #' or left edges of bins are included in the bin. #' @param pad If `TRUE`, adds empty bins at either end of x. This ensures @@ -146,6 +146,9 @@ StatBin <- ggproto("StatBin", Stat, origin = NULL, right = NULL, drop = NULL) { x <- flipped_names(flipped_aes)$x if (!is.null(breaks)) { + if (is.function(breaks)) { + breaks <- breaks(data[[x]]) + } if (!scales[[x]]$is_discrete()) { breaks <- scales[[x]]$transform(breaks) } diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index 7cd907daed..f60ec4b1f5 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -164,7 +164,7 @@ outside the range of the data.} \item{breaks}{Alternatively, you can supply a numeric vector giving the bin boundaries. Overrides \code{binwidth}, \code{bins}, \code{center}, -and \code{boundary}.} +and \code{boundary}. Can also be a function that takes group-wise values as input and returns bin boundaries.} \item{closed}{One of \code{"right"} or \code{"left"} indicating whether right or left edges of bins are included in the bin.} diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index af0ae467f3..9b55054604 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -60,6 +60,14 @@ test_that("can use breaks argument", { expect_equal(out$count, c(1, 2)) }) +test_that("breaks computes bin boundaries for function input", { + df <- data.frame(x = c(0, 0, 0, 1:3)) + out <- layer_data(ggplot(df, aes(x)) + + geom_histogram(breaks = function(x) c(0, 0.5, 2.5, 7.5))) + + expect_equal(out$count, c(3, 2, 1)) +}) + test_that("fuzzy breaks are used when cutting", { df <- data_frame(x = c(-1, -0.5, -0.4, 0)) p <- ggplot(df, aes(x)) + From b8da7afc5823b26c9367c3e8982ddfd7b7c1be10 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 4 Jul 2024 06:47:43 +0200 Subject: [PATCH 061/264] don't require dplyr for `fortify.tbl()` (#5969) --- R/fortify.R | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/R/fortify.R b/R/fortify.R index b9cf025f2a..0e0b67516d 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -17,10 +17,7 @@ fortify.data.frame <- function(model, data, ...) model #' @export fortify.tbl_df <- function(model, data, ...) model #' @export -fortify.tbl <- function(model, data, ...) { - check_installed("dplyr", reason = "to work with `tbl` objects.") - dplyr::collect(model) -} +fortify.tbl <- function(model, data, ...) as.data.frame(model) #' @export fortify.NULL <- function(model, data, ...) waiver() #' @export From 46ae89f6bcad8be8784301b4c11129ac4b88e9f8 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 8 Jul 2024 10:18:15 +0200 Subject: [PATCH 062/264] Consolidate scale definition of position aesthetics (#5640) * Position scales use ggplot_global for aesthetics * Run revdepcheck * Fallbacks for numeric inputs * add news bullet * improve warning * add test --------- Co-authored-by: Thomas Lin Pedersen --- NEWS.md | 5 + R/scale-date.R | 27 +- R/scale-discrete-.R | 4 +- revdep/README.md | 244 +- revdep/cran.md | 372 +- revdep/failures.md | 10030 +++++++++++++++++++++++++++-- revdep/problems.md | 2647 +++++++- tests/testthat/test-scale-date.R | 15 + 8 files changed, 12594 insertions(+), 750 deletions(-) diff --git a/NEWS.md b/NEWS.md index d553c7f924..2696e04410 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,10 @@ # ggplot2 (development version) +* All position scales now use the same definition of `x` and `y` aesthetics. + This lets uncommon aesthetics like `xintercept` expand scales as usual. + (#3342, #4966, @teunbrand) +* Bare numeric values provided to Date or Datetime scales get inversely + transformed (cast to Date/POSIXct) with a warning (@teunbrand). * `stat_bin()` now accepts functions for argument `breaks` (@aijordan, #4561) * (internal) The plot's layout now has a coord parameter that is used to prevent setting up identical panel parameters (#5427) diff --git a/R/scale-date.R b/R/scale-date.R index 9433ccf568..36f8b37d83 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -81,7 +81,7 @@ scale_x_date <- function(name = waiver(), sec.axis = waiver()) { sc <- datetime_scale( - c("x", "xmin", "xmax", "xend"), + ggplot_global$x_aes, "date", name = name, palette = identity, @@ -118,7 +118,7 @@ scale_y_date <- function(name = waiver(), sec.axis = waiver()) { sc <- datetime_scale( - c("y", "ymin", "ymax", "yend"), + ggplot_global$y_aes, "date", name = name, palette = identity, @@ -156,7 +156,7 @@ scale_x_datetime <- function(name = waiver(), sec.axis = waiver()) { sc <- datetime_scale( - c("x", "xmin", "xmax", "xend"), + ggplot_global$x_aes, "time", name = name, palette = identity, @@ -196,7 +196,7 @@ scale_y_datetime <- function(name = waiver(), sec.axis = waiver()) { sc <- datetime_scale( - c("y", "ymin", "ymax", "yend"), + ggplot_global$y_aes, "time", name = name, palette = identity, @@ -317,7 +317,7 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), # x/y position aesthetics should use ScaleContinuousDate or # ScaleContinuousDatetime; others use ScaleContinuous - if (all(aesthetics %in% c("x", "xmin", "xmax", "xend", "y", "ymin", "ymax", "yend"))) { + if (all(aesthetics %in% c(ggplot_global$x_aes, ggplot_global$y_aes))) { scale_class <- switch( transform, date = ScaleContinuousDate, @@ -362,6 +362,13 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous, self$timezone <- tz self$trans <- transform_time(self$timezone) } + if (is_bare_numeric(x)) { + x <- self$trans$inverse(x) + cli::cli_warn(c( + "A {.cls numeric} value was passed to a {.field Datetime} scale.", + i = "The value was converted to {obj_type_friendly(x)}." + ), call = self$call) + } ggproto_parent(ScaleContinuous, self)$transform(x) }, map = function(self, x, limits = self$get_limits()) { @@ -401,6 +408,16 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous, map = function(self, x, limits = self$get_limits()) { self$oob(x, limits) }, + transform = function(self, x) { + if (is_bare_numeric(x)) { + x <- self$trans$inverse(x) + cli::cli_warn(c( + "A {.cls numeric} value was passed to a {.field Date} scale.", + i = "The value was converted to {obj_type_friendly(x)}." + ), call = self$call) + } + ggproto_parent(ScaleContinuous, self)$transform(x) + }, get_breaks = function(self, limits = self$get_limits()) { breaks <- ggproto_parent(ScaleContinuous, self)$get_breaks(limits) if (is.null(breaks)) { diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index b957b97b97..82bb8eb8fe 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -71,7 +71,7 @@ scale_x_discrete <- function(name = waiver(), ..., palette = seq_len, expand = waiver(), guide = waiver(), position = "bottom", sec.axis = waiver()) { sc <- discrete_scale( - aesthetics = c("x", "xmin", "xmax", "xend"), name = name, + aesthetics = ggplot_global$x_aes, name = name, palette = palette, ..., expand = expand, guide = guide, position = position, super = ScaleDiscretePosition @@ -86,7 +86,7 @@ scale_y_discrete <- function(name = waiver(), ..., palette = seq_len, expand = waiver(), guide = waiver(), position = "left", sec.axis = waiver()) { sc <- discrete_scale( - aesthetics = c("y", "ymin", "ymax", "yend"), name = name, + aesthetics = ggplot_global$y_aes, name = name, palette = palette, ..., expand = expand, guide = guide, position = position, super = ScaleDiscretePosition diff --git a/revdep/README.md b/revdep/README.md index b6eff473f2..d6c6b43f5e 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,34 +1,222 @@ # Revdeps -## Failed to check (17) +## Failed to check (146) -|package |version |error |warning |note | -|:----------------|:-------|:-----|:-------|:----| -|bayesdfa |1.3.3 |1 | | | -|bmgarch |2.0.0 |1 | | | -|ctsem |3.9.1 |1 | | | -|EcoEnsemble |1.0.5 |1 | | | -|geostan |0.5.4 |1 | | | -|grandR |? | | | | -|multilevelcoda |1.2.3 |1 | | | -|multinma |0.6.1 |1 | | | -|rmsb |1.1-0 |1 | | | -|rstanarm |2.32.1 |1 | | | -|Seurat |? | | | | -|streamDAG |? | | | | -|treestats |1.0.5 |1 | | | -|TriDimRegression |1.0.2 |1 | | | -|triptych |0.1.2 |1 | | | -|ubms |1.2.6 |1 | | | -|valse |0.1-0 |1 | | | +|package |version |error |warning |note | +|:----------------------|:----------|:------|:-------|:----| +|abctools |1.1.7 |1 | | | +|AnanseSeurat |? | | | | +|animalEKF |1.2 |1 | | | +|ANOM |0.5 |1 | | | +|APackOfTheClones |? | | | | +|atRisk |0.1.0 |1 | | | +|AutoScore |1.0.0 |1 | | | +|bayesdfa |1.3.3 |1 | | | +|bayesDP |1.3.6 |1 | | | +|BayesianFactorZoo |0.0.0.2 |1 | | | +|BCClong |1.0.2 |1 | |1 | +|binsreg |1.0 |1 | | | +|bmstdr |0.7.9 |1 | | | +|bspcov |1.0.0 |1 | | | +|CalibrationCurves |2.0.1 |1 | | | +|Canek |? | | | | +|CARBayesST |4.0 |1 | | | +|CaseBasedReasoning |0.3 |1 | | | +|cellpypes |? | | | | +|CGPfunctions |0.6.3 |1 | | | +|CIARA |? | | | | +|ClustAssess |? | | | | +|clustree |? | | | | +|cmprskcoxmsm |0.2.1 |1 | | | +|combiroc |? | | | | +|conos |? | | | | +|contrast |0.24.2 |1 | | | +|countland |? | | | | +|coxed |0.3.3 |1 | | | +|CRMetrics |? | | | | +|csmpv |1.0.3 |1 | | | +|ctsem |3.10.0 |1 | | | +|CytoSimplex |? | | | | +|DepthProc |2.1.5 |1 | | | +|DIscBIO |? | | | | +|DR.SC |? | | | | +|dyngen |? | | | | +|EcoEnsemble |1.0.5 |1 | | | +|ecolottery |1.0.0 |1 | | | +|EpiEstim |2.2-4 |1 | | | +|evolqg |0.3-4 |1 | | | +|ForecastComb |1.3.1 |1 | | | +|gapfill |0.9.6-1 |1 | |1 | +|GeomComb |1.0 |1 | | | +|[geostan](failures.md#geostan)|0.6.1 |__+1__ | |-3 | +|ggrcs |0.3.8 |1 | | | +|ggrisk |1.3 |1 | | | +|ggsector |? | | | | +|gJLS2 |0.2.0 |1 | | | +|grandR |? | | | | +|Greg |2.0.2 |1 | | | +|greport |0.7-4 |1 | | | +|harmony |? | | | | +|hettx |0.1.3 |1 | | | +|hIRT |0.3.0 |1 | | | +|Hmsc |3.0-13 |1 | | | +|iNZightPlots |2.15.3 |1 | | | +|iNZightRegression |1.3.4 |1 | | | +|IRexamples |0.0.4 |1 | | | +|joineRML |0.4.6 |1 | | | +|JWileymisc |1.4.1 |1 | | | +|kmc |0.4-2 |1 | | | +|L2E |2.0 |1 | | | +|llbayesireg |1.0.0 |1 | | | +|LorenzRegression |1.0.0 |1 | | | +|lsirm12pl |1.3.1 |1 | | | +|mbsts |3.0 |1 | | | +|MendelianRandomization |0.10.0 |1 | | | +|MetabolicSurv |1.1.2 |1 | | | +|miWQS |0.4.4 |1 | | | +|mlmts |1.1.1 |1 | | | +|MRZero |0.2.0 |1 | | | +|Multiaovbay |0.1.0 |1 | | | +|multilevelTools |0.1.1 |1 | | | +|multinma |0.7.0 |1 | | | +|NCA |4.0.1 |1 | | | +|netcmc |1.0.2 |1 | | | +|NetworkChange |0.8 |1 | | | +|nlmeVPC |2.6 |1 | | | +|NMADiagT |0.1.2 |1 | | | +|optweight |0.2.5 |1 | | | +|OVtool |1.0.3 |1 | | | +|paths |0.1.1 |1 | | | +|PLMIX |2.1.1 |1 | | | +|popstudy |1.0.1 |1 | | | +|pould |1.0.1 |1 | | | +|powerly |1.8.6 |1 | | | +|pre |1.0.7 |1 | | | +|PRECAST |? | | | | +|ProFAST |? | | | | +|pscore |0.4.0 |1 | | | +|psfmi |1.4.0 |1 | | | +|qreport |1.0-0 |1 | | | +|qris |1.1.1 |1 | | | +|qte |1.3.1 |1 | | | +|quid |0.0.1 |1 | | | +|RATest |0.1.10 |1 | | | +|RcmdrPlugin.RiskDemo |3.2 |1 | | | +|rddtools |1.6.0 |1 | | | +|riskRegression |2023.12.21 |1 | | | +|rliger |? | | | | +|rms |6.8-0 |1 | |1 | +|rmsb |1.1-0 |1 | | | +|robmed |1.0.2 |1 | | | +|robmedExtra |0.1.0 |1 | | | +|RPPanalyzer |1.4.9 |1 | | | +|rstanarm |2.32.1 |1 | | | +|scCustomize |? | | | | +|SCdeconR |? | | | | +|scDiffCom |? | | | | +|scGate |? | | | | +|scMappR |? | | | | +|SCORPIUS |? | | | | +|scpoisson |? | | | | +|SCpubr |? | | | | +|scRNAstat |? | | | | +|sectorgap |0.1.0 |1 | | | +|SEERaBomb |2019.2 |1 | | | +|semicmprskcoxmsm |0.2.0 |1 | | | +|SensMap |0.7 |1 | | | +|Signac |? | | | | +|SimplyAgree |0.2.0 |1 | | | +|sMSROC |0.1.2 |1 | | | +|SNPassoc |2.1-0 |1 | | | +|snplinkage |? | | | | +|SoupX |? | | | | +|SpaDES.core |2.0.5 |1 | | | +|sparsereg |1.2 |1 | | | +|SPECK |? | | | | +|spikeSlabGAM |1.1-19 |1 | | | +|statsr |0.3.0 |1 | | | +|streamDAG |? | | | | +|survHE |2.0.1 |1 | |1 | +|survidm |1.3.2 |1 | | | +|tempted |0.1.1 |1 | | | +|[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | +|tidyEdSurvey |0.1.3 |1 | | | +|tidyseurat |? | | | | +|tidyvpc |1.5.1 |1 | | | +|treefit |? | | | | +|TriDimRegression |1.0.2 |1 | | | +|TSrepr |1.1.0 |1 | | | +|twang |2.6 |1 | | | +|valse |0.1-0 |1 | | | +|vdg |1.2.3 |1 | | | +|WRTDStidal |1.1.4 |1 | | | -## New problems (5) +## New problems (64) -|package |version |error |warning |note | -|:----------------------|:-------|:------|:-------|:------| -|[ggh4x](problems.md#ggh4x)|0.2.8 |__+3__ | | | -|[MplusAutomation](problems.md#mplusautomation)|1.1.1 | | |__+1__ | -|[PlasmaMutationDetector](problems.md#plasmamutationdetector)|1.7.2 | | |__+1__ | -|[Superpower](problems.md#superpower)|0.2.0 |__+1__ | |1 | -|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |__+1__ | | | +|package |version |error |warning |note | +|:---------------|:--------|:--------|:--------|:--------| +|[asmbPLS](problems.md#asmbpls)|1.0.0 | |__+1__ |1 | +|[bdl](problems.md#bdl)|1.0.5 | |__+1__ | | +|[bdscale](problems.md#bdscale)|2.0.0 |__+1__ | |__+1__ | +|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | +|[brolgar](problems.md#brolgar)|1.0.1 |__+2__ | |__+1__ | +|[bSi](problems.md#bsi)|1.0.0 | |__+1__ | | +|[CausalImpact](problems.md#causalimpact)|1.3.0 |__+2__ | |__+1__ | +|[ClusROC](problems.md#clusroc)|1.0.2 | |__+1__ | | +|[clustEff](problems.md#clusteff)|0.3.1 | |__+1__ | | +|[CLVTools](problems.md#clvtools)|0.10.0 |__+1__ | |1 __+1__ | +|[coda4microbiome](problems.md#coda4microbiome)|0.2.3 | |__+1__ | | +|[CompAREdesign](problems.md#comparedesign)|2.3.1 | |__+1__ | | +|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | +|[Coxmos](problems.md#coxmos)|1.0.2 |1 |__+1__ |1 | +|[csa](problems.md#csa)|0.7.1 | |__+1__ | | +|[deeptime](problems.md#deeptime)|1.1.1 |__+2__ | | | +|[DEGRE](problems.md#degre)|0.2.0 | |__+1__ | | +|[did](problems.md#did)|2.1.2 | |1 __+1__ | | +|[EpiCurve](problems.md#epicurve)|2.4-2 |__+1__ | |1 __+1__ | +|[epiR](problems.md#epir)|2.0.74 |__+1__ | |__+1__ | +|[FuncNN](problems.md#funcnn)|1.0 | |__+1__ |1 | +|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | +|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | +|[ggfortify](problems.md#ggfortify)|0.4.17 | | |__+1__ | +|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | +|[ggheatmap](problems.md#ggheatmap)|2.2 | |__+1__ | | +|[ggScatRidges](problems.md#ggscatridges)|0.1.1 | |__+1__ | | +|[GimmeMyPlot](problems.md#gimmemyplot)|0.1.0 | |__+1__ | | +|[hilldiv](problems.md#hilldiv)|1.5.1 | |__+1__ | | +|[hJAM](problems.md#hjam)|1.0.0 | |__+1__ | | +|[iglu](problems.md#iglu)|4.0.0 |__+2__ | |__+1__ | +|[ImFoR](problems.md#imfor)|0.1.0 | |__+1__ | | +|[iNEXT.4steps](problems.md#inext4steps)|1.0.0 | |__+1__ | | +|[insane](problems.md#insane)|1.0.3 | |__+1__ | | +|[MarketMatching](problems.md#marketmatching)|1.2.1 |__+1__ | | | +|[mc2d](problems.md#mc2d)|0.2.0 | |__+1__ |1 | +|[MetaIntegrator](problems.md#metaintegrator)|2.1.3 | |__+1__ |2 | +|[MF.beta4](problems.md#mfbeta4)|1.0.3 | |1 __+1__ | | +|[MIMSunit](problems.md#mimsunit)|0.11.2 |__+1__ | | | +|[missingHE](problems.md#missinghe)|1.5.0 | |__+1__ |1 | +|[MSPRT](problems.md#msprt)|3.0 | |__+1__ |1 | +|[nzelect](problems.md#nzelect)|0.4.0 |__+1__ | |2 | +|[OenoKPM](problems.md#oenokpm)|2.4.1 | |__+1__ | | +|[posologyr](problems.md#posologyr)|1.2.4 |__+1__ | | | +|[qicharts](problems.md#qicharts)|0.5.8 |__+1__ | | | +|[qicharts2](problems.md#qicharts2)|0.7.5 |__+1__ | |__+1__ | +|[QuadratiK](problems.md#quadratik)|1.1.0 | |__+1__ |1 | +|[RCTrep](problems.md#rctrep)|1.2.0 | |__+1__ | | +|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | +|[SCOUTer](problems.md#scouter)|1.0.0 | |__+1__ | | +|[sievePH](problems.md#sieveph)|1.0.4 | |__+1__ | | +|[SouthParkRshiny](problems.md#southparkrshiny)|1.0.0 | |__+1__ |2 | +|[SqueakR](problems.md#squeakr)|1.3.0 |1 |__+1__ |1 | +|[survminer](problems.md#survminer)|0.4.9 | |__+1__ |1 | +|[symptomcheckR](problems.md#symptomcheckr)|0.1.3 | |__+1__ | | +|[tcgaViz](problems.md#tcgaviz)|1.0.2 | |__+1__ | | +|[TestGardener](problems.md#testgardener)|3.3.3 | |__+1__ | | +|[tis](problems.md#tis)|1.39 |__+1__ | |1 | +|[UniprotR](problems.md#uniprotr)|2.4.0 | |__+1__ | | +|[VALERIE](problems.md#valerie)|1.1.0 | |__+1__ |1 | +|[vannstats](problems.md#vannstats)|1.3.4.14 | |__+1__ | | +|[vici](problems.md#vici)|0.7.3 | |__+1__ | | +|[Wats](problems.md#wats)|1.0.1 |__+2__ | |__+1__ | +|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index ff60632977..f1da4a685a 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,48 +1,370 @@ ## revdepcheck results -We checked 5021 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 5034 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 5 new problems - * We failed to check 17 packages + * We saw 64 new problems + * We failed to check 146 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) +* asmbPLS + checking whether package ‘asmbPLS’ can be installed ... WARNING + +* bdl + checking whether package ‘bdl’ can be installed ... WARNING + +* bdscale + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* biclustermd + checking tests ... ERROR + +* brolgar + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* bSi + checking whether package ‘bSi’ can be installed ... WARNING + +* CausalImpact + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ClusROC + checking whether package ‘ClusROC’ can be installed ... WARNING + +* clustEff + checking whether package ‘clustEff’ can be installed ... WARNING + +* CLVTools + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* coda4microbiome + checking whether package ‘coda4microbiome’ can be installed ... WARNING + +* CompAREdesign + checking whether package ‘CompAREdesign’ can be installed ... WARNING + +* covidcast + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* Coxmos + checking Rd files ... WARNING + +* csa + checking whether package ‘csa’ can be installed ... WARNING + +* deeptime + checking examples ... ERROR + checking tests ... ERROR + +* DEGRE + checking whether package ‘DEGRE’ can be installed ... WARNING + +* did + checking whether package ‘did’ can be installed ... WARNING + +* EpiCurve + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* epiR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* FuncNN + checking whether package ‘FuncNN’ can be installed ... WARNING + +* ggedit + checking examples ... ERROR + +* ggfixest + checking tests ... ERROR + +* ggfortify + checking re-building of vignette outputs ... NOTE + * ggh4x checking examples ... ERROR checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggheatmap + checking whether package ‘ggheatmap’ can be installed ... WARNING + +* ggScatRidges + checking whether package ‘ggScatRidges’ can be installed ... WARNING + +* GimmeMyPlot + checking whether package ‘GimmeMyPlot’ can be installed ... WARNING + +* hilldiv + checking whether package ‘hilldiv’ can be installed ... WARNING + +* hJAM + checking whether package ‘hJAM’ can be installed ... WARNING + +* iglu + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ImFoR + checking whether package ‘ImFoR’ can be installed ... WARNING + +* iNEXT.4steps + checking whether package ‘iNEXT.4steps’ can be installed ... WARNING + +* insane + checking whether package ‘insane’ can be installed ... WARNING + +* MarketMatching checking re-building of vignette outputs ... ERROR -* MplusAutomation - checking installed package size ... NOTE +* mc2d + checking whether package ‘mc2d’ can be installed ... WARNING + +* MetaIntegrator + checking whether package ‘MetaIntegrator’ can be installed ... WARNING + +* MF.beta4 + checking whether package ‘MF.beta4’ can be installed ... WARNING + +* MIMSunit + checking examples ... ERROR + +* missingHE + checking whether package ‘missingHE’ can be installed ... WARNING + +* MSPRT + checking whether package ‘MSPRT’ can be installed ... WARNING + +* nzelect + checking examples ... ERROR + +* OenoKPM + checking whether package ‘OenoKPM’ can be installed ... WARNING + +* posologyr + checking running R code from vignettes ... ERROR + +* qicharts + checking examples ... ERROR + +* qicharts2 + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* QuadratiK + checking whether package ‘QuadratiK’ can be installed ... WARNING -* PlasmaMutationDetector - checking installed package size ... NOTE +* RCTrep + checking whether package ‘RCTrep’ can be installed ... WARNING -* Superpower +* scdtb checking tests ... ERROR +* SCOUTer + checking whether package ‘SCOUTer’ can be installed ... WARNING + +* sievePH + checking whether package ‘sievePH’ can be installed ... WARNING + +* SouthParkRshiny + checking whether package ‘SouthParkRshiny’ can be installed ... WARNING + +* SqueakR + checking whether package ‘SqueakR’ can be installed ... WARNING + +* survminer + checking whether package ‘survminer’ can be installed ... WARNING + +* symptomcheckR + checking whether package ‘symptomcheckR’ can be installed ... WARNING + +* tcgaViz + checking whether package ‘tcgaViz’ can be installed ... WARNING + +* TestGardener + checking whether package ‘TestGardener’ can be installed ... WARNING + +* tis + checking examples ... ERROR + +* UniprotR + checking whether package ‘UniprotR’ can be installed ... WARNING + +* VALERIE + checking whether package ‘VALERIE’ can be installed ... WARNING + +* vannstats + checking whether package ‘vannstats’ can be installed ... WARNING + +* vici + checking whether package ‘vici’ can be installed ... WARNING + +* Wats + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * xaringanthemer checking tests ... ERROR ### Failed to check -* bayesdfa (NA) -* bmgarch (NA) -* ctsem (NA) -* EcoEnsemble (NA) -* geostan (NA) -* grandR (NA) -* multilevelcoda (NA) -* multinma (NA) -* rmsb (NA) -* rstanarm (NA) -* Seurat (NA) -* streamDAG (NA) -* treestats (NA) -* TriDimRegression (NA) -* triptych (NA) -* ubms (NA) -* valse (NA) +* abctools (NA) +* AnanseSeurat (NA) +* animalEKF (NA) +* ANOM (NA) +* APackOfTheClones (NA) +* atRisk (NA) +* AutoScore (NA) +* bayesdfa (NA) +* bayesDP (NA) +* BayesianFactorZoo (NA) +* BCClong (NA) +* binsreg (NA) +* bmstdr (NA) +* bspcov (NA) +* CalibrationCurves (NA) +* Canek (NA) +* CARBayesST (NA) +* CaseBasedReasoning (NA) +* cellpypes (NA) +* CGPfunctions (NA) +* CIARA (NA) +* ClustAssess (NA) +* clustree (NA) +* cmprskcoxmsm (NA) +* combiroc (NA) +* conos (NA) +* contrast (NA) +* countland (NA) +* coxed (NA) +* CRMetrics (NA) +* csmpv (NA) +* ctsem (NA) +* CytoSimplex (NA) +* DepthProc (NA) +* DIscBIO (NA) +* DR.SC (NA) +* dyngen (NA) +* EcoEnsemble (NA) +* ecolottery (NA) +* EpiEstim (NA) +* evolqg (NA) +* ForecastComb (NA) +* gapfill (NA) +* GeomComb (NA) +* geostan (NA) +* ggrcs (NA) +* ggrisk (NA) +* ggsector (NA) +* gJLS2 (NA) +* grandR (NA) +* Greg (NA) +* greport (NA) +* harmony (NA) +* hettx (NA) +* hIRT (NA) +* Hmsc (NA) +* iNZightPlots (NA) +* iNZightRegression (NA) +* IRexamples (NA) +* joineRML (NA) +* JWileymisc (NA) +* kmc (NA) +* L2E (NA) +* llbayesireg (NA) +* LorenzRegression (NA) +* lsirm12pl (NA) +* mbsts (NA) +* MendelianRandomization (NA) +* MetabolicSurv (NA) +* miWQS (NA) +* mlmts (NA) +* MRZero (NA) +* Multiaovbay (NA) +* multilevelTools (NA) +* multinma (NA) +* NCA (NA) +* netcmc (NA) +* NetworkChange (NA) +* nlmeVPC (NA) +* NMADiagT (NA) +* optweight (NA) +* OVtool (NA) +* paths (NA) +* PLMIX (NA) +* popstudy (NA) +* pould (NA) +* powerly (NA) +* pre (NA) +* PRECAST (NA) +* ProFAST (NA) +* pscore (NA) +* psfmi (NA) +* qreport (NA) +* qris (NA) +* qte (NA) +* quid (NA) +* RATest (NA) +* RcmdrPlugin.RiskDemo (NA) +* rddtools (NA) +* riskRegression (NA) +* rliger (NA) +* rms (NA) +* rmsb (NA) +* robmed (NA) +* robmedExtra (NA) +* RPPanalyzer (NA) +* rstanarm (NA) +* scCustomize (NA) +* SCdeconR (NA) +* scDiffCom (NA) +* scGate (NA) +* scMappR (NA) +* SCORPIUS (NA) +* scpoisson (NA) +* SCpubr (NA) +* scRNAstat (NA) +* sectorgap (NA) +* SEERaBomb (NA) +* semicmprskcoxmsm (NA) +* SensMap (NA) +* Signac (NA) +* SimplyAgree (NA) +* sMSROC (NA) +* SNPassoc (NA) +* snplinkage (NA) +* SoupX (NA) +* SpaDES.core (NA) +* sparsereg (NA) +* SPECK (NA) +* spikeSlabGAM (NA) +* statsr (NA) +* streamDAG (NA) +* survHE (NA) +* survidm (NA) +* tempted (NA) +* tidydr (NA) +* tidyEdSurvey (NA) +* tidyseurat (NA) +* tidyvpc (NA) +* treefit (NA) +* TriDimRegression (NA) +* TSrepr (NA) +* twang (NA) +* valse (NA) +* vdg (NA) +* WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index ca00cbc9ae..5eb2ead6c6 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,23 +1,23 @@ -# bayesdfa +# abctools
-* Version: 1.3.3 -* GitHub: https://github.com/fate-ewi/bayesdfa -* Source code: https://github.com/cran/bayesdfa -* Date/Publication: 2024-02-26 20:50:06 UTC -* Number of recursive dependencies: 89 +* Version: 1.1.7 +* GitHub: https://github.com/dennisprangle/abctools +* Source code: https://github.com/cran/abctools +* Date/Publication: 2023-09-18 10:40:02 UTC +* Number of recursive dependencies: 75 -Run `revdepcheck::cloud_details(, "bayesdfa")` for more info +Run `revdepcheck::cloud_details(, "abctools")` for more info
## In both -* checking whether package ‘bayesdfa’ can be installed ... ERROR +* checking whether package ‘abctools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/abctools/new/abctools.Rcheck/00install.out’ for details. ``` ## Installation @@ -25,77 +25,147 @@ Run `revdepcheck::cloud_details(, "bayesdfa")` for more info ### Devel ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked +* installing *source* package ‘abctools’ ... +** package ‘abctools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c abctools.c -o abctools.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o abctools.so abctools.o init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/abctools/new/abctools.Rcheck/00LOCK-abctools/00new/abctools/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘abctools’ +* removing ‘/tmp/workdir/abctools/new/abctools.Rcheck/abctools’ ``` ### CRAN ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked +* installing *source* package ‘abctools’ ... +** package ‘abctools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c abctools.c -o abctools.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o abctools.so abctools.o init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/abctools/old/abctools.Rcheck/00LOCK-abctools/00new/abctools/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘abctools’ +* removing ‘/tmp/workdir/abctools/old/abctools.Rcheck/abctools’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +``` +# AnanseSeurat + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/JGASmits/AnanseSeurat +* Source code: https://github.com/cran/AnanseSeurat +* Date/Publication: 2023-11-11 21:43:17 UTC +* Number of recursive dependencies: 201 + +Run `revdepcheck::cloud_details(, "AnanseSeurat")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/AnanseSeurat/new/AnanseSeurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +Package suggested but not available for checking: ‘Signac’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/AnanseSeurat/old/AnanseSeurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +Package suggested but not available for checking: ‘Signac’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# bmgarch +# animalEKF
-* Version: 2.0.0 -* GitHub: https://github.com/ph-rast/bmgarch -* Source code: https://github.com/cran/bmgarch -* Date/Publication: 2023-09-12 00:40:02 UTC -* Number of recursive dependencies: 82 +* Version: 1.2 +* GitHub: NA +* Source code: https://github.com/cran/animalEKF +* Date/Publication: 2023-09-29 15:32:41 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "bmgarch")` for more info +Run `revdepcheck::cloud_details(, "animalEKF")` for more info
## In both -* checking whether package ‘bmgarch’ can be installed ... ERROR +* checking whether package ‘animalEKF’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bmgarch/new/bmgarch.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/animalEKF/new/animalEKF.Rcheck/00install.out’ for details. ``` ## Installation @@ -103,77 +173,61 @@ Run `revdepcheck::cloud_details(, "bmgarch")` for more info ### Devel ``` -* installing *source* package ‘bmgarch’ ... -** package ‘bmgarch’ successfully unpacked and MD5 sums checked +* installing *source* package ‘animalEKF’ ... +** package ‘animalEKF’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_DCCMGARCH_namespace::model_DCCMGARCH; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_DCCMGARCH.o] Error 1 -ERROR: compilation failed for package ‘bmgarch’ -* removing ‘/tmp/workdir/bmgarch/new/bmgarch.Rcheck/bmgarch’ +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘animalEKF’ +* removing ‘/tmp/workdir/animalEKF/new/animalEKF.Rcheck/animalEKF’ ``` ### CRAN ``` -* installing *source* package ‘bmgarch’ ... -** package ‘bmgarch’ successfully unpacked and MD5 sums checked +* installing *source* package ‘animalEKF’ ... +** package ‘animalEKF’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_DCCMGARCH_namespace::model_DCCMGARCH; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_DCCMGARCH.o] Error 1 -ERROR: compilation failed for package ‘bmgarch’ -* removing ‘/tmp/workdir/bmgarch/old/bmgarch.Rcheck/bmgarch’ +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘animalEKF’ +* removing ‘/tmp/workdir/animalEKF/old/animalEKF.Rcheck/animalEKF’ ``` -# ctsem +# ANOM
-* Version: 3.9.1 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2023-10-30 14:20:02 UTC -* Number of recursive dependencies: 143 +* Version: 0.5 +* GitHub: https://github.com/PhilipPallmann/ANOM +* Source code: https://github.com/cran/ANOM +* Date/Publication: 2017-04-12 13:32:33 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "ctsem")` for more info +Run `revdepcheck::cloud_details(, "ANOM")` for more info
## In both -* checking whether package ‘ctsem’ can be installed ... ERROR +* checking whether package ‘ANOM’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ANOM/new/ANOM.Rcheck/00install.out’ for details. ``` ## Installation @@ -181,77 +235,139 @@ Run `revdepcheck::cloud_details(, "ctsem")` for more info ### Devel ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ANOM’ ... +** package ‘ANOM’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ANOM’ +* removing ‘/tmp/workdir/ANOM/new/ANOM.Rcheck/ANOM’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +``` +### CRAN + +``` +* installing *source* package ‘ANOM’ ... +** package ‘ANOM’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ANOM’ +* removing ‘/tmp/workdir/ANOM/old/ANOM.Rcheck/ANOM’ + + +``` +# APackOfTheClones + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/Qile0317/APackOfTheClones +* Source code: https://github.com/cran/APackOfTheClones +* Date/Publication: 2024-04-16 09:50:02 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "APackOfTheClones")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/APackOfTheClones/new/APackOfTheClones.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ +* this is package ‘APackOfTheClones’ version ‘1.2.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/APackOfTheClones/old/APackOfTheClones.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK +... +* this is package ‘APackOfTheClones’ version ‘1.2.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ ``` -# EcoEnsemble +# atRisk
-* Version: 1.0.5 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/EcoEnsemble -* Date/Publication: 2023-09-18 11:50:02 UTC -* Number of recursive dependencies: 91 +* Source code: https://github.com/cran/atRisk +* Date/Publication: 2023-08-08 14:50:05 UTC +* Number of recursive dependencies: 37 -Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info +Run `revdepcheck::cloud_details(, "atRisk")` for more info
## In both -* checking whether package ‘EcoEnsemble’ can be installed ... ERROR +* checking whether package ‘atRisk’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/atRisk/new/atRisk.Rcheck/00install.out’ for details. ``` ## Installation @@ -259,77 +375,8629 @@ Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info ### Devel ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘atRisk’ ... +** package ‘atRisk’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘atRisk’ +* removing ‘/tmp/workdir/atRisk/new/atRisk.Rcheck/atRisk’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_namespace::model_ensemble_model; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ +``` +### CRAN + +``` +* installing *source* package ‘atRisk’ ... +** package ‘atRisk’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘atRisk’ +* removing ‘/tmp/workdir/atRisk/old/atRisk.Rcheck/atRisk’ + + +``` +# AutoScore + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/nliulab/AutoScore +* Source code: https://github.com/cran/AutoScore +* Date/Publication: 2022-10-15 22:15:26 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "AutoScore")` for more info + +
+ +## In both + +* checking whether package ‘AutoScore’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘AutoScore’ ... +** package ‘AutoScore’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘AutoScore’ +* removing ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/AutoScore’ + + +``` +### CRAN + +``` +* installing *source* package ‘AutoScore’ ... +** package ‘AutoScore’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘AutoScore’ +* removing ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck/AutoScore’ + + +``` +# bayesdfa + +
+ +* Version: 1.3.3 +* GitHub: https://github.com/fate-ewi/bayesdfa +* Source code: https://github.com/cran/bayesdfa +* Date/Publication: 2024-02-26 20:50:06 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "bayesdfa")` for more info + +
+ +## In both + +* checking whether package ‘bayesdfa’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘bayesdfa’ ... +** package ‘bayesdfa’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 +ERROR: compilation failed for package ‘bayesdfa’ +* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’ + + +``` +### CRAN + +``` +* installing *source* package ‘bayesdfa’ ... +** package ‘bayesdfa’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 +ERROR: compilation failed for package ‘bayesdfa’ +* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’ + + +``` +# bayesDP + +
+ +* Version: 1.3.6 +* GitHub: https://github.com/graemeleehickey/bayesDP +* Source code: https://github.com/cran/bayesDP +* Date/Publication: 2022-01-30 22:20:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "bayesDP")` for more info + +
+ +## In both + +* checking whether package ‘bayesDP’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bayesDP/new/bayesDP.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘bayesDP’ ... +** package ‘bayesDP’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o bayesDP.so RcppExports.o bdplm.o ppexp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/bayesDP/new/bayesDP.Rcheck/00LOCK-bayesDP/00new/bayesDP/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bayesDP’ +* removing ‘/tmp/workdir/bayesDP/new/bayesDP.Rcheck/bayesDP’ + + +``` +### CRAN + +``` +* installing *source* package ‘bayesDP’ ... +** package ‘bayesDP’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o bayesDP.so RcppExports.o bdplm.o ppexp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/bayesDP/old/bayesDP.Rcheck/00LOCK-bayesDP/00new/bayesDP/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bayesDP’ +* removing ‘/tmp/workdir/bayesDP/old/bayesDP.Rcheck/bayesDP’ + + +``` +# BayesianFactorZoo + +
+ +* Version: 0.0.0.2 +* GitHub: NA +* Source code: https://github.com/cran/BayesianFactorZoo +* Date/Publication: 2023-11-14 12:43:44 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "BayesianFactorZoo")` for more info + +
+ +## In both + +* checking whether package ‘BayesianFactorZoo’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BayesianFactorZoo/new/BayesianFactorZoo.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BayesianFactorZoo’ ... +** package ‘BayesianFactorZoo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesianFactorZoo’ +* removing ‘/tmp/workdir/BayesianFactorZoo/new/BayesianFactorZoo.Rcheck/BayesianFactorZoo’ + + +``` +### CRAN + +``` +* installing *source* package ‘BayesianFactorZoo’ ... +** package ‘BayesianFactorZoo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesianFactorZoo’ +* removing ‘/tmp/workdir/BayesianFactorZoo/old/BayesianFactorZoo.Rcheck/BayesianFactorZoo’ + + +``` +# BCClong + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/BCClong +* Date/Publication: 2024-02-05 11:50:06 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "BCClong")` for more info + +
+ +## In both + +* checking whether package ‘BCClong’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BCClong/new/BCClong.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘joineRML’ + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BCClong’ ... +** package ‘BCClong’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BCClong/new/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BCClong’ +* removing ‘/tmp/workdir/BCClong/new/BCClong.Rcheck/BCClong’ + + +``` +### CRAN + +``` +* installing *source* package ‘BCClong’ ... +** package ‘BCClong’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BCClong/old/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BCClong’ +* removing ‘/tmp/workdir/BCClong/old/BCClong.Rcheck/BCClong’ + + +``` +# binsreg + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/binsreg +* Date/Publication: 2023-07-11 12:00:24 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "binsreg")` for more info + +
+ +## In both + +* checking whether package ‘binsreg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/binsreg/new/binsreg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘binsreg’ ... +** package ‘binsreg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘binsreg’ +* removing ‘/tmp/workdir/binsreg/new/binsreg.Rcheck/binsreg’ + + +``` +### CRAN + +``` +* installing *source* package ‘binsreg’ ... +** package ‘binsreg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘binsreg’ +* removing ‘/tmp/workdir/binsreg/old/binsreg.Rcheck/binsreg’ + + +``` +# bmstdr + +
+ +* Version: 0.7.9 +* GitHub: https://github.com/sujit-sahu/bmstdr +* Source code: https://github.com/cran/bmstdr +* Date/Publication: 2023-12-18 15:00:02 UTC +* Number of recursive dependencies: 212 + +Run `revdepcheck::cloud_details(, "bmstdr")` for more info + +
+ +## In both + +* checking whether package ‘bmstdr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘bmstdr’ ... +** package ‘bmstdr’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bmstdr’ +* removing ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/bmstdr’ + + +``` +### CRAN + +``` +* installing *source* package ‘bmstdr’ ... +** package ‘bmstdr’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bmstdr’ +* removing ‘/tmp/workdir/bmstdr/old/bmstdr.Rcheck/bmstdr’ + + +``` +# bspcov + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/statjs/bspcov +* Source code: https://github.com/cran/bspcov +* Date/Publication: 2024-02-06 16:50:08 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "bspcov")` for more info + +
+ +## In both + +* checking whether package ‘bspcov’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/bspcov’ + + +``` +### CRAN + +``` +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/old/bspcov.Rcheck/bspcov’ + + +``` +# CalibrationCurves + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/CalibrationCurves +* Date/Publication: 2024-03-01 10:12:35 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info + +
+ +## In both + +* checking whether package ‘CalibrationCurves’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ + + +``` +### CRAN + +``` +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ + + +``` +# Canek + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/MartinLoza/Canek +* Source code: https://github.com/cran/Canek +* Date/Publication: 2023-12-08 05:30:02 UTC +* Number of recursive dependencies: 220 + +Run `revdepcheck::cloud_details(, "Canek")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/Canek/new/Canek.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Canek/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘toy_example.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/Canek/old/Canek.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Canek/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘toy_example.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +# CARBayesST + +
+ +* Version: 4.0 +* GitHub: https://github.com/duncanplee/CARBayesST +* Source code: https://github.com/cran/CARBayesST +* Date/Publication: 2023-10-30 16:40:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "CARBayesST")` for more info + +
+ +## In both + +* checking whether package ‘CARBayesST’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CARBayesST/new/CARBayesST.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘CARBayesST’ ... +** package ‘CARBayesST’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayesST.so CARBayesST.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/CARBayesST/new/CARBayesST.Rcheck/00LOCK-CARBayesST/00new/CARBayesST/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CARBayesST’ +* removing ‘/tmp/workdir/CARBayesST/new/CARBayesST.Rcheck/CARBayesST’ + + +``` +### CRAN + +``` +* installing *source* package ‘CARBayesST’ ... +** package ‘CARBayesST’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayesST.so CARBayesST.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/00LOCK-CARBayesST/00new/CARBayesST/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CARBayesST’ +* removing ‘/tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/CARBayesST’ + + +``` +# CaseBasedReasoning + +
+ +* Version: 0.3 +* GitHub: https://github.com/sipemu/case-based-reasoning +* Source code: https://github.com/cran/CaseBasedReasoning +* Date/Publication: 2023-05-02 08:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "CaseBasedReasoning")` for more info + +
+ +## In both + +* checking whether package ‘CaseBasedReasoning’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘CaseBasedReasoning’ ... +** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o +... +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CaseBasedReasoning’ +* removing ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ + + +``` +### CRAN + +``` +* installing *source* package ‘CaseBasedReasoning’ ... +** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o +... +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CaseBasedReasoning’ +* removing ‘/tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ + + +``` +# cellpypes + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/FelixTheStudent/cellpypes +* Source code: https://github.com/cran/cellpypes +* Date/Publication: 2024-01-27 07:30:07 UTC +* Number of recursive dependencies: 183 + +Run `revdepcheck::cloud_details(, "cellpypes")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/cellpypes/new/cellpypes.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cellpypes/DESCRIPTION’ ... OK +... +* checking contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/cellpypes/old/cellpypes.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cellpypes/DESCRIPTION’ ... OK +... +* checking contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 1 NOTE + + + + + +``` +# CGPfunctions + +
+ +* Version: 0.6.3 +* GitHub: https://github.com/ibecav/CGPfunctions +* Source code: https://github.com/cran/CGPfunctions +* Date/Publication: 2020-11-12 14:50:09 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "CGPfunctions")` for more info + +
+ +## In both + +* checking whether package ‘CGPfunctions’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CGPfunctions/new/CGPfunctions.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘CGPfunctions’ ... +** package ‘CGPfunctions’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CGPfunctions’ +* removing ‘/tmp/workdir/CGPfunctions/new/CGPfunctions.Rcheck/CGPfunctions’ + + +``` +### CRAN + +``` +* installing *source* package ‘CGPfunctions’ ... +** package ‘CGPfunctions’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CGPfunctions’ +* removing ‘/tmp/workdir/CGPfunctions/old/CGPfunctions.Rcheck/CGPfunctions’ + + +``` +# CIARA + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/CIARA +* Date/Publication: 2022-02-22 20:00:02 UTC +* Number of recursive dependencies: 181 + +Run `revdepcheck::cloud_details(, "CIARA")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/CIARA/new/CIARA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CIARA/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘CIARA.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... NOTE +Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' +* DONE +Status: 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CIARA/old/CIARA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CIARA/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘CIARA.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... NOTE +Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' +* DONE +Status: 3 NOTEs + + + + + +``` +# ClustAssess + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/Core-Bioinformatics/ClustAssess +* Source code: https://github.com/cran/ClustAssess +* Date/Publication: 2022-01-26 16:52:46 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "ClustAssess")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ClustAssess/new/ClustAssess.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ClustAssess/DESCRIPTION’ ... OK +... +--- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ + +SUMMARY: processing the following file failed: + ‘ClustAssess.Rmd’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 ERROR, 1 WARNING, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ClustAssess/old/ClustAssess.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ClustAssess/DESCRIPTION’ ... OK +... +--- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ + +SUMMARY: processing the following file failed: + ‘ClustAssess.Rmd’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 ERROR, 1 WARNING, 2 NOTEs + + + + + +``` +# clustree + +
+ +* Version: 0.5.1 +* GitHub: https://github.com/lazappi/clustree +* Source code: https://github.com/cran/clustree +* Date/Publication: 2023-11-05 19:10:02 UTC +* Number of recursive dependencies: 192 + +Run `revdepcheck::cloud_details(, "clustree")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/clustree/new/clustree.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘clustree/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘spelling.R’ + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘clustree.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/clustree/old/clustree.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘clustree/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘spelling.R’ + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘clustree.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# cmprskcoxmsm + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/cmprskcoxmsm +* Date/Publication: 2021-09-04 05:50:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info + +
+ +## In both + +* checking whether package ‘cmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ + + +``` +### CRAN + +``` +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ + + +``` +# combiroc + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/ingmbioinfo/combiroc +* Source code: https://github.com/cran/combiroc +* Date/Publication: 2023-07-06 12:53:12 UTC +* Number of recursive dependencies: 160 + +Run `revdepcheck::cloud_details(, "combiroc")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/combiroc/new/combiroc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘combiroc/DESCRIPTION’ ... OK +... + + When sourcing ‘combiroc_vignette_2.R’: +Error: Cannot find the file(s): "/tmp/RtmpA38BUi/file1c6675fecb04/vignettes/vignettes/atlas_dimplot.png" +Execution halted + + ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK + ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/combiroc/old/combiroc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘combiroc/DESCRIPTION’ ... OK +... + + When sourcing ‘combiroc_vignette_2.R’: +Error: Cannot find the file(s): "/tmp/RtmpD5SHHa/file14446c22f1bc/vignettes/vignettes/atlas_dimplot.png" +Execution halted + + ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK + ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +# conos + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/kharchenkolab/conos +* Source code: https://github.com/cran/conos +* Date/Publication: 2024-02-26 19:30:05 UTC +* Number of recursive dependencies: 239 + +Run `revdepcheck::cloud_details(, "conos")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 2 NOTEs + + + + + +``` +# contrast + +
+ +* Version: 0.24.2 +* GitHub: https://github.com/Alanocallaghan/contrast +* Source code: https://github.com/cran/contrast +* Date/Publication: 2022-10-05 17:20:09 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "contrast")` for more info + +
+ +## In both + +* checking whether package ‘contrast’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ + + +``` +### CRAN + +``` +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ + + +``` +# countland + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/shchurch/countland +* Source code: https://github.com/cran/countland +* Date/Publication: 2024-02-01 18:00:02 UTC +* Number of recursive dependencies: 199 + +Run `revdepcheck::cloud_details(, "countland")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/countland/new/countland.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘countland/DESCRIPTION’ ... OK +... + 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 + 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) + 3. └─base (local) withOneRestart(expr, restarts[[1L]]) + 4. └─base (local) doWithOneRestart(return(expr), restart) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] + Error: Test failures + Execution halted +* DONE +Status: 2 ERRORs, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/countland/old/countland.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘countland/DESCRIPTION’ ... OK +... + 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 + 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) + 3. └─base (local) withOneRestart(expr, restarts[[1L]]) + 4. └─base (local) doWithOneRestart(return(expr), restart) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] + Error: Test failures + Execution halted +* DONE +Status: 2 ERRORs, 1 NOTE + + + + + +``` +# coxed + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/jkropko/coxed +* Source code: https://github.com/cran/coxed +* Date/Publication: 2020-08-02 01:20:07 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "coxed")` for more info + +
+ +## In both + +* checking whether package ‘coxed’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ + + +``` +### CRAN + +``` +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ + + +``` +# CRMetrics + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/khodosevichlab/CRMetrics +* Source code: https://github.com/cran/CRMetrics +* Date/Publication: 2023-09-01 09:00:06 UTC +* Number of recursive dependencies: 235 + +Run `revdepcheck::cloud_details(, "CRMetrics")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ggpmisc’ + +Package suggested but not available for checking: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ggpmisc’ + +Package suggested but not available for checking: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# csmpv + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/csmpv +* Date/Publication: 2024-03-01 18:12:44 UTC +* Number of recursive dependencies: 175 + +Run `revdepcheck::cloud_details(, "csmpv")` for more info + +
+ +## In both + +* checking whether package ‘csmpv’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csmpv’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ + + +``` +### CRAN + +``` +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ + + +``` +# ctsem + +
+ +* Version: 3.10.0 +* GitHub: https://github.com/cdriveraus/ctsem +* Source code: https://github.com/cran/ctsem +* Date/Publication: 2024-05-09 14:40:03 UTC +* Number of recursive dependencies: 159 + +Run `revdepcheck::cloud_details(, "ctsem")` for more info + +
+ +## In both + +* checking whether package ‘ctsem’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ + + +``` +### CRAN + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ + + +``` +# CytoSimplex + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/welch-lab/CytoSimplex +* Source code: https://github.com/cran/CytoSimplex +* Date/Publication: 2023-12-15 09:30:06 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "CytoSimplex")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/CytoSimplex/new/CytoSimplex.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CytoSimplex/old/CytoSimplex.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# DepthProc + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "DepthProc")` for more info + +
+ +## In both + +* checking whether package ‘DepthProc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ + + +``` +### CRAN + +``` +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ + + +``` +# DIscBIO + +
+ +* Version: 1.2.2 +* GitHub: https://github.com/ocbe-uio/DIscBIO +* Source code: https://github.com/cran/DIscBIO +* Date/Publication: 2023-11-06 10:50:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "DIscBIO")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/DIscBIO/new/DIscBIO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DIscBIO/DESCRIPTION’ ... OK +... +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking examples ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/DIscBIO/old/DIscBIO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DIscBIO/DESCRIPTION’ ... OK +... +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking examples ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# DR.SC + +
+ +* Version: 3.4 +* GitHub: https://github.com/feiyoung/DR.SC +* Source code: https://github.com/cran/DR.SC +* Date/Publication: 2024-03-19 08:40:02 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "DR.SC")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DR.SC/DESCRIPTION’ ... OK +... +* this is package ‘DR.SC’ version ‘3.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DR.SC/DESCRIPTION’ ... OK +... +* this is package ‘DR.SC’ version ‘3.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# dyngen + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/dynverse/dyngen +* Source code: https://github.com/cran/dyngen +* Date/Publication: 2022-10-12 15:22:39 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "dyngen")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/dyngen/new/dyngen.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dyngen/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘getting_started.html.asis’ using ‘UTF-8’... OK + ‘installation.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/dyngen/old/dyngen.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dyngen/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘getting_started.html.asis’ using ‘UTF-8’... OK + ‘installation.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# EcoEnsemble + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/EcoEnsemble +* Date/Publication: 2023-09-18 11:50:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info + +
+ +## In both + +* checking whether package ‘EcoEnsemble’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +stanExports_ensemble_model_hierarchical.cc:32:1: fatal error: error writing to /tmp/ccqp74mc.s: Cannot allocate memory + 32 | } + | ^ +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ + + +``` +### CRAN + +``` +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ + + +``` +# ecolottery + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/frmunoz/ecolottery +* Source code: https://github.com/cran/ecolottery +* Date/Publication: 2017-07-03 11:01:29 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "ecolottery")` for more info + +
+ +## In both + +* checking whether package ‘ecolottery’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ + + +``` +### CRAN + +``` +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ + + +``` +# EpiEstim + +
+ +* Version: 2.2-4 +* GitHub: https://github.com/mrc-ide/EpiEstim +* Source code: https://github.com/cran/EpiEstim +* Date/Publication: 2021-01-07 16:20:10 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "EpiEstim")` for more info + +
+ +## In both + +* checking whether package ‘EpiEstim’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ + + +``` +### CRAN + +``` +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ + + +``` +# evolqg + +
+ +* Version: 0.3-4 +* GitHub: https://github.com/lem-usp/evolqg +* Source code: https://github.com/cran/evolqg +* Date/Publication: 2023-12-05 15:20:12 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "evolqg")` for more info + +
+ +## In both + +* checking whether package ‘evolqg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ + + +``` +### CRAN + +``` +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ + + +``` +# ForecastComb + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/ceweiss/ForecastComb +* Source code: https://github.com/cran/ForecastComb +* Date/Publication: 2018-08-07 13:50:08 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "ForecastComb")` for more info + +
+ +## In both + +* checking whether package ‘ForecastComb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ + + +``` +### CRAN + +``` +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ + + +``` +# gapfill + +
+ +* Version: 0.9.6-1 +* GitHub: https://github.com/florafauna/gapfill +* Source code: https://github.com/cran/gapfill +* Date/Publication: 2021-02-12 10:10:05 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "gapfill")` for more info + +
+ +## In both + +* checking whether package ‘gapfill’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'raster', 'doParallel', 'doMPI' + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ + + +``` +### CRAN + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ + + +``` +# GeomComb + +
+ +* Version: 1.0 +* GitHub: https://github.com/ceweiss/GeomComb +* Source code: https://github.com/cran/GeomComb +* Date/Publication: 2016-11-27 16:02:26 +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "GeomComb")` for more info + +
+ +## In both + +* checking whether package ‘GeomComb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ + + +``` +### CRAN + +``` +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ + + +``` +# geostan + +
+ +* Version: 0.6.1 +* GitHub: https://github.com/ConnorDonegan/geostan +* Source code: https://github.com/cran/geostan +* Date/Publication: 2024-05-10 22:23:01 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "geostan")` for more info + +
+ +## Newly broken + +* checking whether package ‘geostan’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 129.8Mb + sub-directories of 1Mb or more: + libs 127.6Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory + 32 | } + | ^ +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 +ERROR: compilation failed for package ‘geostan’ +* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ + + +``` +### CRAN + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** help +*** installing help indices +*** copying figures +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (geostan) + + +``` +# ggrcs + +
+ +* Version: 0.3.8 +* GitHub: NA +* Source code: https://github.com/cran/ggrcs +* Date/Publication: 2024-01-30 03:20:08 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "ggrcs")` for more info + +
+ +## In both + +* checking whether package ‘ggrcs’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ + + +``` +### CRAN + +``` +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ + + +``` +# ggrisk + +
+ +* Version: 1.3 +* GitHub: https://github.com/yikeshu0611/ggrisk +* Source code: https://github.com/cran/ggrisk +* Date/Publication: 2021-08-09 07:40:06 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggrisk")` for more info + +
+ +## In both + +* checking whether package ‘ggrisk’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ + + +``` +### CRAN + +``` +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ + + +``` +# ggsector + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/yanpd01/ggsector +* Source code: https://github.com/cran/ggsector +* Date/Publication: 2022-12-05 15:20:02 UTC +* Number of recursive dependencies: 159 + +Run `revdepcheck::cloud_details(, "ggsector")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ggsector/new/ggsector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ggsector/DESCRIPTION’ ... OK +... +* this is package ‘ggsector’ version ‘1.6.6’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ggsector/old/ggsector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ggsector/DESCRIPTION’ ... OK +... +* this is package ‘ggsector’ version ‘1.6.6’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# gJLS2 + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/gJLS2 +* Date/Publication: 2021-09-30 09:00:05 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "gJLS2")` for more info + +
+ +## In both + +* checking whether package ‘gJLS2’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ + + +``` +### CRAN + +``` +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ + + +``` +# grandR + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/erhard-lab/grandR +* Source code: https://github.com/cran/grandR +* Date/Publication: 2024-02-15 15:30:02 UTC +* Number of recursive dependencies: 265 + +Run `revdepcheck::cloud_details(, "grandR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘grandR/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘getting-started.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘grandR/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘getting-started.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# Greg + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/gforge/Greg +* Source code: https://github.com/cran/Greg +* Date/Publication: 2024-01-29 13:30:21 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "Greg")` for more info + +
+ +## In both + +* checking whether package ‘Greg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ + + +``` +### CRAN + +``` +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ + + +``` +# greport + +
+ +* Version: 0.7-4 +* GitHub: https://github.com/harrelfe/greport +* Source code: https://github.com/cran/greport +* Date/Publication: 2023-09-02 22:20:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "greport")` for more info + +
+ +## In both + +* checking whether package ‘greport’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ + + +``` +### CRAN + +``` +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ + + +``` +# harmony + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/harmony +* Date/Publication: 2023-11-29 08:30:04 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "harmony")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/harmony/new/harmony.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘harmony/DESCRIPTION’ ... OK +... +--- finished re-building ‘quickstart.Rmd’ + +SUMMARY: processing the following file failed: + ‘Seurat.Rmd’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 WARNING, 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/harmony/old/harmony.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘harmony/DESCRIPTION’ ... OK +... +--- finished re-building ‘quickstart.Rmd’ + +SUMMARY: processing the following file failed: + ‘Seurat.Rmd’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 WARNING, 3 NOTEs + + + + + +``` +# hettx + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "hettx")` for more info + +
+ +## In both + +* checking whether package ‘hettx’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ + + +``` +### CRAN + +``` +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ + + +``` +# hIRT + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/xiangzhou09/hIRT +* Source code: https://github.com/cran/hIRT +* Date/Publication: 2020-03-26 17:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "hIRT")` for more info + +
+ +## In both + +* checking whether package ‘hIRT’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ + + +``` +### CRAN + +``` +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ + + +``` +# Hmsc + +
+ +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "Hmsc")` for more info + +
+ +## In both + +* checking whether package ‘Hmsc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ + + +``` +### CRAN + +``` +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ + + +``` +# iNZightPlots + +
+ +* Version: 2.15.3 +* GitHub: https://github.com/iNZightVIT/iNZightPlots +* Source code: https://github.com/cran/iNZightPlots +* Date/Publication: 2023-10-14 05:00:02 UTC +* Number of recursive dependencies: 162 + +Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info + +
+ +## In both + +* checking whether package ‘iNZightPlots’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/iNZightPlots’ + + +``` +### CRAN + +``` +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/old/iNZightPlots.Rcheck/iNZightPlots’ + + +``` +# iNZightRegression + +
+ +* Version: 1.3.4 +* GitHub: https://github.com/iNZightVIT/iNZightRegression +* Source code: https://github.com/cran/iNZightRegression +* Date/Publication: 2024-04-05 02:32:59 UTC +* Number of recursive dependencies: 154 + +Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info + +
+ +## In both + +* checking whether package ‘iNZightRegression’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/iNZightRegression’ + + +``` +### CRAN + +``` +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/old/iNZightRegression.Rcheck/iNZightRegression’ + + +``` +# IRexamples + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/vinhdizzo/IRexamples +* Source code: https://github.com/cran/IRexamples +* Date/Publication: 2023-10-06 06:40:02 UTC +* Number of recursive dependencies: 185 + +Run `revdepcheck::cloud_details(, "IRexamples")` for more info + +
+ +## In both + +* checking whether package ‘IRexamples’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ + + +``` +### CRAN + +``` +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ + + +``` +# joineRML + +
+ +* Version: 0.4.6 +* GitHub: https://github.com/graemeleehickey/joineRML +* Source code: https://github.com/cran/joineRML +* Date/Publication: 2023-01-20 04:50:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "joineRML")` for more info + +
+ +## In both + +* checking whether package ‘joineRML’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ + + +``` +### CRAN + +``` +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ + + +``` +# JWileymisc + +
+ +* Version: 1.4.1 +* GitHub: https://github.com/JWiley/JWileymisc +* Source code: https://github.com/cran/JWileymisc +* Date/Publication: 2023-10-05 04:50:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "JWileymisc")` for more info + +
+ +## In both + +* checking whether package ‘JWileymisc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ + + +``` +### CRAN + +``` +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ + + +``` +# kmc + +
+ +* Version: 0.4-2 +* GitHub: https://github.com/yfyang86/kmc +* Source code: https://github.com/cran/kmc +* Date/Publication: 2022-11-22 08:30:02 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "kmc")` for more info + +
+ +## In both + +* checking whether package ‘kmc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ + + +``` +### CRAN + +``` +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ + + +``` +# L2E + +
+ +* Version: 2.0 +* GitHub: NA +* Source code: https://github.com/cran/L2E +* Date/Publication: 2022-09-08 21:13:00 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "L2E")` for more info + +
+ +## In both + +* checking whether package ‘L2E’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Execution halted +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ + + +``` +### CRAN + +``` +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Execution halted +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ + + +``` +# llbayesireg + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/llbayesireg +* Date/Publication: 2019-04-04 16:20:03 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "llbayesireg")` for more info + +
+ +## In both + +* checking whether package ‘llbayesireg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/llbayesireg’ + + +``` +### CRAN + +``` +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ + + +``` +# LorenzRegression + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/LorenzRegression +* Date/Publication: 2023-02-28 17:32:34 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info + +
+ +## In both + +* checking whether package ‘LorenzRegression’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/LorenzRegression’ + + +``` +### CRAN + +``` +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/old/LorenzRegression.Rcheck/LorenzRegression’ + + +``` +# lsirm12pl + +
+ +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/lsirm12pl +* Date/Publication: 2023-06-22 14:12:35 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info + +
+ +## In both + +* checking whether package ‘lsirm12pl’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/lsirm12pl’ + + +``` +### CRAN + +``` +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ + + +``` +# mbsts + +
+ +* Version: 3.0 +* GitHub: NA +* Source code: https://github.com/cran/mbsts +* Date/Publication: 2023-01-07 01:10:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "mbsts")` for more info + +
+ +## In both + +* checking whether package ‘mbsts’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/mbsts’ + + +``` +### CRAN + +``` +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ + + +``` +# MendelianRandomization + +
+ +* Version: 0.10.0 +* GitHub: NA +* Source code: https://github.com/cran/MendelianRandomization +* Date/Publication: 2024-04-12 10:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info + +
+ +## In both + +* checking whether package ‘MendelianRandomization’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ + + +``` +### CRAN + +``` +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ + + +``` +# MetabolicSurv + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv +* Source code: https://github.com/cran/MetabolicSurv +* Date/Publication: 2021-06-11 08:30:02 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info + +
+ +## In both + +* checking whether package ‘MetabolicSurv’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ + + +``` +### CRAN + +``` +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ + + +``` +# miWQS + +
+ +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "miWQS")` for more info + +
+ +## In both + +* checking whether package ‘miWQS’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ + + +``` +### CRAN + +``` +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ + + +``` +# mlmts + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/mlmts +* Date/Publication: 2023-01-22 21:30:02 UTC +* Number of recursive dependencies: 241 + +Run `revdepcheck::cloud_details(, "mlmts")` for more info + +
+ +## In both + +* checking whether package ‘mlmts’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ +Execution halted +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’ + + +``` +### CRAN + +``` +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ +Execution halted +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’ + + +``` +# MRZero + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/MRZero +* Date/Publication: 2024-04-14 09:30:03 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "MRZero")` for more info + +
+ +## In both + +* checking whether package ‘MRZero’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ + + +``` +### CRAN + +``` +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ + + +``` +# Multiaovbay + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/Multiaovbay +* Date/Publication: 2023-03-17 17:20:02 UTC +* Number of recursive dependencies: 161 + +Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info + +
+ +## In both + +* checking whether package ‘Multiaovbay’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ + + +``` +### CRAN + +``` +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ + + +``` +# multilevelTools + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/JWiley/multilevelTools +* Source code: https://github.com/cran/multilevelTools +* Date/Publication: 2020-03-04 09:50:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "multilevelTools")` for more info + +
+ +## In both + +* checking whether package ‘multilevelTools’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/multilevelTools’ + + +``` +### CRAN + +``` +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ + + +``` +# multinma + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/dmphillippo/multinma +* Source code: https://github.com/cran/multinma +* Date/Publication: 2024-05-07 15:40:02 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "multinma")` for more info + +
+ +## In both + +* checking whether package ‘multinma’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ + + +``` +### CRAN + +``` +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ + + +``` +# NCA + +
+ +* Version: 4.0.1 +* GitHub: NA +* Source code: https://github.com/cran/NCA +* Date/Publication: 2024-02-23 09:30:15 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "NCA")` for more info + +
+ +## In both + +* checking whether package ‘NCA’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/NCA/new/NCA.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/new/NCA.Rcheck/NCA’ + + +``` +### CRAN + +``` +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/old/NCA.Rcheck/NCA’ + + +``` +# netcmc + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/netcmc +* Date/Publication: 2022-11-08 22:30:15 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "netcmc")` for more info + +
+ +## In both + +* checking whether package ‘netcmc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’ + + +``` +### CRAN + +``` +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’ + + +``` +# NetworkChange + +
+ +* Version: 0.8 +* GitHub: https://github.com/jongheepark/NetworkChange +* Source code: https://github.com/cran/NetworkChange +* Date/Publication: 2022-03-04 07:30:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "NetworkChange")` for more info + +
+ +## In both + +* checking whether package ‘NetworkChange’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’ + + +``` +### CRAN + +``` +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’ + + +``` +# nlmeVPC + +
+ +* Version: 2.6 +* GitHub: NA +* Source code: https://github.com/cran/nlmeVPC +* Date/Publication: 2022-12-22 05:20:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info + +
+ +## In both + +* checking whether package ‘nlmeVPC’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs +** R +** data +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/nlmeVPC’ + + +``` +### CRAN + +``` +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs +** R +** data +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/nlmeVPC’ + + +``` +# NMADiagT + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/NMADiagT +* Date/Publication: 2020-02-26 07:00:02 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "NMADiagT")` for more info + +
+ +## In both + +* checking whether package ‘NMADiagT’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/NMADiagT’ + + +``` +### CRAN + +``` +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ + + +``` +# optweight + +
+ +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/optweight +* Date/Publication: 2019-09-16 15:40:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "optweight")` for more info + +
+ +## In both + +* checking whether package ‘optweight’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ + + +``` +### CRAN + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ + + +``` +# OVtool + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "OVtool")` for more info + +
+ +## In both + +* checking whether package ‘OVtool’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ + + +``` +### CRAN + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ + + +``` +# paths + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/paths +* Date/Publication: 2021-06-18 08:40:02 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "paths")` for more info + +
+ +## In both + +* checking whether package ‘paths’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ + + +``` +### CRAN + +``` +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ + + +``` +# PLMIX + +
+ +* Version: 2.1.1 +* GitHub: NA +* Source code: https://github.com/cran/PLMIX +* Date/Publication: 2019-09-04 11:50:02 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "PLMIX")` for more info + +
+ +## In both + +* checking whether package ‘PLMIX’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/PLMIX’ + + +``` +### CRAN + +``` +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ + + +``` +# popstudy + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/popstudy +* Date/Publication: 2023-10-17 23:50:02 UTC +* Number of recursive dependencies: 236 + +Run `revdepcheck::cloud_details(, "popstudy")` for more info + +
+ +## In both + +* checking whether package ‘popstudy’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/popstudy’ + + +``` +### CRAN + +``` +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/old/popstudy.Rcheck/popstudy’ + + +``` +# pould + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/pould +* Date/Publication: 2020-10-16 13:50:03 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "pould")` for more info + +
+ +## In both + +* checking whether package ‘pould’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ + + +``` +### CRAN + +``` +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ + + +``` +# powerly + +
+ +* Version: 1.8.6 +* GitHub: https://github.com/mihaiconstantin/powerly +* Source code: https://github.com/cran/powerly +* Date/Publication: 2022-09-09 14:10:01 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "powerly")` for more info + +
+ +## In both + +* checking whether package ‘powerly’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/powerly/new/powerly.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/new/powerly.Rcheck/powerly’ + + +``` +### CRAN + +``` +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/old/powerly.Rcheck/powerly’ + + +``` +# pre + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/marjoleinF/pre +* Source code: https://github.com/cran/pre +* Date/Publication: 2024-01-12 19:30:02 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "pre")` for more info + +
+ +## In both + +* checking whether package ‘pre’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pre/new/pre.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/new/pre.Rcheck/pre’ + + +``` +### CRAN + +``` +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/old/pre.Rcheck/pre’ + + +``` +# PRECAST + +
+ +* Version: 1.6.5 +* GitHub: https://github.com/feiyoung/PRECAST +* Source code: https://github.com/cran/PRECAST +* Date/Publication: 2024-03-19 08:30:02 UTC +* Number of recursive dependencies: 225 + +Run `revdepcheck::cloud_details(, "PRECAST")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/PRECAST/new/PRECAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PRECAST/DESCRIPTION’ ... OK +... +* this is package ‘PRECAST’ version ‘1.6.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'DR.SC' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/PRECAST/old/PRECAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PRECAST/DESCRIPTION’ ... OK +... +* this is package ‘PRECAST’ version ‘1.6.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'DR.SC' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# ProFAST + +
+ +* Version: 1.4 +* GitHub: https://github.com/feiyoung/ProFAST +* Source code: https://github.com/cran/ProFAST +* Date/Publication: 2024-03-18 08:10:06 UTC +* Number of recursive dependencies: 253 + +Run `revdepcheck::cloud_details(, "ProFAST")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ProFAST/new/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ProFAST/old/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# pscore + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/JWiley/score-project +* Source code: https://github.com/cran/pscore +* Date/Publication: 2022-05-13 22:30:02 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "pscore")` for more info + +
+ +## In both + +* checking whether package ‘pscore’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pscore/new/pscore.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/new/pscore.Rcheck/pscore’ + + +``` +### CRAN + +``` +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ + + +``` +# psfmi + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/mwheymans/psfmi +* Source code: https://github.com/cran/psfmi +* Date/Publication: 2023-06-17 22:40:02 UTC +* Number of recursive dependencies: 160 + +Run `revdepcheck::cloud_details(, "psfmi")` for more info + +
+ +## In both + +* checking whether package ‘psfmi’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ + + +``` +### CRAN + +``` +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ + + +``` +# qreport + +
+ +* Version: 1.0-0 +* GitHub: NA +* Source code: https://github.com/cran/qreport +* Date/Publication: 2023-09-12 22:10:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "qreport")` for more info + +
+ +## In both + +* checking whether package ‘qreport’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ + + +``` +### CRAN + +``` +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ + + +``` +# qris + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/Kyuhyun07/qris +* Source code: https://github.com/cran/qris +* Date/Publication: 2024-03-05 14:40:03 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "qris")` for more info + +
+ +## In both + +* checking whether package ‘qris’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ + + +``` +### CRAN + +``` +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ + + +``` +# qte + +
+ +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/qte +* Date/Publication: 2022-09-01 14:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "qte")` for more info + +
+ +## In both + +* checking whether package ‘qte’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ + + +``` +### CRAN + +``` +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ + + +``` +# quid + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/quid +* Date/Publication: 2021-12-09 09:00:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "quid")` for more info + +
+ +## In both + +* checking whether package ‘quid’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/quid/new/quid.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/new/quid.Rcheck/quid’ + + +``` +### CRAN + +``` +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ + + +``` +# RATest + +
+ +* Version: 0.1.10 +* GitHub: https://github.com/ignaciomsarmiento/RATest +* Source code: https://github.com/cran/RATest +* Date/Publication: 2022-09-29 04:30:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "RATest")` for more info + +
+ +## In both + +* checking whether package ‘RATest’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ + + +``` +### CRAN + +``` +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ + + +``` +# RcmdrPlugin.RiskDemo + +
+ +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 208 + +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info + +
+ +## In both + +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + +``` +### CRAN + +``` +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + +``` +# rddtools + +
+ +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "rddtools")` for more info + +
+ +## In both + +* checking whether package ‘rddtools’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ + + +``` +### CRAN + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ + + +``` +# riskRegression + +
+ +* Version: 2023.12.21 +* GitHub: https://github.com/tagteam/riskRegression +* Source code: https://github.com/cran/riskRegression +* Date/Publication: 2023-12-19 17:00:02 UTC +* Number of recursive dependencies: 186 + +Run `revdepcheck::cloud_details(, "riskRegression")` for more info + +
+ +## In both + +* checking whether package ‘riskRegression’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ + + +``` +### CRAN + +``` +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ + + +``` +# rliger + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/welch-lab/liger +* Source code: https://github.com/cran/rliger +* Date/Publication: 2024-04-04 23:20:02 UTC +* Number of recursive dependencies: 218 + +Run `revdepcheck::cloud_details(, "rliger")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/rliger/new/rliger.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘rliger/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘liger-vignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 ERRORs, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/rliger/old/rliger.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘rliger/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘liger-vignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 ERRORs, 2 NOTEs + + + + + +``` +# rms + +
+ +* Version: 6.8-0 +* GitHub: https://github.com/harrelfe/rms +* Source code: https://github.com/cran/rms +* Date/Publication: 2024-03-11 16:20:02 UTC +* Number of recursive dependencies: 154 + +Run `revdepcheck::cloud_details(, "rms")` for more info + +
+ +## In both + +* checking whether package ‘rms’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘rmsb’ + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... +** R +** demo +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ + + +``` +### CRAN + +``` +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... +** R +** demo +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ + + +``` +# rmsb + +
+ +* Version: 1.1-0 +* GitHub: NA +* Source code: https://github.com/cran/rmsb +* Date/Publication: 2024-03-12 15:50:02 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "rmsb")` for more info + +
+ +## In both + +* checking whether package ‘rmsb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked +** using staged installation +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ + + +``` +### CRAN + +``` +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked +** using staged installation +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ + + +``` +# robmed + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/aalfons/robmed +* Source code: https://github.com/cran/robmed +* Date/Publication: 2023-06-16 23:00:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "robmed")` for more info + +
+ +## In both + +* checking whether package ‘robmed’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ + + +``` +### CRAN + +``` +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ + + +``` +# robmedExtra + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2023-06-02 14:40:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "robmedExtra")` for more info + +
+ +## In both + +* checking whether package ‘robmedExtra’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ + + +``` +### CRAN + +``` +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ + + +``` +# RPPanalyzer + +
+ +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/RPPanalyzer +* Date/Publication: 2024-01-25 11:00:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info + +
+ +## In both + +* checking whether package ‘RPPanalyzer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ + + +``` +### CRAN + +``` +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ + + +``` +# rstanarm + +
+ +* Version: 2.32.1 +* GitHub: https://github.com/stan-dev/rstanarm +* Source code: https://github.com/cran/rstanarm +* Date/Publication: 2024-01-18 23:00:03 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "rstanarm")` for more info + +
+ +## In both + +* checking whether package ‘rstanarm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 +rm stan_files/bernoulli.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ + + +``` +### CRAN + +``` +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 +rm stan_files/bernoulli.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ + + +``` +# scCustomize + +
+ +* Version: 2.1.2 +* GitHub: https://github.com/samuel-marsh/scCustomize +* Source code: https://github.com/cran/scCustomize +* Date/Publication: 2024-02-28 19:40:02 UTC +* Number of recursive dependencies: 274 + +Run `revdepcheck::cloud_details(, "scCustomize")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +Package suggested but not available for checking: ‘Nebulosa’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +Package suggested but not available for checking: ‘Nebulosa’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SCdeconR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/Liuy12/SCdeconR +* Source code: https://github.com/cran/SCdeconR +* Date/Publication: 2024-03-22 19:20:02 UTC +* Number of recursive dependencies: 235 + +Run `revdepcheck::cloud_details(, "SCdeconR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCdeconR/DESCRIPTION’ ... OK +... +* this is package ‘SCdeconR’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SCdeconR/old/SCdeconR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCdeconR/DESCRIPTION’ ... OK +... +* this is package ‘SCdeconR’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# scDiffCom + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/scDiffCom +* Date/Publication: 2023-11-03 18:40:02 UTC +* Number of recursive dependencies: 259 + +Run `revdepcheck::cloud_details(, "scDiffCom")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scDiffCom/DESCRIPTION’ ... OK +... +* this is package ‘scDiffCom’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scDiffCom/DESCRIPTION’ ... OK +... +* this is package ‘scDiffCom’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# scGate + +
+ +* Version: 1.6.2 +* GitHub: https://github.com/carmonalab/scGate +* Source code: https://github.com/cran/scGate +* Date/Publication: 2024-04-23 08:50:02 UTC +* Number of recursive dependencies: 178 + +Run `revdepcheck::cloud_details(, "scGate")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scGate/new/scGate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scGate/DESCRIPTION’ ... OK +... +* this is package ‘scGate’ version ‘1.6.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scGate/old/scGate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scGate/DESCRIPTION’ ... OK +... +* this is package ‘scGate’ version ‘1.6.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# scMappR + +
+ +* Version: 1.0.11 +* GitHub: NA +* Source code: https://github.com/cran/scMappR +* Date/Publication: 2023-06-30 08:40:08 UTC +* Number of recursive dependencies: 233 + +Run `revdepcheck::cloud_details(, "scMappR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scMappR/new/scMappR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scMappR/DESCRIPTION’ ... OK +... +* this is package ‘scMappR’ version ‘1.0.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scMappR/old/scMappR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scMappR/DESCRIPTION’ ... OK +... +* this is package ‘scMappR’ version ‘1.0.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SCORPIUS + +
+ +* Version: 1.0.9 +* GitHub: https://github.com/rcannood/SCORPIUS +* Source code: https://github.com/cran/SCORPIUS +* Date/Publication: 2023-08-07 17:30:05 UTC +* Number of recursive dependencies: 202 + +Run `revdepcheck::cloud_details(, "SCORPIUS")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SCORPIUS/new/SCORPIUS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK +... +Run `reticulate::py_last_error()` for details. +Execution halted + + ‘anndata.Rmd’ using ‘UTF-8’... failed + ‘ginhoux.Rmd’ using ‘UTF-8’... OK + ‘simulated-data.Rmd’ using ‘UTF-8’... OK + ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SCORPIUS/old/SCORPIUS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK +... +Run `reticulate::py_last_error()` for details. +Execution halted + + ‘anndata.Rmd’ using ‘UTF-8’... failed + ‘ginhoux.Rmd’ using ‘UTF-8’... OK + ‘simulated-data.Rmd’ using ‘UTF-8’... OK + ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +# scpoisson + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/scpoisson +* Date/Publication: 2022-08-17 06:50:02 UTC +* Number of recursive dependencies: 203 + +Run `revdepcheck::cloud_details(, "scpoisson")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scpoisson/new/scpoisson.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scpoisson/DESCRIPTION’ ... OK +... +* this is package ‘scpoisson’ version ‘0.0.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scpoisson/old/scpoisson.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scpoisson/DESCRIPTION’ ... OK +... +* this is package ‘scpoisson’ version ‘0.0.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'Seurat', 'SeuratObject' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SCpubr + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/enblacar/SCpubr +* Source code: https://github.com/cran/SCpubr +* Date/Publication: 2023-10-11 09:50:02 UTC +* Number of recursive dependencies: 306 + +Run `revdepcheck::cloud_details(, "SCpubr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SCpubr/new/SCpubr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCpubr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘reference_manual.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SCpubr/old/SCpubr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCpubr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘reference_manual.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# scRNAstat + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/scRNAstat +* Date/Publication: 2021-09-22 08:10:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "scRNAstat")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +... +* this is package ‘scRNAstat’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scRNAstat/old/scRNAstat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +... +* this is package ‘scRNAstat’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# sectorgap + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/sectorgap +* Date/Publication: 2024-01-22 17:40:02 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "sectorgap")` for more info + +
+ +## In both + +* checking whether package ‘sectorgap’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/sectorgap/new/sectorgap.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘sectorgap’ ... +** package ‘sectorgap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sectorgap’ +* removing ‘/tmp/workdir/sectorgap/new/sectorgap.Rcheck/sectorgap’ + + +``` +### CRAN + +``` +* installing *source* package ‘sectorgap’ ... +** package ‘sectorgap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sectorgap’ +* removing ‘/tmp/workdir/sectorgap/old/sectorgap.Rcheck/sectorgap’ + + +``` +# SEERaBomb + +
+ +* Version: 2019.2 +* GitHub: NA +* Source code: https://github.com/cran/SEERaBomb +* Date/Publication: 2019-12-12 18:50:03 UTC +* Number of recursive dependencies: 184 + +Run `revdepcheck::cloud_details(, "SEERaBomb")` for more info + +
+ +## In both + +* checking whether package ‘SEERaBomb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SEERaBomb/new/SEERaBomb.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SEERaBomb’ ... +** package ‘SEERaBomb’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SEERaBomb.so RcppExports.o SEERaBomb_init.o fillPYM.o -L/opt/R/4.3.1/lib/R/lib -lR +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘demography’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘SEERaBomb’ +* removing ‘/tmp/workdir/SEERaBomb/new/SEERaBomb.Rcheck/SEERaBomb’ + + +``` +### CRAN + +``` +* installing *source* package ‘SEERaBomb’ ... +** package ‘SEERaBomb’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SEERaBomb.so RcppExports.o SEERaBomb_init.o fillPYM.o -L/opt/R/4.3.1/lib/R/lib -lR +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘demography’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘SEERaBomb’ +* removing ‘/tmp/workdir/SEERaBomb/old/SEERaBomb.Rcheck/SEERaBomb’ + + +``` +# semicmprskcoxmsm + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/semicmprskcoxmsm +* Date/Publication: 2022-04-29 23:40:02 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info + +
+ +## In both + +* checking whether package ‘semicmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +### CRAN + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/old/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +# SensMap + +
+ +* Version: 0.7 +* GitHub: https://github.com/IbtihelRebhi/SensMap +* Source code: https://github.com/cran/SensMap +* Date/Publication: 2022-07-04 19:00:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "SensMap")` for more info + +
+ +## In both + +* checking whether package ‘SensMap’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/SensMap’ + + +``` +### CRAN + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ + + +``` +# Signac + +
+ +* Version: 1.13.0 +* GitHub: https://github.com/stuart-lab/signac +* Source code: https://github.com/cran/Signac +* Date/Publication: 2024-04-04 02:42:57 UTC +* Number of recursive dependencies: 249 + +Run `revdepcheck::cloud_details(, "Signac")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SeuratObject’ + +Package suggested but not available for checking: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SeuratObject’ + +Package suggested but not available for checking: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SimplyAgree + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/arcaldwell49/SimplyAgree +* Source code: https://github.com/cran/SimplyAgree +* Date/Publication: 2024-03-21 14:20:06 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info + +
+ +## In both + +* checking whether package ‘SimplyAgree’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SimplyAgree/new/SimplyAgree.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SimplyAgree’ ... +** package ‘SimplyAgree’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SimplyAgree’ +* removing ‘/tmp/workdir/SimplyAgree/new/SimplyAgree.Rcheck/SimplyAgree’ + + +``` +### CRAN + +``` +* installing *source* package ‘SimplyAgree’ ... +** package ‘SimplyAgree’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SimplyAgree’ +* removing ‘/tmp/workdir/SimplyAgree/old/SimplyAgree.Rcheck/SimplyAgree’ + + +``` +# sMSROC + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/sMSROC +* Date/Publication: 2023-12-07 15:50:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "sMSROC")` for more info + +
+ +## In both + +* checking whether package ‘sMSROC’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘sMSROC’ ... +** package ‘sMSROC’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sMSROC’ +* removing ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/sMSROC’ + + +``` +### CRAN + +``` +* installing *source* package ‘sMSROC’ ... +** package ‘sMSROC’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sMSROC’ +* removing ‘/tmp/workdir/sMSROC/old/sMSROC.Rcheck/sMSROC’ + + +``` +# SNPassoc + +
+ +* Version: 2.1-0 +* GitHub: https://github.com/isglobal-brge/SNPassoc +* Source code: https://github.com/cran/SNPassoc +* Date/Publication: 2022-12-14 20:20:02 UTC +* Number of recursive dependencies: 166 + +Run `revdepcheck::cloud_details(, "SNPassoc")` for more info + +
+ +## In both + +* checking whether package ‘SNPassoc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SNPassoc’ ... +** package ‘SNPassoc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SNPassoc’ +* removing ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/SNPassoc’ + + +``` +### CRAN + +``` +* installing *source* package ‘SNPassoc’ ... +** package ‘SNPassoc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SNPassoc’ +* removing ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/SNPassoc’ + + +``` +# snplinkage + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/snplinkage +* Date/Publication: 2023-05-04 08:10:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "snplinkage")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/snplinkage/new/snplinkage.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘snplinkage/DESCRIPTION’ ... OK +... +* this is package ‘snplinkage’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘GWASTools’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/snplinkage/old/snplinkage.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘snplinkage/DESCRIPTION’ ... OK +... +* this is package ‘snplinkage’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘GWASTools’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SoupX + +
+ +* Version: 1.6.2 +* GitHub: https://github.com/constantAmateur/SoupX +* Source code: https://github.com/cran/SoupX +* Date/Publication: 2022-11-01 14:00:03 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "SoupX")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SoupX/new/SoupX.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SoupX/DESCRIPTION’ ... OK +... +* this is package ‘SoupX’ version ‘1.6.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SoupX/old/SoupX.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SoupX/DESCRIPTION’ ... OK +... +* this is package ‘SoupX’ version ‘1.6.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘Seurat’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# SpaDES.core + +
+ +* Version: 2.0.5 +* GitHub: https://github.com/PredictiveEcology/SpaDES.core +* Source code: https://github.com/cran/SpaDES.core +* Date/Publication: 2024-04-25 17:20:02 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info + +
+ +## In both + +* checking whether package ‘SpaDES.core’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SpaDES.core’ ... +** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ +Error in get(x, envir = ns, inherits = FALSE) : + object '.addingToMemoisedMsg' not found +Error: unable to load R code in package ‘SpaDES.core’ +Execution halted +ERROR: lazy loading failed for package ‘SpaDES.core’ +* removing ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core’ + + +``` +### CRAN + +``` +* installing *source* package ‘SpaDES.core’ ... +** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ +Error in get(x, envir = ns, inherits = FALSE) : + object '.addingToMemoisedMsg' not found +Error: unable to load R code in package ‘SpaDES.core’ +Execution halted +ERROR: lazy loading failed for package ‘SpaDES.core’ +* removing ‘/tmp/workdir/SpaDES.core/old/SpaDES.core.Rcheck/SpaDES.core’ + + +``` +# sparsereg + +
+ +* Version: 1.2 +* GitHub: NA +* Source code: https://github.com/cran/sparsereg +* Date/Publication: 2016-03-10 23:32:18 +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "sparsereg")` for more info + +
+ +## In both + +* checking whether package ‘sparsereg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘sparsereg’ ... +** package ‘sparsereg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sparsereg/new/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/sparsereg’ + + +``` +### CRAN + +``` +* installing *source* package ‘sparsereg’ ... +** package ‘sparsereg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ + + +``` +# SPECK + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/SPECK +* Date/Publication: 2023-11-17 17:30:02 UTC +* Number of recursive dependencies: 161 + +Run `revdepcheck::cloud_details(, "SPECK")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SPECK/new/SPECK.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SPECK/DESCRIPTION’ ... OK +... +Package required but not available: ‘Seurat’ + +Package required and available but unsuitable version: ‘Matrix’ + +Package suggested but not available for checking: ‘SeuratObject’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SPECK/old/SPECK.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SPECK/DESCRIPTION’ ... OK +... +Package required but not available: ‘Seurat’ + +Package required and available but unsuitable version: ‘Matrix’ + +Package suggested but not available for checking: ‘SeuratObject’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# spikeSlabGAM + +
+ +* Version: 1.1-19 +* GitHub: https://github.com/fabian-s/spikeSlabGAM +* Source code: https://github.com/cran/spikeSlabGAM +* Date/Publication: 2022-06-10 15:50:07 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "spikeSlabGAM")` for more info + +
+ +## In both + +* checking whether package ‘spikeSlabGAM’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘spikeSlabGAM’ ... +** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/00LOCK-spikeSlabGAM/00new/spikeSlabGAM/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘spikeSlabGAM’ +* removing ‘/tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/spikeSlabGAM’ ``` ### CRAN ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘spikeSlabGAM’ ... +** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_namespace::model_ensemble_model; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/spikeSlabGAM/old/spikeSlabGAM.Rcheck/00LOCK-spikeSlabGAM/00new/spikeSlabGAM/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘spikeSlabGAM’ +* removing ‘/tmp/workdir/spikeSlabGAM/old/spikeSlabGAM.Rcheck/spikeSlabGAM’ ``` -# geostan +# statsr
-* Version: 0.5.4 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-03-03 15:22:39 UTC -* Number of recursive dependencies: 108 +* Version: 0.3.0 +* GitHub: https://github.com/StatsWithR/statsr +* Source code: https://github.com/cran/statsr +* Date/Publication: 2021-01-22 20:40:03 UTC +* Number of recursive dependencies: 98 -Run `revdepcheck::cloud_details(, "geostan")` for more info +Run `revdepcheck::cloud_details(, "statsr")` for more info
## In both -* checking whether package ‘geostan’ can be installed ... ERROR +* checking whether package ‘statsr’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/statsr/new/statsr.Rcheck/00install.out’ for details. ``` ## Installation @@ -337,68 +9005,52 @@ Run `revdepcheck::cloud_details(, "geostan")` for more info ### Devel ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘statsr’ ... +** package ‘statsr’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘statsr’ +* removing ‘/tmp/workdir/statsr/new/statsr.Rcheck/statsr’ ``` ### CRAN ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘statsr’ ... +** package ‘statsr’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/old/geostan.Rcheck/geostan’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘statsr’ +* removing ‘/tmp/workdir/statsr/old/statsr.Rcheck/statsr’ ``` -# grandR +# streamDAG
-* Version: 0.2.5 -* GitHub: https://github.com/erhard-lab/grandR -* Source code: https://github.com/cran/grandR -* Date/Publication: 2024-02-15 15:30:02 UTC -* Number of recursive dependencies: 266 +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/streamDAG +* Date/Publication: 2023-10-06 18:50:02 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "grandR")` for more info +Run `revdepcheck::cloud_details(, "streamDAG")` for more info
@@ -407,27 +9059,25 @@ Run `revdepcheck::cloud_details(, "grandR")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’ +* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 2 NOTEs +Status: 1 ERROR @@ -437,53 +9087,57 @@ Status: 2 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’ +* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 2 NOTEs +Status: 1 ERROR ``` -# multilevelcoda +# survHE
-* Version: 1.2.3 -* GitHub: https://github.com/florale/multilevelcoda -* Source code: https://github.com/cran/multilevelcoda -* Date/Publication: 2024-03-10 23:00:03 UTC -* Number of recursive dependencies: 159 +* Version: 2.0.1 +* GitHub: https://github.com/giabaio/survHE +* Source code: https://github.com/cran/survHE +* Date/Publication: 2023-03-19 22:10:02 UTC +* Number of recursive dependencies: 130 -Run `revdepcheck::cloud_details(, "multilevelcoda")` for more info +Run `revdepcheck::cloud_details(, "survHE")` for more info
## In both -* checking whether package ‘multilevelcoda’ can be installed ... ERROR +* checking whether package ‘survHE’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multilevelcoda/new/multilevelcoda.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/survHE/new/survHE.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Packages suggested but not available for checking: + 'survHEinla', 'survHEhmc' ``` ## Installation @@ -491,59 +9145,63 @@ Run `revdepcheck::cloud_details(, "multilevelcoda")` for more info ### Devel ``` -* installing *source* package ‘multilevelcoda’ ... -** package ‘multilevelcoda’ successfully unpacked and MD5 sums checked +* installing *source* package ‘survHE’ ... +** package ‘survHE’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: object ‘launch_shinystan’ is not exported by 'namespace:brms' +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelcoda’ -* removing ‘/tmp/workdir/multilevelcoda/new/multilevelcoda.Rcheck/multilevelcoda’ +ERROR: lazy loading failed for package ‘survHE’ +* removing ‘/tmp/workdir/survHE/new/survHE.Rcheck/survHE’ ``` ### CRAN ``` -* installing *source* package ‘multilevelcoda’ ... -** package ‘multilevelcoda’ successfully unpacked and MD5 sums checked +* installing *source* package ‘survHE’ ... +** package ‘survHE’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: object ‘launch_shinystan’ is not exported by 'namespace:brms' +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelcoda’ -* removing ‘/tmp/workdir/multilevelcoda/old/multilevelcoda.Rcheck/multilevelcoda’ +ERROR: lazy loading failed for package ‘survHE’ +* removing ‘/tmp/workdir/survHE/old/survHE.Rcheck/survHE’ ``` -# multinma +# survidm
-* Version: 0.6.1 -* GitHub: https://github.com/dmphillippo/multinma -* Source code: https://github.com/cran/multinma -* Date/Publication: 2024-03-06 01:00:05 UTC -* Number of recursive dependencies: 151 +* Version: 1.3.2 +* GitHub: NA +* Source code: https://github.com/cran/survidm +* Date/Publication: 2021-06-24 23:20:02 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "multinma")` for more info +Run `revdepcheck::cloud_details(, "survidm")` for more info
## In both -* checking whether package ‘multinma’ can be installed ... ERROR +* checking whether package ‘survidm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/survidm/new/survidm.Rcheck/00install.out’ for details. ``` ## Installation @@ -551,77 +9209,73 @@ Run `revdepcheck::cloud_details(, "multinma")` for more info ### Devel ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘survidm’ ... +** package ‘survidm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -In file included from stanExports_survival_mspline.cc:5: -stanExports_survival_mspline.h: In constructor ‘model_survival_mspline_namespace::model_survival_mspline::model_survival_mspline(stan::io::var_context&, unsigned int, std::ostream*)’: -stanExports_survival_mspline.h:2252:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without - 2252 | model_survival_mspline(stan::io::var_context& context__, unsigned int - | ^~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o survidm.so survidm_init.o survivalBIV.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/survidm/new/survidm.Rcheck/00LOCK-survidm/00new/survidm/libs +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘survidm’ +* removing ‘/tmp/workdir/survidm/new/survidm.Rcheck/survidm’ ``` ### CRAN ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘survidm’ ... +** package ‘survidm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -In file included from stanExports_survival_mspline.cc:5: -stanExports_survival_mspline.h: In constructor ‘model_survival_mspline_namespace::model_survival_mspline::model_survival_mspline(stan::io::var_context&, unsigned int, std::ostream*)’: -stanExports_survival_mspline.h:2252:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without - 2252 | model_survival_mspline(stan::io::var_context& context__, unsigned int - | ^~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o survidm.so survidm_init.o survivalBIV.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/survidm/old/survidm.Rcheck/00LOCK-survidm/00new/survidm/libs +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘survidm’ +* removing ‘/tmp/workdir/survidm/old/survidm.Rcheck/survidm’ ``` -# rmsb +# tempted
-* Version: 1.1-0 -* GitHub: NA -* Source code: https://github.com/cran/rmsb -* Date/Publication: 2024-03-12 15:50:02 UTC -* Number of recursive dependencies: 144 +* Version: 0.1.1 +* GitHub: https://github.com/pixushi/tempted +* Source code: https://github.com/cran/tempted +* Date/Publication: 2024-05-09 02:40:02 UTC +* Number of recursive dependencies: 37 -Run `revdepcheck::cloud_details(, "rmsb")` for more info +Run `revdepcheck::cloud_details(, "tempted")` for more info
## In both -* checking whether package ‘rmsb’ can be installed ... ERROR +* checking whether package ‘tempted’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/tempted/new/tempted.Rcheck/00install.out’ for details. ``` ## Installation @@ -629,51 +9283,61 @@ Run `revdepcheck::cloud_details(, "rmsb")` for more info ### Devel ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tempted’ ... +** package ‘tempted’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘tempted’ +* removing ‘/tmp/workdir/tempted/new/tempted.Rcheck/tempted’ ``` ### CRAN ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tempted’ ... +** package ‘tempted’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘tempted’ +* removing ‘/tmp/workdir/tempted/old/tempted.Rcheck/tempted’ ``` -# rstanarm +# tidydr
-* Version: 2.32.1 -* GitHub: https://github.com/stan-dev/rstanarm -* Source code: https://github.com/cran/rstanarm -* Date/Publication: 2024-01-18 23:00:03 UTC -* Number of recursive dependencies: 138 +* Version: 0.0.5 +* GitHub: https://github.com/YuLab-SMU/tidydr +* Source code: https://github.com/cran/tidydr +* Date/Publication: 2023-03-08 09:20:02 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "rstanarm")` for more info +Run `revdepcheck::cloud_details(, "tidydr")` for more info
-## In both +## Newly broken -* checking whether package ‘rstanarm’ can be installed ... ERROR +* checking whether package ‘tidydr’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. ``` ## Installation @@ -681,144 +9345,108 @@ Run `revdepcheck::cloud_details(, "rstanarm")` for more info ### Devel ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan -Wrote C++ file "stan_files/lm.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/mvmer.o] Error 1 -rm stan_files/lm.cc stan_files/mvmer.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ +** R +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'len0_null' not found +Error: unable to load R code in package ‘tidydr’ +Execution halted +ERROR: lazy loading failed for package ‘tidydr’ +* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ ``` ### CRAN ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan -Wrote C++ file "stan_files/lm.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/mvmer.o] Error 1 -rm stan_files/lm.cc stan_files/mvmer.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (tidydr) ``` -# Seurat +# tidyEdSurvey
-* Version: 5.0.3 -* GitHub: https://github.com/satijalab/seurat -* Source code: https://github.com/cran/Seurat -* Date/Publication: 2024-03-18 23:40:02 UTC -* Number of recursive dependencies: 264 +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/tidyEdSurvey +* Date/Publication: 2024-05-14 20:20:03 UTC +* Number of recursive dependencies: 107 -Run `revdepcheck::cloud_details(, "Seurat")` for more info +Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info
-## Error before installation +## In both + +* checking whether package ‘tidyEdSurvey’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidyEdSurvey/new/tidyEdSurvey.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 3 NOTEs - - - +* installing *source* package ‘tidyEdSurvey’ ... +** package ‘tidyEdSurvey’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyEdSurvey’ +* removing ‘/tmp/workdir/tidyEdSurvey/new/tidyEdSurvey.Rcheck/tidyEdSurvey’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 3 NOTEs - - - +* installing *source* package ‘tidyEdSurvey’ ... +** package ‘tidyEdSurvey’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyEdSurvey’ +* removing ‘/tmp/workdir/tidyEdSurvey/old/tidyEdSurvey.Rcheck/tidyEdSurvey’ ``` -# streamDAG +# tidyseurat
-* Version: 1.5 -* GitHub: NA -* Source code: https://github.com/cran/streamDAG -* Date/Publication: 2023-10-06 18:50:02 UTC -* Number of recursive dependencies: 133 +* Version: 0.8.0 +* GitHub: https://github.com/stemangiola/tidyseurat +* Source code: https://github.com/cran/tidyseurat +* Date/Publication: 2024-01-10 04:50:02 UTC +* Number of recursive dependencies: 206 -Run `revdepcheck::cloud_details(, "streamDAG")` for more info +Run `revdepcheck::cloud_details(, "tidyseurat")` for more info
@@ -827,20 +9455,22 @@ Run `revdepcheck::cloud_details(, "streamDAG")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’ +* using log directory ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘streamDAG/DESCRIPTION’ ... OK -* this is package ‘streamDAG’ version ‘1.5’ +* checking for file ‘tidyseurat/DESCRIPTION’ ... OK +... +* this is package ‘tidyseurat’ version ‘0.8.0’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘asbio’ +Packages required but not available: 'SeuratObject', 'Seurat' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -855,20 +9485,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’ +* using log directory ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘streamDAG/DESCRIPTION’ ... OK -* this is package ‘streamDAG’ version ‘1.5’ +* checking for file ‘tidyseurat/DESCRIPTION’ ... OK +... +* this is package ‘tidyseurat’ version ‘0.8.0’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘asbio’ +Packages required but not available: 'SeuratObject', 'Seurat' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -880,26 +9512,26 @@ Status: 1 ERROR ``` -# treestats +# tidyvpc
-* Version: 1.0.5 -* GitHub: https://github.com/thijsjanzen/treestats -* Source code: https://github.com/cran/treestats -* Date/Publication: 2024-01-30 15:50:02 UTC -* Number of recursive dependencies: 232 +* Version: 1.5.1 +* GitHub: https://github.com/certara/tidyvpc +* Source code: https://github.com/cran/tidyvpc +* Date/Publication: 2024-01-18 13:10:02 UTC +* Number of recursive dependencies: 176 -Run `revdepcheck::cloud_details(, "treestats")` for more info +Run `revdepcheck::cloud_details(, "tidyvpc")` for more info
## In both -* checking whether package ‘treestats’ can be installed ... ERROR +* checking whether package ‘tidyvpc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/treestats/new/treestats.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/00install.out’ for details. ``` ## Installation @@ -907,24 +9539,116 @@ Run `revdepcheck::cloud_details(, "treestats")` for more info ### Devel ``` -* installing *source* package ‘treestats’ ... -** package ‘treestats’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tidyvpc’ ... +** package ‘tidyvpc’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -Error: C++20 standard requested but CXX20 is not defined -* removing ‘/tmp/workdir/treestats/new/treestats.Rcheck/treestats’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘tidyvpc’ +* removing ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/tidyvpc’ ``` ### CRAN ``` -* installing *source* package ‘treestats’ ... -** package ‘treestats’ successfully unpacked and MD5 sums checked +* installing *source* package ‘tidyvpc’ ... +** package ‘tidyvpc’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -Error: C++20 standard requested but CXX20 is not defined -* removing ‘/tmp/workdir/treestats/old/treestats.Rcheck/treestats’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘tidyvpc’ +* removing ‘/tmp/workdir/tidyvpc/old/tidyvpc.Rcheck/tidyvpc’ + + +``` +# treefit + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/hayamizu-lab/treefit-r +* Source code: https://github.com/cran/treefit +* Date/Publication: 2022-01-18 07:50:02 UTC +* Number of recursive dependencies: 159 + +Run `revdepcheck::cloud_details(, "treefit")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/treefit/new/treefit.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘treefit/DESCRIPTION’ ... OK +... + + When sourcing ‘working-with-seurat.R’: +Error: there is no package called ‘Seurat’ +Execution halted + + ‘treefit.Rmd’ using ‘UTF-8’... OK + ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/treefit/old/treefit.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘treefit/DESCRIPTION’ ... OK +... + + When sourcing ‘working-with-seurat.R’: +Error: there is no package called ‘Seurat’ +Execution halted + + ‘treefit.Rmd’ using ‘UTF-8’... OK + ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + ``` @@ -980,26 +9704,26 @@ ERROR: configuration failed for package ‘TriDimRegression’ ``` -# triptych +# TSrepr
-* Version: 0.1.2 -* GitHub: https://github.com/aijordan/triptych -* Source code: https://github.com/cran/triptych -* Date/Publication: 2023-10-03 16:30:02 UTC -* Number of recursive dependencies: 64 +* Version: 1.1.0 +* GitHub: https://github.com/PetoLau/TSrepr +* Source code: https://github.com/cran/TSrepr +* Date/Publication: 2020-07-13 06:50:15 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "triptych")` for more info +Run `revdepcheck::cloud_details(, "TSrepr")` for more info
## In both -* checking whether package ‘triptych’ can be installed ... ERROR +* checking whether package ‘TSrepr’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/triptych/new/triptych.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/TSrepr/new/TSrepr.Rcheck/00install.out’ for details. ``` ## Installation @@ -1007,47 +9731,77 @@ Run `revdepcheck::cloud_details(, "triptych")` for more info ### Devel ``` -* installing *source* package ‘triptych’ ... -** package ‘triptych’ successfully unpacked and MD5 sums checked +* installing *source* package ‘TSrepr’ ... +** package ‘TSrepr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -Error: C++20 standard requested but CXX20 is not defined -* removing ‘/tmp/workdir/triptych/new/triptych.Rcheck/triptych’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘TSrepr’ +* removing ‘/tmp/workdir/TSrepr/new/TSrepr.Rcheck/TSrepr’ ``` ### CRAN ``` -* installing *source* package ‘triptych’ ... -** package ‘triptych’ successfully unpacked and MD5 sums checked +* installing *source* package ‘TSrepr’ ... +** package ‘TSrepr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -Error: C++20 standard requested but CXX20 is not defined -* removing ‘/tmp/workdir/triptych/old/triptych.Rcheck/triptych’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘TSrepr’ +* removing ‘/tmp/workdir/TSrepr/old/TSrepr.Rcheck/TSrepr’ ``` -# ubms +# twang
-* Version: 1.2.6 -* GitHub: https://github.com/kenkellner/ubms -* Source code: https://github.com/cran/ubms -* Date/Publication: 2023-09-11 18:50:02 UTC -* Number of recursive dependencies: 145 +* Version: 2.6 +* GitHub: NA +* Source code: https://github.com/cran/twang +* Date/Publication: 2023-12-06 00:30:02 UTC +* Number of recursive dependencies: 53 -Run `revdepcheck::cloud_details(, "ubms")` for more info +Run `revdepcheck::cloud_details(, "twang")` for more info
## In both -* checking whether package ‘ubms’ can be installed ... ERROR +* checking whether package ‘twang’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ubms/new/ubms.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/twang/new/twang.Rcheck/00install.out’ for details. ``` ## Installation @@ -1055,54 +9809,50 @@ Run `revdepcheck::cloud_details(, "ubms")` for more info ### Devel ``` -* installing *source* package ‘ubms’ ... -** package ‘ubms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘twang’ ... +** package ‘twang’ successfully unpacked and MD5 sums checked ** using staged installation -Registered S3 methods overwritten by 'RcppEigen': - method from - predict.fastLm RcppArmadillo - print.fastLm RcppArmadillo - summary.fastLm RcppArmadillo - print.summary.fastLm RcppArmadillo -Warning message: -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_colext_namespace::model_colext; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_colext.o] Error 1 -ERROR: compilation failed for package ‘ubms’ -* removing ‘/tmp/workdir/ubms/new/ubms.Rcheck/ubms’ +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks.c -o ks.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o twang.so init.o ks.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/twang/new/twang.Rcheck/00LOCK-twang/00new/twang/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘twang’ +* removing ‘/tmp/workdir/twang/new/twang.Rcheck/twang’ ``` ### CRAN ``` -* installing *source* package ‘ubms’ ... -** package ‘ubms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘twang’ ... +** package ‘twang’ successfully unpacked and MD5 sums checked ** using staged installation -Registered S3 methods overwritten by 'RcppEigen': - method from - predict.fastLm RcppArmadillo - print.fastLm RcppArmadillo - summary.fastLm RcppArmadillo - print.summary.fastLm RcppArmadillo -Warning message: -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_colext_namespace::model_colext; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_colext.o] Error 1 -ERROR: compilation failed for package ‘ubms’ -* removing ‘/tmp/workdir/ubms/old/ubms.Rcheck/ubms’ +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks.c -o ks.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o twang.so init.o ks.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/twang/old/twang.Rcheck/00LOCK-twang/00new/twang/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘twang’ +* removing ‘/tmp/workdir/twang/old/twang.Rcheck/twang’ ``` @@ -1137,7 +9887,7 @@ Run `revdepcheck::cloud_details(, "valse")` for more info ** package ‘valse’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o @@ -1149,7 +9899,7 @@ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_vector_free + /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free Error: loading failed Execution halted ERROR: loading failed @@ -1164,7 +9914,7 @@ ERROR: loading failed ** package ‘valse’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o @@ -1176,11 +9926,147 @@ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_vector_free + /tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free Error: loading failed Execution halted ERROR: loading failed * removing ‘/tmp/workdir/valse/old/valse.Rcheck/valse’ +``` +# vdg + +
+ +* Version: 1.2.3 +* GitHub: NA +* Source code: https://github.com/cran/vdg +* Date/Publication: 2024-04-23 13:00:02 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "vdg")` for more info + +
+ +## In both + +* checking whether package ‘vdg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/vdg/new/vdg.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/new/vdg.Rcheck/vdg’ + + +``` +### CRAN + +``` +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ + + +``` +# WRTDStidal + +
+ +* Version: 1.1.4 +* GitHub: https://github.com/fawda123/WRTDStidal +* Source code: https://github.com/cran/WRTDStidal +* Date/Publication: 2023-10-20 09:00:11 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "WRTDStidal")` for more info + +
+ +## In both + +* checking whether package ‘WRTDStidal’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/WRTDStidal/new/WRTDStidal.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘WRTDStidal’ ... +** package ‘WRTDStidal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘WRTDStidal’ +* removing ‘/tmp/workdir/WRTDStidal/new/WRTDStidal.Rcheck/WRTDStidal’ + + +``` +### CRAN + +``` +* installing *source* package ‘WRTDStidal’ ... +** package ‘WRTDStidal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘WRTDStidal’ +* removing ‘/tmp/workdir/WRTDStidal/old/WRTDStidal.Rcheck/WRTDStidal’ + + ``` diff --git a/revdep/problems.md b/revdep/problems.md index 8151dae476..1280d2fbbb 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,14 +1,2365 @@ +# asmbPLS + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/asmbPLS +* Date/Publication: 2023-04-17 09:50:05 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "asmbPLS")` for more info + +
+ +## Newly broken + +* checking whether package ‘asmbPLS’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘asmbPLS’ + See ‘/tmp/workdir/asmbPLS/new/asmbPLS.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 19.7Mb + sub-directories of 1Mb or more: + data 2.1Mb + libs 16.5Mb + ``` + +# bdl + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/statisticspoland/R_Package_to_API_BDL +* Source code: https://github.com/cran/bdl +* Date/Publication: 2023-02-24 15:00:02 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "bdl")` for more info + +
+ +## Newly broken + +* checking whether package ‘bdl’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bdl’ + See ‘/tmp/workdir/bdl/new/bdl.Rcheck/00install.out’ for details. + ``` + +# bdscale + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/dvmlls/bdscale +* Source code: https://github.com/cran/bdscale +* Date/Publication: 2016-03-17 13:27:37 +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "bdscale")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘bdscale.Rmd’ + ... + > options <- as.Date(c("2014-08-15", "2014-09-19")) + + > plot + geom_vline(xintercept = as.numeric(options), + + size = 2, alpha = 0.25) + ggtitle("calendar dates, option expiry") + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘bdscale.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘bdscale.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘bdscale.Rmd’ using rmarkdown + ``` + +# biclustermd + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/jreisner/biclustermd +* Source code: https://github.com/cran/biclustermd +* Date/Publication: 2021-06-17 15:10:06 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "biclustermd")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(biclustermd) + Loading required package: ggplot2 + Loading required package: tidyr + + Attaching package: 'tidyr' + + ... + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── + ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. + Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘nycflights13’ + All declared Imports should be used. + ``` + +# brolgar + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/njtierney/brolgar +* Source code: https://github.com/cran/brolgar +* Date/Publication: 2024-05-10 14:50:34 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "brolgar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘brolgar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_sample + > ### Title: Facet data into groups to facilitate exploration + > ### Aliases: facet_sample + > + > ### ** Examples + > + > library(ggplot2) + > ggplot(heights, + + aes(x = year, + + y = height_cm, + + group = country)) + + + geom_line() + + + facet_sample() + Error in if (params$as.table) { : argument is of length zero + Calls: ... -> setup -> -> compute_layout + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started.Rmd’ + ... + > set.seed(2019 - 7 - 23 - 1936) + + > library(ggplot2) + + > ggplot(wages, aes(x = xp, y = ln_wages, group = id)) + + + geom_line() + facet_strata() + + ... + Error: argument is of length zero + Execution halted + + ‘exploratory-modelling.Rmd’ using ‘UTF-8’... OK + ‘finding-features.Rmd’ using ‘UTF-8’... OK + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK + ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK + ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed + ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown + ``` + +# bSi + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/bSi +* Date/Publication: 2024-01-24 15:52:57 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "bSi")` for more info + +
+ +## Newly broken + +* checking whether package ‘bSi’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bSi’ + See ‘/tmp/workdir/bSi/new/bSi.Rcheck/00install.out’ for details. + ``` + +# CausalImpact + +
+ +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/CausalImpact +* Date/Publication: 2022-11-09 08:40:40 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "CausalImpact")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘CausalImpact_import_test.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # Copyright 2014-2022 Google Inc. All rights reserved. + > # + > # Licensed under the Apache License, Version 2.0 (the "License"); + > # you may not use this file except in compliance with the License. + > # You may obtain a copy of the License at + > # + ... + 20. └─base::lapply(df[aesthetics], self$transform) + 21. └─ggplot2 (local) FUN(X[[i]], ...) + 22. └─ggplot2 (local) transform(..., self = self) + 23. └─transformation$transform(x) + 24. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") + 25. └─rlang::abort(...) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 739 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CausalImpact.Rmd’ + ... + + > impact <- CausalImpact(data, pre.period, post.period) + + > q <- plot(impact) + theme_bw(base_size = 11) + + > suppressWarnings(plot(q)) + + When sourcing ‘CausalImpact.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘CausalImpact.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘CausalImpact.Rmd’ using rmarkdown + ``` + +# ClusROC + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/toduckhanh/ClusROC +* Source code: https://github.com/cran/ClusROC +* Date/Publication: 2022-11-17 15:00:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "ClusROC")` for more info + +
+ +## Newly broken + +* checking whether package ‘ClusROC’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ClusROC’ + See ‘/tmp/workdir/ClusROC/new/ClusROC.Rcheck/00install.out’ for details. + ``` + +# clustEff + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/clustEff +* Date/Publication: 2024-01-23 08:52:55 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "clustEff")` for more info + +
+ +## Newly broken + +* checking whether package ‘clustEff’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘clustEff’ + See ‘/tmp/workdir/clustEff/new/clustEff.Rcheck/00install.out’ for details. + ``` + +# CLVTools + +
+ +* Version: 0.10.0 +* GitHub: https://github.com/bachmannpatrick/CLVTools +* Source code: https://github.com/cran/CLVTools +* Date/Publication: 2023-10-23 20:10:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "CLVTools")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CLVTools.Rmd’ + ... + 248: 39.95483 2.336902 + 249: 34.28958 38.969738 + 250: 47.35500 7.284870 + + > plot(clv.apparel) + Plotting from 2005-01-03 until 2006-07-16. + + When sourcing ‘CLVTools.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘CLVTools.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CLVTools.Rmd’ using rmarkdown + + Quitting from lines 270-272 [plot-actual] (CLVTools.Rmd) + Error: processing vignette 'CLVTools.Rmd' failed with diagnostics: + `transform_date()` works with objects of class only + --- failed re-building ‘CLVTools.Rmd’ + + SUMMARY: processing the following file failed: + ‘CLVTools.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 17.4Mb + sub-directories of 1Mb or more: + libs 15.5Mb + ``` + +# coda4microbiome + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/malucalle/coda4microbiome +* Source code: https://github.com/cran/coda4microbiome +* Date/Publication: 2024-02-21 08:30:06 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "coda4microbiome")` for more info + +
+ +## Newly broken + +* checking whether package ‘coda4microbiome’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘coda4microbiome’ + See ‘/tmp/workdir/coda4microbiome/new/coda4microbiome.Rcheck/00install.out’ for details. + ``` + +# CompAREdesign + +
+ +* Version: 2.3.1 +* GitHub: NA +* Source code: https://github.com/cran/CompAREdesign +* Date/Publication: 2024-02-15 13:00:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "CompAREdesign")` for more info + +
+ +## Newly broken + +* checking whether package ‘CompAREdesign’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘CompAREdesign’ + See ‘/tmp/workdir/CompAREdesign/new/CompAREdesign.Rcheck/00install.out’ for details. + ``` + +# covidcast + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/cmu-delphi/covidcast +* Source code: https://github.com/cran/covidcast +* Date/Publication: 2023-07-12 23:40:06 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "covidcast")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(covidcast) + We encourage COVIDcast API users to register on our mailing list: + https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api + We'll send announcements about new data sources, package updates, + server maintenance, and new features. + > + ... + • plot/default-county-choropleth.svg + • plot/default-hrr-choropleth-with-include.svg + • plot/default-msa-choropleth-with-include.svg + • plot/default-state-choropleth-with-include.svg + • plot/default-state-choropleth-with-range.svg + • plot/state-choropleth-with-no-metadata.svg + • plot/state-line-graph-with-range.svg + • plot/state-line-graph-with-stderrs.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘plotting-signals.Rmd’ + ... + > plot(inum, choro_col = colors, choro_params = list(breaks = breaks), + + title = "New COVID cases (7-day trailing average) on 2020-07-14") + + When sourcing ‘plotting-signals.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 5th layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (3078). + ✖ Fix the following mappings: `fill`. + Execution halted + + ‘correlation-utils.Rmd’ using ‘UTF-8’... OK + ‘covidcast.Rmd’ using ‘UTF-8’... OK + ‘external-data.Rmd’ using ‘UTF-8’... OK + ‘multi-signals.Rmd’ using ‘UTF-8’... OK + ‘plotting-signals.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘correlation-utils.Rmd’ using rmarkdown + --- finished re-building ‘correlation-utils.Rmd’ + + --- re-building ‘covidcast.Rmd’ using rmarkdown + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 20 marked UTF-8 strings + ``` + +# Coxmos + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/BiostatOmics/Coxmos +* Source code: https://github.com/cran/Coxmos +* Date/Publication: 2024-03-25 20:32:38 UTC +* Number of recursive dependencies: 204 + +Run `revdepcheck::cloud_details(, "Coxmos")` for more info + +
+ +## Newly broken + +* checking Rd files ... WARNING + ``` + prepare_Rd: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Coxmos-pipeline.Rmd’ + ... + Warning in data("X_proteomic") : data set ‘X_proteomic’ not found + + > data("Y_proteomic") + Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found + + > X <- X_proteomic + + When sourcing ‘Coxmos-pipeline.R’: + Error: object 'X_proteomic' not found + Execution halted + + ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... OK + ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + data 2.1Mb + doc 2.9Mb + ``` + +# csa + +
+ +* Version: 0.7.1 +* GitHub: https://github.com/imarkonis/csa +* Source code: https://github.com/cran/csa +* Date/Publication: 2023-10-24 13:40:11 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "csa")` for more info + +
+ +## Newly broken + +* checking whether package ‘csa’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csa’ + See ‘/tmp/workdir/csa/new/csa.Rcheck/00install.out’ for details. + ``` + +# deeptime + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/willgearty/deeptime +* Source code: https://github.com/cran/deeptime +* Date/Publication: 2024-03-08 17:10:10 UTC +* Number of recursive dependencies: 181 + +Run `revdepcheck::cloud_details(, "deeptime")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘deeptime-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_wrap_color + > ### Title: Wrap a 1d ribbon of panels into 2d with colored strips + > ### Aliases: facet_wrap_color FacetWrapColor + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 6. │ └─ggplot2 (local) setup(..., self = self) + 7. │ └─self$facet$compute_layout(data, self$facet_params) + 8. │ └─ggplot2 (local) compute_layout(..., self = self) + 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) + 10. │ └─ggplot2:::data_frame0(...) + 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") + 12. └─vctrs:::stop_recycle_incompatible_size(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(deeptime) + > + > test_check("deeptime") + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + ... + • gggeo_scale/gggeo-scale-top-new.svg + • gggeo_scale/gggeo-scale-top-old.svg + • points_range/geom-points-range-aes-new.svg + • points_range/geom-points-range-aes-old.svg + • points_range/geom-points-range-bg-new.svg + • points_range/geom-points-range-bg-old.svg + • points_range/geom-points-range-h-new.svg + • points_range/geom-points-range-h-old.svg + Error: Test failures + Execution halted + ``` + +# DEGRE + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/DEGRE +* Date/Publication: 2022-11-02 09:32:57 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "DEGRE")` for more info + +
+ +## Newly broken + +* checking whether package ‘DEGRE’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘DEGRE’ + See ‘/tmp/workdir/DEGRE/new/DEGRE.Rcheck/00install.out’ for details. + ``` + +# did + +
+ +* Version: 2.1.2 +* GitHub: https://github.com/bcallaway11/did +* Source code: https://github.com/cran/did +* Date/Publication: 2022-07-20 16:00:05 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "did")` for more info + +
+ +## Newly broken + +* checking whether package ‘did’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘did’ + See ‘/tmp/workdir/did/new/did.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking running R code from vignettes ... WARNING + ``` + Errors in running code in vignettes: + when running code in ‘TWFE.Rmd’ + ... + + > knitr::opts_chunk$set(collapse = TRUE, comment = "#>", + + echo = TRUE, eval = FALSE) + + > library(tidyverse) + + When sourcing ‘TWFE.R’: + ... + + When sourcing ‘pre-testing.R’: + Error: cannot open the connection + Execution halted + + ‘TWFE.Rmd’ using ‘UTF-8’... failed + ‘did-basics.Rmd’ using ‘UTF-8’... OK + ‘extensions.Rmd’ using ‘UTF-8’... failed + ‘multi-period-did.Rmd’ using ‘UTF-8’... OK + ‘pre-testing.Rmd’ using ‘UTF-8’... failed + ``` + +# EpiCurve + +
+ +* Version: 2.4-2 +* GitHub: https://github.com/IamKDO/EpiCurve +* Source code: https://github.com/cran/EpiCurve +* Date/Publication: 2021-07-14 16:20:05 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "EpiCurve")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘EpiCurve.Rmd’ + ... + |2016-11-06 | 6.60| 116| + |2016-11-07 | 7.68| 141| + |2016-11-07 | 10.08| 126| + + > EpiCurve(DF, date = "UTS", period = "day", colors = "#9900ef", + + xlabel = sprintf("From %s to %s", min(DF$UTS), max(DF$UTS))) + + When sourcing ‘EpiCurve.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘EpiCurve.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘EpiCurve.Rmd’ using rmarkdown + + Quitting from lines 103-106 [unnamed-chunk-3] (EpiCurve.Rmd) + Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics: + `transform_date()` works with objects of class only + --- failed re-building ‘EpiCurve.Rmd’ + + SUMMARY: processing the following file failed: + ‘EpiCurve.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tibble’ + All declared Imports should be used. + ``` + +# epiR + +
+ +* Version: 2.0.74 +* GitHub: NA +* Source code: https://github.com/cran/epiR +* Date/Publication: 2024-04-27 12:30:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "epiR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘epiR_descriptive.Rmd’ + ... + + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", + + li .... [TRUNCATED] + + > ggplot(data = dat.df, aes(x = as.Date(odate))) + theme_bw() + + + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", + + li .... [TRUNCATED] + + When sourcing ‘epiR_descriptive.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘epiR_descriptive.Rmd’... failed + ‘epiR_measures_of_association.Rmd’... OK + ‘epiR_sample_size.Rmd’... OK + ‘epiR_surveillance.Rmd’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘epiR_descriptive.Rmd’ using rmarkdown + ``` + +# FuncNN + +
+ +* Version: 1.0 +* GitHub: https://github.com/b-thi/FuncNN +* Source code: https://github.com/cran/FuncNN +* Date/Publication: 2020-09-15 09:40:15 UTC +* Number of recursive dependencies: 170 + +Run `revdepcheck::cloud_details(, "FuncNN")` for more info + +
+ +## Newly broken + +* checking whether package ‘FuncNN’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘FuncNN’ + See ‘/tmp/workdir/FuncNN/new/FuncNN.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘foreach’ + All declared Imports should be used. + ``` + +# geostan + +
+ +* Version: 0.6.1 +* GitHub: https://github.com/ConnorDonegan/geostan +* Source code: https://github.com/cran/geostan +* Date/Publication: 2024-05-10 22:23:01 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "geostan")` for more info + +
+ +## Newly broken + +* checking whether package ‘geostan’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 129.8Mb + sub-directories of 1Mb or more: + libs 127.6Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory + 32 | } + | ^ +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 +ERROR: compilation failed for package ‘geostan’ +* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ + + +``` +### CRAN + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** help +*** installing help indices +*** copying figures +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (geostan) + + +``` +# ggedit + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/yonicd/ggedit +* Source code: https://github.com/cran/ggedit +* Date/Publication: 2024-03-04 14:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "ggedit")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggedit-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.ggedit + > ### Title: Print ggedit objects + > ### Aliases: print.ggedit + > + > ### ** Examples + > + > p <- as.gglist(pList[1:2]) + ... + 8. │ └─ggplot2 (local) setup(..., self = self) + 9. │ └─self$facet$compute_layout(data, self$facet_params) + 10. │ └─ggplot2 (local) compute_layout(..., self = self) + 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) + 12. │ └─ggplot2:::data_frame0(...) + 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") + 14. └─vctrs:::stop_recycle_incompatible_size(...) + 15. └─vctrs:::stop_vctrs(...) + 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +# ggfixest + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/grantmcdermott/ggfixest +* Source code: https://github.com/cran/ggfixest +* Date/Publication: 2023-12-14 08:00:06 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "ggfixest")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > ## Throttle CPU threads if R CMD check (for CRAN) + > + > if (any(grepl("_R_CHECK", names(Sys.getenv()), fixed = TRUE))) { + + # fixest + + if (requireNamespace("fixest", quietly = TRUE)) { + + library(fixest) + + setFixest_nthreads(1) + ... + ----- FAILED[]: test_ggcoefplot.R<66--66> + call| expect_snapshot_plot(p_did_iid_summ, label = "ggcoefplot_did_iid") + diff| 7580 + info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png + ----- FAILED[]: test_ggcoefplot.R<67--67> + call| expect_snapshot_plot(p_did_iid, label = "ggcoefplot_did_iid") + diff| 7580 + info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png + Error: 12 out of 101 tests failed + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggiplot.Rmd’ + ... + > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), + + ref.line = -1, main = "Staggered treatment: Split mutli-sample") + The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. + Note that you can provide the argument `df.t` directly. + + When sourcing ‘ggiplot.R’: + Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: + The 1st element of 'object' raises and error: + Error in nb * sd : non-numeric argument to binary operator + Execution halted + + ‘ggiplot.Rmd’ using ‘UTF-8’... failed + ``` + +# ggfortify + +
+ +* Version: 0.4.17 +* GitHub: https://github.com/sinhrks/ggfortify +* Source code: https://github.com/cran/ggfortify +* Date/Publication: 2024-04-17 04:30:04 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "ggfortify")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basics.Rmd’ using knitr + + Attaching package: 'zoo' + + The following objects are masked from 'package:base': + + as.Date, as.Date.numeric + ``` + # ggh4x
-* Version: 0.2.8 -* GitHub: https://github.com/teunbrand/ggh4x -* Source code: https://github.com/cran/ggh4x -* Date/Publication: 2024-01-23 21:00:02 UTC -* Number of recursive dependencies: 77 +* Version: 0.2.8 +* GitHub: https://github.com/teunbrand/ggh4x +* Source code: https://github.com/cran/ggh4x +* Date/Publication: 2024-01-23 21:00:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "ggh4x")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggh4x-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_nested_wrap + > ### Title: Ribbon of panels with nested strips. + > ### Aliases: facet_nested_wrap + > + > ### ** Examples + > + > # A standard plot + ... + 6. │ └─ggplot2 (local) setup(..., self = self) + 7. │ └─self$facet$compute_layout(data, self$facet_params) + 8. │ └─ggplot2 (local) compute_layout(..., self = self) + 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) + 10. │ └─ggplot2:::data_frame0(...) + 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") + 12. └─vctrs:::stop_recycle_incompatible_size(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggh4x) + Loading required package: ggplot2 + > + > test_check("ggh4x") + [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] + + ... + 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) + 12. │ └─ggplot2:::data_frame0(...) + 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") + 14. └─vctrs:::stop_recycle_incompatible_size(...) + 15. └─vctrs:::stop_vctrs(...) + 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + + [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Facets.Rmd’ using rmarkdown + + Quitting from lines 33-39 [wrap_mimick] (Facets.Rmd) + Error: processing vignette 'Facets.Rmd' failed with diagnostics: + Can't recycle `ROW` (size 0) to size 7. + --- failed re-building ‘Facets.Rmd’ + + --- re-building ‘Miscellaneous.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Facets.Rmd’ + ... + Loading required package: ggplot2 + + > p <- ggplot(mpg, aes(displ, hwy, colour = as.factor(cyl))) + + + geom_point() + labs(x = "Engine displacement", y = "Highway miles per gallon") + .... [TRUNCATED] + + > p + facet_wrap2(vars(class)) + + ... + ℹ Error occurred in the 1st layer. + Caused by error in `setup_params()`: + ! A discrete 'nbinom' distribution cannot be fitted to continuous data. + Execution halted + + ‘Facets.Rmd’ using ‘UTF-8’... failed + ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK + ‘PositionGuides.Rmd’ using ‘UTF-8’... OK + ‘Statistics.Rmd’ using ‘UTF-8’... failed + ‘ggh4x.Rmd’ using ‘UTF-8’... OK + ``` + +# ggheatmap + +
+ +* Version: 2.2 +* GitHub: NA +* Source code: https://github.com/cran/ggheatmap +* Date/Publication: 2022-09-10 13:32:55 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ggheatmap")` for more info + +
+ +## Newly broken + +* checking whether package ‘ggheatmap’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggheatmap’ + See ‘/tmp/workdir/ggheatmap/new/ggheatmap.Rcheck/00install.out’ for details. + ``` + +# ggScatRidges + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/matbou85/ggScatRidges +* Source code: https://github.com/cran/ggScatRidges +* Date/Publication: 2024-03-25 10:20:05 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "ggScatRidges")` for more info + +
+ +## Newly broken + +* checking whether package ‘ggScatRidges’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggScatRidges’ + See ‘/tmp/workdir/ggScatRidges/new/ggScatRidges.Rcheck/00install.out’ for details. + ``` + +# GimmeMyPlot + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/GimmeMyPlot +* Date/Publication: 2023-10-18 16:10:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info + +
+ +## Newly broken + +* checking whether package ‘GimmeMyPlot’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘GimmeMyPlot’ + See ‘/tmp/workdir/GimmeMyPlot/new/GimmeMyPlot.Rcheck/00install.out’ for details. + ``` + +# hilldiv + +
+ +* Version: 1.5.1 +* GitHub: https://github.com/anttonalberdi/hilldiv +* Source code: https://github.com/cran/hilldiv +* Date/Publication: 2019-10-01 14:40:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "hilldiv")` for more info + +
+ +## Newly broken + +* checking whether package ‘hilldiv’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hilldiv’ + See ‘/tmp/workdir/hilldiv/new/hilldiv.Rcheck/00install.out’ for details. + ``` + +# hJAM + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/lailylajiang/hJAM +* Source code: https://github.com/cran/hJAM +* Date/Publication: 2020-02-20 14:50:05 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "hJAM")` for more info + +
+ +## Newly broken + +* checking whether package ‘hJAM’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hJAM’ + See ‘/tmp/workdir/hJAM/new/hJAM.Rcheck/00install.out’ for details. + ``` + +# iglu + +
+ +* Version: 4.0.0 +* GitHub: https://github.com/irinagain/iglu +* Source code: https://github.com/cran/iglu +* Date/Publication: 2024-02-23 17:50:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "iglu")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘iglu-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mage_ma_single + > ### Title: Calculates Mean Amplitude of Glycemic Excursions (see "mage") + > ### Aliases: mage_ma_single + > + > ### ** Examples + > + > data(example_data_1_subject) + ... + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) + 17. └─ggplot2 (local) transform(..., self = self) + 18. └─transformation$transform(x) + 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MAGE.Rmd’ + ... + + > fig1data <- example_data_1_subject[1:200, ] + + > mage(fig1data, plot = TRUE, show_ma = TRUE, title = "Glucose Trace - Subject 1") + + When sourcing ‘MAGE.R’: + Error: ℹ In index: 1. + Caused by error in `transformation$transform()`: + ! `transform_time()` works with objects of class only + Execution halted + + ‘AGP_and_Episodes.Rmd’ using ‘UTF-8’... OK + ‘MAGE.Rmd’ using ‘UTF-8’... failed + ‘iglu.Rmd’ using ‘UTF-8’... OK + ‘lasagna_plots.Rmd’ using ‘UTF-8’... OK + ‘metrics_list.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘AGP_and_Episodes.Rmd’ using rmarkdown + ``` + +# ImFoR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ImFoR +* Date/Publication: 2023-09-21 18:50:02 UTC +* Number of recursive dependencies: 173 + +Run `revdepcheck::cloud_details(, "ImFoR")` for more info + +
+ +## Newly broken + +* checking whether package ‘ImFoR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ImFoR’ + See ‘/tmp/workdir/ImFoR/new/ImFoR.Rcheck/00install.out’ for details. + ``` + +# iNEXT.4steps + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/KaiHsiangHu/iNEXT.4steps +* Source code: https://github.com/cran/iNEXT.4steps +* Date/Publication: 2024-04-10 20:00:05 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "iNEXT.4steps")` for more info + +
+ +## Newly broken + +* checking whether package ‘iNEXT.4steps’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘iNEXT.4steps’ + See ‘/tmp/workdir/iNEXT.4steps/new/iNEXT.4steps.Rcheck/00install.out’ for details. + ``` + +# insane + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/mcanouil/insane +* Source code: https://github.com/cran/insane +* Date/Publication: 2023-11-14 21:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "insane")` for more info + +
+ +## Newly broken + +* checking whether package ‘insane’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘insane’ + See ‘/tmp/workdir/insane/new/insane.Rcheck/00install.out’ for details. + ``` + +# MarketMatching + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/MarketMatching +* Date/Publication: 2024-01-31 09:40:02 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "MarketMatching")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle + + Quitting from lines 114-115 [unnamed-chunk-3] (MarketMatching-Vignette.Rmd) + Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics: + `transform_date()` works with objects of class only + --- failed re-building ‘MarketMatching-Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘MarketMatching-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mc2d + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/mc2d +* Date/Publication: 2023-07-17 16:00:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "mc2d")` for more info + +
+ +## Newly broken + +* checking whether package ‘mc2d’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ + See ‘/tmp/workdir/mc2d/new/mc2d.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘docmcEnglish.Rnw’ using Sweave + Loading required package: mvtnorm + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ + + Attaching package: ‘mc2d’ + + The following objects are masked from ‘package:base’: + + pmax, pmin + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘mc2dLmEnglish.rnw’ + + SUMMARY: processing the following files failed: + ‘docmcEnglish.Rnw’ ‘mc2dLmEnglish.rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MetaIntegrator + +
+ +* Version: 2.1.3 +* GitHub: NA +* Source code: https://github.com/cran/MetaIntegrator +* Date/Publication: 2020-02-26 13:00:11 UTC +* Number of recursive dependencies: 178 + +Run `revdepcheck::cloud_details(, "MetaIntegrator")` for more info + +
+ +## Newly broken + +* checking whether package ‘MetaIntegrator’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MetaIntegrator’ + See ‘/tmp/workdir/MetaIntegrator/new/MetaIntegrator.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + data 3.9Mb + doc 2.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’ + ‘readr’ + All declared Imports should be used. + ``` + +# MF.beta4 + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/AnneChao/MF.beta4 +* Source code: https://github.com/cran/MF.beta4 +* Date/Publication: 2024-04-16 16:30:02 UTC +* Number of recursive dependencies: 173 + +Run `revdepcheck::cloud_details(, "MF.beta4")` for more info + +
+ +## Newly broken + +* checking whether package ‘MF.beta4’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MF.beta4’ + See ‘/tmp/workdir/MF.beta4/new/MF.beta4.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Introduction.Rnw’ using Sweave + Error: processing vignette 'Introduction.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'Introduction.tex' failed. + LaTeX errors: + ! LaTeX Error: File `pdfpages.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.4 ^^M + + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘Introduction.Rnw’ + + SUMMARY: processing the following file failed: + ‘Introduction.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MIMSunit + +
+ +* Version: 0.11.2 +* GitHub: https://github.com/mhealthgroup/MIMSunit +* Source code: https://github.com/cran/MIMSunit +* Date/Publication: 2022-06-21 11:00:09 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "MIMSunit")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MIMSunit-Ex.R’ failed + The error most likely occurred in: + + > ### Name: illustrate_extrapolation + > ### Title: Plot illustrations about extrapolation in illustration style. + > ### Aliases: illustrate_extrapolation + > + > ### ** Examples + > + > # Use the maxed-out data for the conceptual diagram + ... + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) + 17. └─ggplot2 (local) transform(..., self = self) + 18. └─transformation$transform(x) + 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") + 20. └─rlang::abort(...) + Execution halted + ``` + +# missingHE + +
+ +* Version: 1.5.0 +* GitHub: NA +* Source code: https://github.com/cran/missingHE +* Date/Publication: 2023-03-21 08:50:02 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "missingHE")` for more info + +
+ +## Newly broken + +* checking whether package ‘missingHE’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘missingHE’ + See ‘/tmp/workdir/missingHE/new/missingHE.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘mcmcr’ + All declared Imports should be used. + ``` + +# MSPRT + +
+ +* Version: 3.0 +* GitHub: NA +* Source code: https://github.com/cran/MSPRT +* Date/Publication: 2020-11-13 10:20:05 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "MSPRT")` for more info + +
+ +## Newly broken + +* checking whether package ‘MSPRT’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MSPRT’ + See ‘/tmp/workdir/MSPRT/new/MSPRT.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’ + All declared Imports should be used. + ``` + +# nzelect + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/nzelect +* Date/Publication: 2017-10-02 20:35:23 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "nzelect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nzelect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: polls + > ### Title: New Zealand Opinion Polls + > ### Aliases: polls + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 10. └─ggplot2 (local) FUN(X[[i]], ...) + 11. └─scale$transform_df(df = df) + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─transformation$transform(x) + 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") + 18. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + data 5.6Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6409 marked UTF-8 strings + ``` + +# OenoKPM + +
+ +* Version: 2.4.1 +* GitHub: NA +* Source code: https://github.com/cran/OenoKPM +* Date/Publication: 2024-04-08 19:20:10 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "OenoKPM")` for more info + +
+ +## Newly broken + +* checking whether package ‘OenoKPM’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘OenoKPM’ + See ‘/tmp/workdir/OenoKPM/new/OenoKPM.Rcheck/00install.out’ for details. + ``` + +# posologyr + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/levenc/posologyr +* Source code: https://github.com/cran/posologyr +* Date/Publication: 2024-02-09 11:50:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "posologyr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘a_priori_dosing.Rmd’ + ... + 16: source(output, echo = TRUE) + 17: doTryCatch(return(expr), name, parentenv, handler) + 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) + 19: tryCatchList(expr, classes, parentenv, handlers) + 20: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)}) + 21: tools:::.run_one_vignette("a_priori_dosing.Rmd", "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr/vignettes", encoding = "UTF-8", pkgdir = "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr") + An irrecoverable exception occurred. R is aborting now ... + ... + Segmentation fault + + ... incomplete output. Crash? + + ‘a_posteriori_dosing.Rmd’ using ‘UTF-8’... OK + ‘a_priori_dosing.Rmd’ using ‘UTF-8’... failed to complete the test + ‘auc_based_dosing.Rmd’ using ‘UTF-8’... OK + ‘multiple_endpoints.Rmd’ using ‘UTF-8’... OK + ‘patient_data_input.Rmd’ using ‘UTF-8’... OK + ‘posologyr_user_defined_models.Rmd’ using ‘UTF-8’... OK + ``` + +# qicharts + +
+ +* Version: 0.5.8 +* GitHub: NA +* Source code: https://github.com/cran/qicharts +* Date/Publication: 2021-04-20 12:20:03 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "qicharts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qicharts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tcc + > ### Title: Trellis Control Charts + > ### Aliases: tcc + > + > ### ** Examples + > + > # Run chart of 24 random normal variables + ... + 10. └─ggplot2 (local) FUN(X[[i]], ...) + 11. └─scale$transform_df(df = df) + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─transformation$transform(x) + 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") + 18. └─rlang::abort(...) + Execution halted + ``` + +# qicharts2 + +
+ +* Version: 0.7.5 +* GitHub: https://github.com/anhoej/qicharts2 +* Source code: https://github.com/cran/qicharts2 +* Date/Publication: 2024-05-09 06:20:03 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "qicharts2")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘qicharts2.Rmd’ + ... + > qic(month, n, notes = notes, data = cdi, decimals = 0, + + title = "Hospital acquired Clostridium difficile infections", + + ylab = "Count", x .... [TRUNCATED] + + > qic(month, n, data = cdi, decimals = 0, freeze = 24, + + part.labels = c("Baseline", "Intervention"), title = "Hospital acquired Clostridium diff ..." ... [TRUNCATED] + + When sourcing ‘qicharts2.R’: + Error: `transform_time()` works with objects of class only + Execution halted + + ‘qicharts2.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘qicharts2.Rmd’ using rmarkdown + ``` + +# QuadratiK + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/giovsaraceno/QuadratiK-package +* Source code: https://github.com/cran/QuadratiK +* Date/Publication: 2024-05-14 13:50:06 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "QuadratiK")` for more info + +
+ +## Newly broken + +* checking whether package ‘QuadratiK’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘QuadratiK’ + See ‘/tmp/workdir/QuadratiK/new/QuadratiK.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 14.6Mb + sub-directories of 1Mb or more: + libs 12.9Mb + ``` + +# RCTrep + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/duolajiang/RCTrep +* Source code: https://github.com/cran/RCTrep +* Date/Publication: 2023-11-02 14:40:02 UTC +* Number of recursive dependencies: 166 + +Run `revdepcheck::cloud_details(, "RCTrep")` for more info + +
+ +## Newly broken + +* checking whether package ‘RCTrep’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘RCTrep’ + See ‘/tmp/workdir/RCTrep/new/RCTrep.Rcheck/00install.out’ for details. + ``` + +# scdtb + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mightymetrika/scdtb +* Source code: https://github.com/cran/scdtb +* Date/Publication: 2024-04-30 08:50:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "scdtb")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + Error in `nlme::gls(model = mod_form, data = .df, method = "REML", correlation = nlme::corAR1(form = re_form), + ...)`: false convergence (8) + Backtrace: + ▆ + 1. └─scdtb::mixed_model_analysis(...) at test-mixed_model_analysis.R:114:3 + 2. └─nlme::gls(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ] + Error: Test failures + Execution halted + ``` + +# SCOUTer + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/SCOUTer +* Date/Publication: 2020-06-30 09:30:03 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "SCOUTer")` for more info + +
+ +## Newly broken + +* checking whether package ‘SCOUTer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SCOUTer’ + See ‘/tmp/workdir/SCOUTer/new/SCOUTer.Rcheck/00install.out’ for details. + ``` + +# sievePH + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/mjuraska/sievePH +* Source code: https://github.com/cran/sievePH +* Date/Publication: 2023-02-03 18:40:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "ggh4x")` for more info +Run `revdepcheck::cloud_details(, "sievePH")` for more info + +
+ +## Newly broken + +* checking whether package ‘sievePH’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘sievePH’ + See ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/00install.out’ for details. + ``` + +# SouthParkRshiny + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/Amalan-ConStat/SouthParkRshiny +* Source code: https://github.com/cran/SouthParkRshiny +* Date/Publication: 2024-03-09 11:10:08 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "SouthParkRshiny")` for more info + +
+ +## Newly broken + +* checking whether package ‘SouthParkRshiny’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SouthParkRshiny’ + See ‘/tmp/workdir/SouthParkRshiny/new/SouthParkRshiny.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + data 8.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1562 marked UTF-8 strings + ``` + +# SqueakR + +
+ +* Version: 1.3.0 +* GitHub: https://github.com/osimon81/SqueakR +* Source code: https://github.com/cran/SqueakR +* Date/Publication: 2022-06-28 09:20:04 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "SqueakR")` for more info + +
+ +## Newly broken + +* checking whether package ‘SqueakR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SqueakR’ + See ‘/tmp/workdir/SqueakR/new/SqueakR.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘SqueakR.Rmd’ + ... + $ experimenters : NULL + $ experimental_data: list() + + > my_new_data <- add_timepoint_data(data_path = "../inst/extdata/Example_Mouse_Data.xlsx", + + t1 = 5, t2 = 25) + Adding call features Excel file to workspace... + + When sourcing ‘SqueakR.R’: + Error: `path` does not exist: ‘../inst/extdata/Example_Mouse_Data.xlsx’ + Execution halted + + ‘SqueakR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + doc 8.2Mb + ``` + +# survminer + +
+ +* Version: 0.4.9 +* GitHub: https://github.com/kassambara/survminer +* Source code: https://github.com/cran/survminer +* Date/Publication: 2021-03-09 09:50:03 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "survminer")` for more info + +
+ +## Newly broken + +* checking whether package ‘survminer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ + See ‘/tmp/workdir/survminer/new/survminer.Rcheck/00install.out’ for details. + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + doc 5.5Mb + ``` + +# symptomcheckR + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/ma-kopka/symptomcheckR +* Source code: https://github.com/cran/symptomcheckR +* Date/Publication: 2024-04-16 20:40:06 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "symptomcheckR")` for more info + +
+ +## Newly broken + +* checking whether package ‘symptomcheckR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘symptomcheckR’ + See ‘/tmp/workdir/symptomcheckR/new/symptomcheckR.Rcheck/00install.out’ for details. + ``` + +# tcgaViz + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/tcgaViz +* Date/Publication: 2023-04-04 15:40:02 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "tcgaViz")` for more info + +
+ +## Newly broken + +* checking whether package ‘tcgaViz’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘tcgaViz’ + See ‘/tmp/workdir/tcgaViz/new/tcgaViz.Rcheck/00install.out’ for details. + ``` + +# TestGardener + +
+ +* Version: 3.3.3 +* GitHub: NA +* Source code: https://github.com/cran/TestGardener +* Date/Publication: 2024-03-20 13:50:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "TestGardener")` for more info + +
+ +## Newly broken + +* checking whether package ‘TestGardener’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘TestGardener’ + See ‘/tmp/workdir/TestGardener/new/TestGardener.Rcheck/00install.out’ for details. + ``` + +# tidydr + +
+ +* Version: 0.0.5 +* GitHub: https://github.com/YuLab-SMU/tidydr +* Source code: https://github.com/cran/tidydr +* Date/Publication: 2023-03-08 09:20:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "tidydr")` for more info + +
+ +## Newly broken + +* checking whether package ‘tidydr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'len0_null' not found +Error: unable to load R code in package ‘tidydr’ +Execution halted +ERROR: lazy loading failed for package ‘tidydr’ +* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ + + +``` +### CRAN + +``` +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (tidydr) + + +``` +# tis + +
+ +* Version: 1.39 +* GitHub: NA +* Source code: https://github.com/cran/tis +* Date/Publication: 2021-09-28 19:50:02 UTC +* Number of recursive dependencies: 15 + +Run `revdepcheck::cloud_details(, "tis")` for more info
@@ -16,174 +2367,213 @@ Run `revdepcheck::cloud_details(, "ggh4x")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggh4x-Ex.R’ failed + Running examples in ‘tis-Ex.R’ failed The error most likely occurred in: - > ### Name: coord_axes_inside - > ### Title: Cartesian coordinates with interior axes - > ### Aliases: coord_axes_inside + > ### Name: fortify.tis + > ### Title: Fortify a tis object + > ### Aliases: fortify.tis > > ### ** Examples > - > # A standard plot + > if(require("ggplot2") && require("reshape")) { ... - > p + coord_axes_inside() - Theme element `panel.background` is missing - Theme element `panel.grid.minor.y` is missing - Theme element `panel.grid.minor.x` is missing - Theme element `panel.grid.major.y` is missing - Theme element `panel.grid.major.x` is missing - Error in UseMethod("element_grob") : - no applicable method for 'element_grob' applied to an object of class "NULL" - Calls: ... lapply -> FUN -> draw_axis_labels -> exec -> + 10. └─ggplot2 (local) FUN(X[[i]], ...) + 11. └─scale$transform_df(df = df) + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─transformation$transform(x) + 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") + 18. └─rlang::abort(...) Execution halted ``` -* checking tests ... ERROR +## In both + +* checking package dependencies ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggh4x) - Loading required package: ggplot2 - > - > test_check("ggh4x") - Theme element `panel.background` is missing - Theme element `panel.grid.minor.y` is missing - ... - 16. └─ggplot2 (local) build_labels(...) - 17. └─base::lapply(...) - 18. └─ggplot2 (local) FUN(X[[i]], ...) - 19. └─ggplot2:::draw_axis_labels(...) - 20. ├─rlang::exec(...) - 21. └─ggplot2 (local) ``(...) - - [ FAIL 1 | WARN 0 | SKIP 18 | PASS 750 ] - Error: Test failures - Execution halted + Package which this enhances but not available for checking: ‘zoo’ ``` -* checking re-building of vignette outputs ... ERROR +# UniprotR + +
+ +* Version: 2.4.0 +* GitHub: https://github.com/Proteomicslab57357/UniprotR +* Source code: https://github.com/cran/UniprotR +* Date/Publication: 2024-03-05 15:10:02 UTC +* Number of recursive dependencies: 192 + +Run `revdepcheck::cloud_details(, "UniprotR")` for more info + +
+ +## Newly broken + +* checking whether package ‘UniprotR’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Facets.Rmd’ using rmarkdown - --- finished re-building ‘Facets.Rmd’ - - --- re-building ‘Miscellaneous.Rmd’ using rmarkdown - - Quitting from lines 199-204 [unnamed-chunk-13] (Miscellaneous.Rmd) - Error: processing vignette 'Miscellaneous.Rmd' failed with diagnostics: - no applicable method for 'element_grob' applied to an object of class "NULL" - ... - --- finished re-building ‘Statistics.Rmd’ - - --- re-building ‘ggh4x.Rmd’ using rmarkdown - --- finished re-building ‘ggh4x.Rmd’ - - SUMMARY: processing the following file failed: - ‘Miscellaneous.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘UniprotR’ + See ‘/tmp/workdir/UniprotR/new/UniprotR.Rcheck/00install.out’ for details. ``` -# MplusAutomation +# VALERIE
-* Version: 1.1.1 -* GitHub: https://github.com/michaelhallquist/MplusAutomation -* Source code: https://github.com/cran/MplusAutomation -* Date/Publication: 2024-01-30 23:40:02 UTC -* Number of recursive dependencies: 89 +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/VALERIE +* Date/Publication: 2020-07-10 10:20:13 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "MplusAutomation")` for more info +Run `revdepcheck::cloud_details(, "VALERIE")` for more info
## Newly broken +* checking whether package ‘VALERIE’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘VALERIE’ + See ‘/tmp/workdir/VALERIE/new/VALERIE.Rcheck/00install.out’ for details. + ``` + +## In both + * checking installed package size ... NOTE ``` - installed size is 5.4Mb + installed size is 9.6Mb sub-directories of 1Mb or more: - R 3.1Mb - data 1.0Mb + extdata 8.7Mb ``` -# PlasmaMutationDetector +# vannstats
-* Version: 1.7.2 +* Version: 1.3.4.14 * GitHub: NA -* Source code: https://github.com/cran/PlasmaMutationDetector -* Date/Publication: 2018-06-11 07:43:09 UTC -* Number of recursive dependencies: 107 +* Source code: https://github.com/cran/vannstats +* Date/Publication: 2023-04-15 04:30:02 UTC +* Number of recursive dependencies: 101 -Run `revdepcheck::cloud_details(, "PlasmaMutationDetector")` for more info +Run `revdepcheck::cloud_details(, "vannstats")` for more info
## Newly broken -* checking installed package size ... NOTE +* checking whether package ‘vannstats’ can be installed ... WARNING ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - extdata 4.0Mb + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vannstats’ + See ‘/tmp/workdir/vannstats/new/vannstats.Rcheck/00install.out’ for details. ``` -# Superpower +# vici
-* Version: 0.2.0 -* GitHub: https://github.com/arcaldwell49/Superpower -* Source code: https://github.com/cran/Superpower -* Date/Publication: 2022-05-17 13:50:02 UTC -* Number of recursive dependencies: 112 +* Version: 0.7.3 +* GitHub: https://github.com/sistm/vici +* Source code: https://github.com/cran/vici +* Date/Publication: 2024-02-02 16:20:02 UTC +* Number of recursive dependencies: 113 -Run `revdepcheck::cloud_details(, "Superpower")` for more info +Run `revdepcheck::cloud_details(, "vici")` for more info
## Newly broken -* checking tests ... ERROR +* checking whether package ‘vici’ can be installed ... WARNING ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(Superpower) - > - > - > test_check("Superpower") - [ FAIL 2 | WARN 18 | SKIP 13 | PASS 397 ] - ... - 1/1 mismatches - [1] -0.00304 - 0 == -0.00304 - ── Failure ('test_sim_cor.R:38:3'): simulated correlations fit expected values ── - `res5` not equal to 0. - 1/1 mismatches - [1] -0.00322 - 0 == -0.00322 - - [ FAIL 2 | WARN 18 | SKIP 13 | PASS 397 ] - Error: Test failures - Execution halted + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vici’ + See ‘/tmp/workdir/vici/new/vici.Rcheck/00install.out’ for details. ``` -## In both +# Wats -* checking dependencies in R code ... NOTE +
+ +* Version: 1.0.1 +* GitHub: https://github.com/OuhscBbmc/Wats +* Source code: https://github.com/cran/Wats +* Date/Publication: 2023-03-10 22:50:05 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "Wats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR ``` - Namespaces in Imports field not imported from: - ‘gridExtra’ ‘mvtnorm’ - All declared Imports should be used. + Running examples in ‘Wats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cartesian_periodic + > ### Title: Linear Plot with Periodic Elements + > ### Aliases: cartesian_periodic + > ### Keywords: Cartesian + > + > ### ** Examples + > + ... + 10. └─ggplot2 (local) FUN(X[[i]], ...) + 11. └─scale$transform_df(df = df) + 12. └─ggplot2 (local) transform_df(..., self = self) + 13. └─base::lapply(df[aesthetics], self$transform) + 14. └─ggplot2 (local) FUN(X[[i]], ...) + 15. └─ggplot2 (local) transform(..., self = self) + 16. └─transformation$transform(x) + 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") + 18. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘mbr-figures.Rmd’ + ... + + dv_name = "birth_rate", center_function = stats::median, + + spread_function = h_sprea .... [TRUNCATED] + + > cartesian_rolling(ds_linear = portfolio_cartesian$ds_linear, + + x_name = "date", y_name = "birth_rate", stage_id_name = "stage_id", + + chang .... [TRUNCATED] + + When sourcing ‘mbr-figures.R’: + Error: `transform_date()` works with objects of class only + Execution halted + + ‘mbr-figures.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘mbr-figures.Rmd’ using rmarkdown + + Quitting from lines 135-165 [fig-2-individual-basic] (mbr-figures.Rmd) + Error: processing vignette 'mbr-figures.Rmd' failed with diagnostics: + `transform_date()` works with objects of class only + --- failed re-building ‘mbr-figures.Rmd’ + + SUMMARY: processing the following file failed: + ‘mbr-figures.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` # xaringanthemer @@ -227,3 +2617,24 @@ Run `revdepcheck::cloud_details(, "xaringanthemer")` for more info Execution halted ``` +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘xaringanthemer.Rmd’ + ... + Warning in file(con, "r") : + cannot open file './../man/fragments/_quick-intro.Rmd': No such file or directory + + Quitting from lines 43-43 [unnamed-chunk-2] (xaringanthemer.Rmd) + + When tangling ‘xaringanthemer.Rmd’: + Error: cannot open the connection + Execution halted + + ‘ggplot2-themes.Rmd’ using ‘UTF-8’... OK + ‘template-variables.Rmd’ using ‘UTF-8’... OK + ‘xaringanthemer.Rmd’ using ‘UTF-8’... failed + ``` + diff --git a/tests/testthat/test-scale-date.R b/tests/testthat/test-scale-date.R index 83b95c6827..1183fcd756 100644 --- a/tests/testthat/test-scale-date.R +++ b/tests/testthat/test-scale-date.R @@ -68,3 +68,18 @@ test_that("datetime colour scales work", { expect_equal(range(get_layer_data(p)$colour), c("#132B43", "#56B1F7")) }) + +test_that("date(time) scales throw warnings when input is numeric", { + p <- ggplot(data.frame(x = 1, y = 1), aes(x, y)) + geom_point() + + expect_warning( + ggplot_build(p + scale_x_date()), + "The value was converted to a object." + ) + + expect_warning( + ggplot_build(p + scale_x_datetime()), + "The value was converted to a object." + ) + +}) From fb33e266ebed79cd5e0a3026ed5cee63f5d9b234 Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Mon, 8 Jul 2024 18:14:27 +0900 Subject: [PATCH 063/264] Expose position arg on geom_hline() and geom_vline() (#5965) --- NEWS.md | 2 ++ R/geom-hline.R | 3 ++- R/geom-vline.R | 3 ++- man/geom_abline.Rd | 15 +++++++++++++++ 4 files changed, 21 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 2696e04410..7e8594b4da 100644 --- a/NEWS.md +++ b/NEWS.md @@ -104,6 +104,8 @@ the `nbin` argument (@teunbrand, #5882, #5036) * `after_stat()` and `after_scale()` throw warnings when the computed aesthetics are not of the correct length (#5901). +* `geom_hline()` and `geom_vline()` now have `position` argument + (@yutannihilation, #4285). # ggplot2 3.5.1 diff --git a/R/geom-hline.R b/R/geom-hline.R index 924b41f40a..6b80d0bb08 100644 --- a/R/geom-hline.R +++ b/R/geom-hline.R @@ -4,6 +4,7 @@ NULL #' @export #' @rdname geom_abline geom_hline <- function(mapping = NULL, data = NULL, + position = "identity", ..., yintercept, na.rm = FALSE, @@ -29,7 +30,7 @@ geom_hline <- function(mapping = NULL, data = NULL, mapping = mapping, stat = StatIdentity, geom = GeomHline, - position = PositionIdentity, + position = position, show.legend = show.legend, inherit.aes = FALSE, params = list2( diff --git a/R/geom-vline.R b/R/geom-vline.R index 2705093f05..85cacf3e63 100644 --- a/R/geom-vline.R +++ b/R/geom-vline.R @@ -4,6 +4,7 @@ NULL #' @export #' @rdname geom_abline geom_vline <- function(mapping = NULL, data = NULL, + position = "identity", ..., xintercept, na.rm = FALSE, @@ -29,7 +30,7 @@ geom_vline <- function(mapping = NULL, data = NULL, mapping = mapping, stat = StatIdentity, geom = GeomVline, - position = PositionIdentity, + position = position, show.legend = show.legend, inherit.aes = FALSE, params = list2( diff --git a/man/geom_abline.Rd b/man/geom_abline.Rd index 9e13bc3de8..8fd63ae8e0 100644 --- a/man/geom_abline.Rd +++ b/man/geom_abline.Rd @@ -19,6 +19,7 @@ geom_abline( geom_hline( mapping = NULL, data = NULL, + position = "identity", ..., yintercept, na.rm = FALSE, @@ -28,6 +29,7 @@ geom_hline( geom_vline( mapping = NULL, data = NULL, + position = "identity", ..., xintercept, na.rm = FALSE, @@ -89,6 +91,19 @@ a warning. If \code{TRUE}, missing values are silently removed.} It can also be a named logical vector to finely select the aesthetics to display.} +\item{position}{A position adjustment to use on the data for this layer. This +can be used in various ways, including to prevent overplotting and +improving the display. The \code{position} argument accepts the following: +\itemize{ +\item The result of calling a position function, such as \code{position_jitter()}. +This method allows for passing extra arguments to the position. +\item A string naming the position adjustment. To give the position as a +string, strip the function name of the \code{position_} prefix. For example, +to use \code{position_jitter()}, give the position as \code{"jitter"}. +\item For more information and other ways to specify the position, see the +\link[=layer_positions]{layer position} documentation. +}} + \item{xintercept, yintercept, slope, intercept}{Parameters that control the position of the line. If these are set, \code{data}, \code{mapping} and \code{show.legend} are overridden.} From c6a9a14d5b8aebe05a206681acd901629e4e322b Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 10 Jul 2024 09:58:34 +0200 Subject: [PATCH 064/264] `geom_rect()` can derive corners from `x`/`width` or `y`/`height` (#5862) * required aesthetics to non-missing aes * doesn't inherit `optional_aes` * fill missing aes * throw error when unresolveable * protect against partial matching * add tests * add news bullet * adjust docs * fallback for corners wired through `params` * Revert " doesn't inherit `optional_aes`" This reverts commit 65030f5ecb3a63f7cdb650f900867d654d08c39a. * adapt `check_required_aesthetics()` to deal with multiple or-logic * undo aesthetic field voodoo * fill data from params more reliably * throw error from `resolve_rect()` * document --- NEWS.md | 2 + R/geom-rect.R | 72 +++++++++++++++++++++++++++++- R/geom-tile.R | 25 ++++++----- R/utilities-help.R | 2 +- R/utilities.R | 56 +++++++++++++++++------ man/geom_tile.Rd | 28 +++++------- tests/testthat/_snaps/utilities.md | 2 +- tests/testthat/test-geom-rect.R | 36 +++++++++++++++ 8 files changed, 178 insertions(+), 45 deletions(-) create mode 100644 tests/testthat/test-geom-rect.R diff --git a/NEWS.md b/NEWS.md index 7e8594b4da..ce5f733099 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_rect()` can now derive the required corners positions from `x`/`width` + or `y`/`height` parameterisation (@teunbrand, #5861). * All position scales now use the same definition of `x` and `y` aesthetics. This lets uncommon aesthetics like `xintercept` expand scales as usual. (#3342, #4966, @teunbrand) diff --git a/R/geom-rect.R b/R/geom-rect.R index f5eee4d4c5..0a9d4bdeed 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -31,7 +31,39 @@ GeomRect <- ggproto("GeomRect", Geom, default_aes = aes(colour = NA, fill = "grey35", linewidth = 0.5, linetype = 1, alpha = NA), - required_aes = c("xmin", "xmax", "ymin", "ymax"), + required_aes = c("x|width|xmin|xmax", "y|height|ymin|ymax"), + + setup_data = function(self, data, params) { + if (all(c("xmin", "xmax", "ymin", "ymax") %in% names(data))) { + return(data) + } + + # Fill in missing aesthetics from parameters + required <- strsplit(self$required_aes, "|", fixed = TRUE) + missing <- setdiff(unlist(required), names(data)) + default <- params[intersect(missing, names(params))] + data[names(default)] <- default + + if (is.null(data$xmin) || is.null(data$xmax)) { + x <- resolve_rect( + data[["xmin"]], data[["xmax"]], + data[["x"]], data[["width"]], + fun = snake_class(self), type = "x" + ) + i <- lengths(x) > 1 + data[c("xmin", "xmax")[i]] <- x[i] + } + if (is.null(data$ymin) || is.null(data$ymax)) { + y <- resolve_rect( + data[["ymin"]], data[["ymax"]], + data[["y"]], data[["height"]], + fun = snake_class(self), type = "y" + ) + i <- lengths(y) > 1 + data[c("ymin", "ymax")[i]] <- y[i] + } + data + }, draw_panel = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre") { data <- check_linewidth(data, snake_class(self)) @@ -73,3 +105,41 @@ GeomRect <- ggproto("GeomRect", Geom, rename_size = TRUE ) + +resolve_rect <- function(min = NULL, max = NULL, center = NULL, length = NULL, + fun, type) { + absent <- c(is.null(min), is.null(max), is.null(center), is.null(length)) + if (sum(absent) > 2) { + missing <- switch( + type, + x = c("xmin", "xmax", "x", "width"), + y = c("ymin", "ymax", "y", "height") + ) + cli::cli_abort(c( + "{.fn {fun}} requires two of the following aesthetics: \\ + {.or {.field {missing}}}.", + i = "Currently, {.field {missing[!absent]}} is present." + )) + } + + if (absent[1] && absent[2]) { + min <- center - 0.5 * length + max <- center + 0.5 * length + return(list(min = min, max = max)) + } + if (absent[1]) { + if (is.null(center)) { + min <- max - length + } else { + min <- max - 2 * (max - center) + } + } + if (absent[2]) { + if (is.null(center)) { + max <- min + length + } else { + max <- min + 2 * (center - min) + } + } + list(min = min, max = max) +} diff --git a/R/geom-tile.R b/R/geom-tile.R index ad01b1248f..a5e3232080 100644 --- a/R/geom-tile.R +++ b/R/geom-tile.R @@ -1,25 +1,26 @@ #' Rectangles #' #' `geom_rect()` and `geom_tile()` do the same thing, but are -#' parameterised differently: `geom_rect()` uses the locations of the four -#' corners (`xmin`, `xmax`, `ymin` and `ymax`), while -#' `geom_tile()` uses the center of the tile and its size (`x`, -#' `y`, `width`, `height`). `geom_raster()` is a high -#' performance special case for when all the tiles are the same size, and no -#' pattern fills are applied. +#' parameterised differently: `geom_tile()` uses the center of the tile and its +#' size (`x`, `y`, `width`, `height`), while `geom_rect()` can use those or the +#' locations of the corners (`xmin`, `xmax`, `ymin` and `ymax`). +#' `geom_raster()` is a high performance special case for when all the tiles +#' are the same size, and no pattern fills are applied. #' -#' @eval rd_aesthetics("geom", "tile", "Note that `geom_raster()` ignores `colour`.") +#' @eval rd_aesthetics( +#' "geom", "rect", +#' "`geom_tile()` understands only the `x`/`width` and `y`/`height` combinations. +#' Note that `geom_raster()` ignores `colour`." +#' ) #' @inheritParams layer #' @inheritParams geom_point #' @inheritParams geom_segment #' @export #' #' @details -#' `geom_rect()` and `geom_tile()`'s respond differently to scale -#' transformations due to their parameterisation. In `geom_rect()`, the scale -#' transformation is applied to the corners of the rectangles. In `geom_tile()`, -#' the transformation is applied only to the centres and its size is determined -#' after transformation. +#' Please note that the `width` and `height` aesthetics are not true position +#' aesthetics and therefore are not subject to scale transformation. It is +#' only after transformation that these aesthetics are applied. #' #' @examples #' # The most common use for rectangles is to draw a surface. You always want diff --git a/R/utilities-help.R b/R/utilities-help.R index 4a2312b549..87f5419612 100644 --- a/R/utilities-help.R +++ b/R/utilities-help.R @@ -23,7 +23,7 @@ rd_aesthetics <- function(type, name, extra_note = NULL) { rd_aesthetics_item <- function(x) { req <- x$required_aes - req <- sub("|", "} \\emph{or} \\code{", req, fixed = TRUE) + req <- gsub("|", "} \\emph{or} \\code{", req, fixed = TRUE) req_aes <- unlist(strsplit(x$required_aes, "|", fixed = TRUE)) optional_aes <- setdiff(x$aesthetics(), req_aes) all <- union(req, sort(optional_aes)) diff --git a/R/utilities.R b/R/utilities.R index 1a9181be69..a3357e6119 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -24,25 +24,53 @@ scales::alpha # @param name of object for error message # @keyword internal check_required_aesthetics <- function(required, present, name, call = caller_env()) { - if (is.null(required)) return() + if (is.null(required)) { + return() + } required <- strsplit(required, "|", fixed = TRUE) - if (any(lengths(required) > 1)) { - required <- lapply(required, rep_len, 2) - required <- list( - vapply(required, `[`, character(1), 1), - vapply(required, `[`, character(1), 2) + n <- lengths(required) + + is_present <- vapply( + required, + function(req) any(req %in% present), + logical(1) + ) + if (all(is_present)) { + return() + } + + # Deal with paired (bidirectional) aesthetics + pairs <- character() + missing_pairs <- n == 2 + if (any(missing_pairs)) { + pairs <- lapply(required[missing_pairs], rep_len, 2) + pairs <- list( + vapply(pairs, `[`, character(1), 1), + vapply(pairs, `[`, character(1), 2) ) - } else { - required <- list(unlist(required)) + pairs <- lapply(pairs, setdiff, present) + pairs <- vapply(pairs, function(x) { + as_cli("{.and {.field {x}}}") + }, character(1)) + pairs <- as_cli("{.or {pairs}}") } - missing_aes <- lapply(required, setdiff, present) - if (any(lengths(missing_aes) == 0)) return() - message <- "{.fn {name}} requires the following missing aesthetics: {.field {missing_aes[[1]]}}" - if (length(missing_aes) > 1) { - message <- paste0(message, " {.strong or} {.field {missing_aes[[2]]}}") + + other <- character() + missing_other <- !is_present & n != 2 + if (any(missing_other)) { + other <- lapply(required[missing_other], setdiff, present) + other <- vapply(other, function(x) { + as_cli("{.or {.field {x}}}") + }, character(1)) } - cli::cli_abort(paste0(message, "."), call = call) + + missing <- c(other, pairs) + + cli::cli_abort( + "{.fn {name}} requires the following missing aesthetics: {.and {missing}}.", + call = call + ) } # Concatenate a named list for output diff --git a/man/geom_tile.Rd b/man/geom_tile.Rd index a45ca07008..ac32298ee7 100644 --- a/man/geom_tile.Rd +++ b/man/geom_tile.Rd @@ -144,35 +144,31 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} } \description{ \code{geom_rect()} and \code{geom_tile()} do the same thing, but are -parameterised differently: \code{geom_rect()} uses the locations of the four -corners (\code{xmin}, \code{xmax}, \code{ymin} and \code{ymax}), while -\code{geom_tile()} uses the center of the tile and its size (\code{x}, -\code{y}, \code{width}, \code{height}). \code{geom_raster()} is a high -performance special case for when all the tiles are the same size, and no -pattern fills are applied. +parameterised differently: \code{geom_tile()} uses the center of the tile and its +size (\code{x}, \code{y}, \code{width}, \code{height}), while \code{geom_rect()} can use those or the +locations of the corners (\code{xmin}, \code{xmax}, \code{ymin} and \code{ymax}). +\code{geom_raster()} is a high performance special case for when all the tiles +are the same size, and no pattern fills are applied. } \details{ -\code{geom_rect()} and \code{geom_tile()}'s respond differently to scale -transformations due to their parameterisation. In \code{geom_rect()}, the scale -transformation is applied to the corners of the rectangles. In \code{geom_tile()}, -the transformation is applied only to the centres and its size is determined -after transformation. +Please note that the \code{width} and \code{height} aesthetics are not true position +aesthetics and therefore are not subject to scale transformation. It is +only after transformation that these aesthetics are applied. } \section{Aesthetics}{ -\code{geom_tile()} understands the following aesthetics (required aesthetics are in bold): +\code{geom_rect()} understands the following aesthetics (required aesthetics are in bold): \itemize{ -\item \strong{\code{\link[=aes_position]{x}}} -\item \strong{\code{\link[=aes_position]{y}}} +\item \strong{\code{\link[=aes_position]{x}} \emph{or} \code{width} \emph{or} \code{\link[=aes_position]{xmin}} \emph{or} \code{\link[=aes_position]{xmax}}} +\item \strong{\code{\link[=aes_position]{y}} \emph{or} \code{height} \emph{or} \code{\link[=aes_position]{ymin}} \emph{or} \code{\link[=aes_position]{ymax}}} \item \code{\link[=aes_colour_fill_alpha]{alpha}} \item \code{\link[=aes_colour_fill_alpha]{colour}} \item \code{\link[=aes_colour_fill_alpha]{fill}} \item \code{\link[=aes_group_order]{group}} -\item \code{height} \item \code{\link[=aes_linetype_size_shape]{linetype}} \item \code{\link[=aes_linetype_size_shape]{linewidth}} -\item \code{width} } +\code{geom_tile()} understands only the \code{x}/\code{width} and \code{y}/\code{height} combinations. Note that \code{geom_raster()} ignores \code{colour}. Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. diff --git a/tests/testthat/_snaps/utilities.md b/tests/testthat/_snaps/utilities.md index 804ce1ad27..0101c1edd1 100644 --- a/tests/testthat/_snaps/utilities.md +++ b/tests/testthat/_snaps/utilities.md @@ -12,7 +12,7 @@ --- - `test()` requires the following missing aesthetics: x and fill or y and fill. + `test()` requires the following missing aesthetics: fill and x or y. # remove_missing checks input diff --git a/tests/testthat/test-geom-rect.R b/tests/testthat/test-geom-rect.R new file mode 100644 index 0000000000..a0d90899f8 --- /dev/null +++ b/tests/testthat/test-geom-rect.R @@ -0,0 +1,36 @@ +test_that("geom_rect can derive corners", { + + corners <- c("xmin", "xmax", "ymin", "ymax") + full <- data.frame( + xmin = c(1, 2), xmax = c(3, 6), + ymin = c(1, 2), ymax = c(3, 6), + width = c(2, 4), height = c(2, 4), + x = c(2, 4), y = c(2, 4) + ) + + test <- full[, c("xmin", "ymin", "width", "height")] + test <- GeomRect$setup_data(test, NULL) + expect_equal(full[, corners], test[, corners]) + + test <- full[, c("xmin", "ymin", "x", "y")] + test <- GeomRect$setup_data(test, NULL) + expect_equal(full[, corners], test[, corners]) + + test <- full[, c("x", "y", "width", "height")] + test <- GeomRect$setup_data(test, NULL) + expect_equal(full[, corners], test[, corners]) + + test <- full[, c("xmax", "ymax", "width", "height")] + test <- GeomRect$setup_data(test, NULL) + expect_equal(full[, corners], test[, corners]) + + test <- full[, c("xmax", "ymax", "x", "y")] + test <- GeomRect$setup_data(test, NULL) + expect_equal(full[, corners], test[, corners]) + + test <- full[, c("x", "y")] + expect_error( + GeomRect$setup_data(test, NULL), + "requires two of the following aesthetics" + ) +}) From cd9410c8c9c7b1a15e9f8f6a10f0810937e9642e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 10 Jul 2024 10:17:10 +0200 Subject: [PATCH 065/264] Remove {glue} dependency (#5988) * replace `glue::glue()` with `paste0()` * remove glue imports * accept snapshot * add news bullet --- DESCRIPTION | 1 - NAMESPACE | 2 -- NEWS.md | 1 + R/aes-evaluation.R | 8 ++++---- R/fortify.R | 14 ++++++------- R/ggplot2-package.R | 1 - R/labels.R | 36 +++++++++++++++------------------ tests/testthat/_snaps/labels.md | 2 +- 8 files changed, 29 insertions(+), 36 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dcaf992c7f..3f34454b36 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,6 @@ Depends: R (>= 3.5) Imports: cli, - glue, grDevices, grid, gtable (>= 0.1.1), diff --git a/NAMESPACE b/NAMESPACE index 9068973de0..d6093fe7e9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -727,8 +727,6 @@ import(gtable) import(rlang) import(scales) import(vctrs) -importFrom(glue,glue) -importFrom(glue,glue_collapse) importFrom(grid,arrow) importFrom(grid,unit) importFrom(lifecycle,deprecated) diff --git a/NEWS.md b/NEWS.md index ce5f733099..381ba4c097 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* ggplot2 no longer imports {glue} (@teunbrand, #5986). * `geom_rect()` can now derive the required corners positions from `x`/`width` or `y`/`height` parameterisation (@teunbrand, #5861). * All position scales now use the same definition of `x` and `y` aesthetics. diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index e128fd2c15..4c682e3f63 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -231,9 +231,9 @@ is_calculated <- function(x, warn = FALSE) { } else if (is.symbol(x)) { res <- is_dotted_var(as.character(x)) if (res && warn) { - what <- I(glue("The dot-dot notation (`{x}`)")) + what <- I(paste0("The dot-dot notation (`", x, "`)")) var <- gsub(match_calculated_aes, "\\1", as.character(x)) - with <- I(glue("`after_stat({var})`")) + with <- I(paste0("`after_stat(", var, ")`")) deprecate_warn0("3.4.0", what, with, id = "ggplot-warn-aes-dot-dot") } res @@ -242,9 +242,9 @@ is_calculated <- function(x, warn = FALSE) { } else if (is.call(x)) { if (identical(x[[1]], quote(stat))) { if (warn) { - what <- I(glue("`{expr_deparse(x)}`")) + what <- I(paste0("`", expr_deparse(x), "`")) x[[1]] <- quote(after_stat) - with <- I(glue("`{expr_deparse(x)}`")) + with <- I(paste0("`", expr_deparse(x), "`")) deprecate_warn0("3.4.0", what, with, id = "ggplot-warn-aes-stat") } TRUE diff --git a/R/fortify.R b/R/fortify.R index 0e0b67516d..3a61e3ce49 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -74,21 +74,21 @@ validate_as_data_frame <- function(data) { #' @export fortify.default <- function(model, data, ...) { - msg0 <- paste0( - "{{.arg data}} must be a {{.cls data.frame}}, ", - "or an object coercible by {{.fn fortify}}, or a valid ", - "{{.cls data.frame}}-like object coercible by {{.fn as.data.frame}}" + msg <- paste0( + "{.arg data} must be a {.cls data.frame}, ", + "or an object coercible by {.fn fortify}, or a valid ", + "{.cls data.frame}-like object coercible by {.fn as.data.frame}" ) if (inherits(model, "uneval")) { msg <- c( - glue(msg0, ", not {obj_type_friendly(model)}."), + paste0(msg, ", not ", obj_type_friendly(model), "."), "i" = "Did you accidentally pass {.fn aes} to the {.arg data} argument?" ) cli::cli_abort(msg) } - msg0 <- paste0(msg0, ". ") + msg <- paste0(msg, ".") try_fetch( validate_as_data_frame(model), - error = function(cnd) cli::cli_abort(glue(msg0), parent = cnd) + error = function(cnd) cli::cli_abort(msg, parent = cnd) ) } diff --git a/R/ggplot2-package.R b/R/ggplot2-package.R index 539f03db97..46c1b334f0 100644 --- a/R/ggplot2-package.R +++ b/R/ggplot2-package.R @@ -3,7 +3,6 @@ ## usethis namespace: start #' @import scales grid gtable rlang vctrs -#' @importFrom glue glue glue_collapse #' @importFrom lifecycle deprecated #' @importFrom stats setNames #' @importFrom utils head tail diff --git a/R/labels.R b/R/labels.R index 66401683cb..d617bd9238 100644 --- a/R/labels.R +++ b/R/labels.R @@ -205,10 +205,11 @@ get_alt_text.gtable <- function(p, ...) { generate_alt_text <- function(p) { # Combine titles if (!is.null(p$label$title %||% p$labels$subtitle)) { - title <- glue(glue_collapse( - sub("\\.?$", "", c(p$labels$title, p$labels$subtitle)), - last = ": " - ), ". ") + title <- sub("\\.?$", "", c(p$labels$title, p$labels$subtitle)) + if (length(title) == 2) { + title <- paste0(title[1], ": ", title[2]) + } + title <- paste0(title, ". ") title <- safe_string(title) } else { title <- "" @@ -216,29 +217,24 @@ generate_alt_text <- function(p) { # Get axes descriptions - axes <- glue(" showing ", glue_collapse( - c(scale_description(p, "x"), scale_description(p, "y")), - last = " and " - )) + axes <- paste0(" showing ", scale_description(p, "x"), " and ", scale_description(p, "y")) axes <- safe_string(axes) # Get layer types layers <- vapply(p$layers, function(l) snake_class(l$geom), character(1)) layers <- sub("_", " ", sub("^geom_", "", unique0(layers))) - layers <- glue( - " using ", - if (length(layers) == 1) "a " else "", - glue_collapse(layers, sep = ", ", last = " and "), - " layer", - if (length(layers) == 1) "" else "s" - ) + if (length(layers) == 1) { + layers <- paste0(" using a ", layers, " layer") + } else { + layers <- paste0(" using ", oxford_comma(layers), " layers") + } layers <- safe_string(layers) # Combine - alt <- glue_collapse( - c(glue("{title}A plot{axes}{layers}"), p$labels$alt_insight), - last = ". " - ) + alt <- paste0(title, "A plot", axes, layers, ".") + if (!is.null(p$labels$alt_insight)) { + alt <- paste0(alt, " ", p$labels$alt_insight) + } as.character(alt) } safe_string <- function(string) { @@ -258,5 +254,5 @@ scale_description <- function(p, name) { if (is.null(lab)) { return(NULL) } - glue("{lab} on {type} {name}-axis") + paste0(lab, " on ", type, " ", name, "-axis") } diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index 8c673cfe11..87b2cb4fe2 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -3,7 +3,7 @@ Code get_alt_text(p) Output - [1] "A plot showing class on the x-axis and count on the y-axis using a bar layer" + [1] "A plot showing class on the x-axis and count on the y-axis using a bar layer." # plot.tag.position rejects invalid input From 76bb2cdd287423032f6bb56348ca8f4ec0a9b357 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 19:21:14 +0200 Subject: [PATCH 066/264] Default labels from attributes (option 2) (#5879) * resolve layers in `ggplot_build()` * remove label updates from `ggplot_add()` methods * pre-build for label tests * fix bug * add test * `get_alt_text()` applies to build plot --- R/labels.R | 57 ++++++++++++++++++++++++++++++++- R/plot-build.R | 1 + R/plot-construction.R | 19 +---------- R/plot.R | 2 -- tests/testthat/_snaps/labels.md | 2 +- tests/testthat/test-aes.R | 6 ++-- tests/testthat/test-labels.R | 21 +++++++++--- 7 files changed, 80 insertions(+), 28 deletions(-) diff --git a/R/labels.R b/R/labels.R index d617bd9238..3012868874 100644 --- a/R/labels.R +++ b/R/labels.R @@ -16,6 +16,56 @@ update_labels <- function(p, labels) { p } +# Called in `ggplot_build()` to set default labels not specified by user. +setup_plot_labels <- function(plot, layers, data) { + # Initiate from user-defined labels + labels <- plot$labels + + # Find labels from every layer + for (i in seq_along(layers)) { + layer <- layers[[i]] + mapping <- layer$computed_mapping + mapping <- strip_stage(mapping) + mapping <- strip_dots(mapping, strip_pronoun = TRUE) + + # Acquire default labels + mapping_default <- make_labels(mapping) + stat_default <- lapply( + make_labels(layer$stat$default_aes), + function(l) { + attr(l, "fallback") <- TRUE + l + } + ) + default <- defaults(mapping_default, stat_default) + + # Search for label attribute in symbolic mappings + symbolic <- vapply( + mapping, FUN.VALUE = logical(1), + function(x) is_quosure(x) && quo_is_symbol(x) + ) + symbols <- intersect(names(mapping)[symbolic], names(data[[i]])) + attribs <- lapply(setNames(nm = symbols), function(x) { + attr(data[[i]][[x]], "label", exact = TRUE) + }) + attribs <- attribs[lengths(attribs) > 0] + layer_labels <- defaults(attribs, default) + + # Set label priority: + # 1. Existing labels that aren't fallback labels + # 2. The labels of this layer, including fallback labels + # 3. Existing fallback labels + current <- labels + fallbacks <- vapply(current, function(l) isTRUE(attr(l, "fallback")), logical(1)) + + labels <- defaults(current[!fallbacks], layer_labels) + if (any(fallbacks)) { + labels <- defaults(labels, current) + } + } + labels +} + #' Modify axis, legend, and plot labels #' #' Good labels are critical for making your plots accessible to a wider @@ -144,8 +194,13 @@ get_alt_text <- function(p, ...) { #' @export get_alt_text.ggplot <- function(p, ...) { alt <- p$labels[["alt"]] %||% "" + if (!is.function(alt)) { + return(alt) + } p$labels[["alt"]] <- NULL - if (is.function(alt)) alt(p) else alt + build <- ggplot_build(p) + build$plot$labels[["alt"]] <- alt + get_alt_text(build) } #' @export get_alt_text.ggplot_built <- function(p, ...) { diff --git a/R/plot-build.R b/R/plot-build.R index 7b90d9cf26..2a68dd550f 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -60,6 +60,7 @@ ggplot_build.ggplot <- function(plot) { # Compute aesthetics to produce data with generalised variable names data <- by_layer(function(l, d) l$compute_aesthetics(d, plot), layers, data, "computing aesthetics") + plot$labels <- setup_plot_labels(plot, layers, data) data <- .ignore_data(data) # Transform all scales diff --git a/R/plot-construction.R b/R/plot-construction.R index b6d83fe1f0..de1306098f 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -133,10 +133,7 @@ ggplot_add.uneval <- function(object, plot, object_name) { plot$mapping <- defaults(object, plot$mapping) # defaults() doesn't copy class, so copy it. class(plot$mapping) <- class(object) - - labels <- make_labels(object) - names(labels) <- names(object) - update_labels(plot, labels) + plot } #' @export ggplot_add.Coord <- function(object, plot, object_name) { @@ -167,19 +164,5 @@ ggplot_add.by <- function(object, plot, object_name) { #' @export ggplot_add.Layer <- function(object, plot, object_name) { plot$layers <- append(plot$layers, object) - - # Add any new labels - mapping <- make_labels(object$mapping) - default <- lapply(make_labels(object$stat$default_aes), function(l) { - attr(l, "fallback") <- TRUE - l - }) - new_labels <- defaults(mapping, default) - current_labels <- plot$labels - current_fallbacks <- vapply(current_labels, function(l) isTRUE(attr(l, "fallback")), logical(1)) - plot$labels <- defaults(current_labels[!current_fallbacks], new_labels) - if (any(current_fallbacks)) { - plot$labels <- defaults(plot$labels, current_labels) - } plot } diff --git a/R/plot.R b/R/plot.R index 0d1df80f98..6bdcabc23f 100644 --- a/R/plot.R +++ b/R/plot.R @@ -133,8 +133,6 @@ ggplot.default <- function(data = NULL, mapping = aes(), ..., layout = ggproto(NULL, Layout) ), class = c("gg", "ggplot")) - p$labels <- make_labels(mapping) - set_last_plot(p) p } diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index 87b2cb4fe2..e1f6ed4140 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -3,7 +3,7 @@ Code get_alt_text(p) Output - [1] "A plot showing class on the x-axis and count on the y-axis using a bar layer." + [1] "A plot showing class on a discrete x-axis and count on a continuous y-axis using a bar layer." # plot.tag.position rejects invalid input diff --git a/tests/testthat/test-aes.R b/tests/testthat/test-aes.R index e407562082..1cb333fcac 100644 --- a/tests/testthat/test-aes.R +++ b/tests/testthat/test-aes.R @@ -94,12 +94,14 @@ test_that("assignment methods pull unwrap constants from quosures", { test_that("quosures are squashed when creating default label for a mapping", { p <- ggplot(mtcars) + aes(!!quo(identity(!!quo(cyl)))) - expect_identical(p$labels$x, "identity(cyl)") + labels <- ggplot_build(p)$plot$labels + expect_identical(labels$x, "identity(cyl)") }) test_that("labelling doesn't cause error if aesthetic is NULL", { p <- ggplot(mtcars) + aes(x = NULL) - expect_identical(p$labels$x, "x") + labels <- ggplot_build(p)$plot$labels + expect_identical(labels$x, "x") }) test_that("aes standardises aesthetic names", { diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index e119637f94..e338226bd4 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -52,13 +52,26 @@ test_that("setting guide labels works", { test_that("Labels from default stat mapping are overwritten by default labels", { p <- ggplot(mpg, aes(displ, hwy)) + geom_density2d() + labels <- ggplot_build(p)$plot$labels - expect_equal(p$labels$colour[1], "colour") - expect_true(attr(p$labels$colour, "fallback")) + expect_equal(labels$colour[1], "colour") + expect_true(attr(labels$colour, "fallback")) - p <- p + geom_smooth(aes(color = drv)) + p <- p + geom_smooth(aes(color = drv), method = "lm", formula = y ~ x) + labels <- ggplot_build(p)$plot$labels - expect_equal(p$labels$colour, "drv") + expect_equal(labels$colour, "drv") +}) + +test_that("Labels can be extracted from attributes", { + df <- mtcars + attr(df$mpg, "label") <- "Miles per gallon" + + p <- ggplot(df, aes(mpg, disp)) + geom_point() + labels <- ggplot_build(p)$plot$labels + + expect_equal(labels$x, "Miles per gallon") + expect_equal(labels$y, "disp") }) test_that("alt text is returned", { From 096b9663e53d4d28040ce0f252ddadab79bc7e14 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 19:23:38 +0200 Subject: [PATCH 067/264] Themes accept header font family (#5887) * new `header_family` theme argument * allow new underscore argument for consistency * caption and subtitle inherit from root text * add news bullets * add test * reoxygenate * set the default `header_family` to `NULL` * document * `plot.tag` inherits from root `text` element --- NEWS.md | 4 +++ R/theme-defaults.R | 24 ++++++++++++++- R/theme-elements.R | 6 ++-- man/ggtheme.Rd | 14 +++++++++ tests/testthat/_snaps/prohibited-functions.md | 30 ++++++++++++------- tests/testthat/test-theme.R | 11 +++++++ 6 files changed, 75 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 381ba4c097..89f06dfb20 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* Themes gain an additional `header_family` argument to easily set the font + for headers and titles (#5886). +* The `plot.subtitle`, `plot.caption` and `plot.tag` theme elements now inherit + from the root `text` element instead of the `title` element (#5886). * ggplot2 no longer imports {glue} (@teunbrand, #5986). * `geom_rect()` can now derive the required corners positions from `x`/`width` or `y`/`height` parameterisation (@teunbrand, #5861). diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 6ecd6d68c0..951f20a01c 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -6,6 +6,9 @@ #' #' @param base_size base font size, given in pts. #' @param base_family base font family +#' @param header_family font family for titles and headers. The default, `NULL`, +#' uses theme inheritance to set the font. This setting affects axis titles, +#' legend titles, the plot title and tag text. #' @param base_line_size base size for line elements #' @param base_rect_size base size for rect elements #' @@ -101,6 +104,7 @@ NULL #' @export #' @rdname ggtheme theme_grey <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { @@ -133,6 +137,9 @@ theme_grey <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + + title = element_text(family = header_family), + spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), @@ -257,12 +264,14 @@ theme_gray <- theme_grey #' @export #' @rdname ggtheme theme_bw <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { # Starts with theme_grey and then modify some parts theme_grey( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -283,6 +292,7 @@ theme_bw <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_linedraw <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { half_line <- base_size / 2 @@ -292,6 +302,7 @@ theme_linedraw <- function(base_size = 11, base_family = "", theme_bw( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -323,6 +334,7 @@ theme_linedraw <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_light <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { half_line <- base_size / 2 @@ -331,6 +343,7 @@ theme_light <- function(base_size = 11, base_family = "", theme_grey( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -363,6 +376,7 @@ theme_light <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_dark <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { half_line <- base_size / 2 @@ -371,6 +385,7 @@ theme_dark <- function(base_size = 11, base_family = "", theme_grey( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -401,12 +416,14 @@ theme_dark <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_minimal <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { # Starts with theme_bw and remove most parts theme_bw( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -426,11 +443,13 @@ theme_minimal <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_classic <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { theme_bw( base_size = base_size, base_family = base_family, + header_family = header_family, base_line_size = base_line_size, base_rect_size = base_rect_size ) %+replace% @@ -454,6 +473,7 @@ theme_classic <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_void <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { half_line <- base_size / 2 @@ -468,6 +488,7 @@ theme_void <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + title = element_text(family = header_family), spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), axis.text = element_blank(), @@ -530,6 +551,7 @@ theme_void <- function(base_size = 11, base_family = "", #' @export #' @rdname ggtheme theme_test <- function(base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size / 22, base_rect_size = base_size / 22) { half_line <- base_size / 2 @@ -549,9 +571,9 @@ theme_test <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + title = element_text(family = header_family), spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), - axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, diff --git a/R/theme-elements.R b/R/theme-elements.R index bf3c693f3b..4a0bfce774 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -600,10 +600,10 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { plot.background = el_def("element_rect", "rect"), plot.title = el_def("element_text", "title"), plot.title.position = el_def("character"), - plot.subtitle = el_def("element_text", "title"), - plot.caption = el_def("element_text", "title"), + plot.subtitle = el_def("element_text", "text"), + plot.caption = el_def("element_text", "text"), plot.caption.position = el_def("character"), - plot.tag = el_def("element_text", "title"), + plot.tag = el_def("element_text", "text"), plot.tag.position = el_def(c("character", "numeric", "integer")), # Need to also accept numbers plot.tag.location = el_def("character"), plot.margin = el_def(c("margin", "unit", "rel"), "margins"), diff --git a/man/ggtheme.Rd b/man/ggtheme.Rd index b3594db3f2..642319bcc9 100644 --- a/man/ggtheme.Rd +++ b/man/ggtheme.Rd @@ -16,6 +16,7 @@ theme_grey( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -23,6 +24,7 @@ theme_grey( theme_gray( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -30,6 +32,7 @@ theme_gray( theme_bw( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -37,6 +40,7 @@ theme_bw( theme_linedraw( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -44,6 +48,7 @@ theme_linedraw( theme_light( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -51,6 +56,7 @@ theme_light( theme_dark( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -58,6 +64,7 @@ theme_dark( theme_minimal( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -65,6 +72,7 @@ theme_minimal( theme_classic( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -72,6 +80,7 @@ theme_classic( theme_void( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -79,6 +88,7 @@ theme_void( theme_test( base_size = 11, base_family = "", + header_family = NULL, base_line_size = base_size/22, base_rect_size = base_size/22 ) @@ -88,6 +98,10 @@ theme_test( \item{base_family}{base font family} +\item{header_family}{font family for titles and headers. The default, \code{NULL}, +uses theme inheritance to set the font. This setting affects axis titles, +legend titles, the plot title and tag text.} + \item{base_line_size}{base size for line elements} \item{base_rect_size}{base size for rect elements} diff --git a/tests/testthat/_snaps/prohibited-functions.md b/tests/testthat/_snaps/prohibited-functions.md index f2aa9bf4d2..afc77c3c60 100644 --- a/tests/testthat/_snaps/prohibited-functions.md +++ b/tests/testthat/_snaps/prohibited-functions.md @@ -184,34 +184,44 @@ [1] "contour_var" $theme_bw - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_classic - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_dark - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_gray - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_grey - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_light - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_linedraw - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_minimal - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_test - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $theme_void - [1] "base_size" "base_family" "base_line_size" "base_rect_size" + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" $transform_position [1] "trans_x" "trans_y" diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index b201602963..a9568cfd72 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -583,6 +583,17 @@ test_that("Minor tick length supports biparental inheritance", { ) }) +test_that("header_family is passed on correctly", { + + td <- theme_dark(base_family = "x", header_family = "y") + + test <- calc_element("plot.title", td) + expect_equal(test$family, "y") + + test <- calc_element("plot.subtitle", td) + expect_equal(test$family, "x") +}) + test_that("complete_theme completes a theme", { # `NULL` should match default gray <- theme_gray() From 744e021087cd209ea836ea5653ed7aa13a143110 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 19:44:31 +0200 Subject: [PATCH 068/264] Encapsulate `sf_grob()` in `GeomSf$draw_panel()` (#5904) * migrate removing missing values to `GeomSf$handle_na` * handle grob wrapping in `GeomSf$draw_panel()` * remove `sf_grob()` --- R/geom-sf.R | 110 ++++++++++++++++++---------------- tests/testthat/test-geom-sf.R | 2 +- 2 files changed, 59 insertions(+), 53 deletions(-) diff --git a/R/geom-sf.R b/R/geom-sf.R index ba559c1243..c6298e4b3a 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -201,10 +201,36 @@ GeomSf <- ggproto("GeomSf", Geom, cli::cli_abort("{.fn {snake_class(self)}} can only be used with {.fn coord_sf}.") } - # Need to refactor this to generate one grob per geometry type - coord <- coord$transform(data, panel_params) - sf_grob(coord, lineend = lineend, linejoin = linejoin, linemitre = linemitre, - arrow = arrow, arrow.fill = arrow.fill, na.rm = na.rm) + data <- coord$transform(data, panel_params) + + type <- sf_types[sf::st_geometry_type(data$geometry)] + is_point <- type == "point" + is_line <- type == "line" + is_collection <- type == "collection" + + fill <- fill_alpha(data$fill %||% rep(NA, nrow(data)), data$alpha) + fill[is_line] <- arrow.fill %||% fill[is_line] + + colour <- data$colour + colour[is_point | is_line] <- + alpha(colour[is_point | is_line], data$alpha[is_point | is_line]) + + point_size <- data$size + point_size[!(is_point | is_collection)] <- + data$linewidth[!(is_point | is_collection)] + + stroke <- data$stroke * .stroke / 2 + font_size <- point_size * .pt + stroke + + linewidth <- data$linewidth * .pt + linewidth[is_point] <- stroke[is_point] + + gp <- gpar( + col = colour, fill = fill, fontsize = font_size, lwd = linewidth, + lineend = lineend, linejoin = linejoin, linemitre = linemitre + ) + + sf::st_as_grob(data$geometry, pch = data$shape, gp = gp, arrow = arrow) }, draw_key = function(data, params, size) { @@ -214,57 +240,37 @@ GeomSf <- ggproto("GeomSf", Geom, line = draw_key_path(data, params, size), draw_key_polygon(data, params, size) ) - } -) + }, -sf_grob <- function(x, lineend = "butt", linejoin = "round", linemitre = 10, - arrow = NULL, arrow.fill = NULL, na.rm = TRUE) { - type <- sf_types[sf::st_geometry_type(x$geometry)] - is_point <- type == "point" - is_line <- type == "line" - is_other <- type == "other" - is_collection <- type == "collection" - type_ind <- match(type, c("point", "line", "other", "collection")) - remove <- rep_len(FALSE, nrow(x)) - remove[is_point] <- detect_missing(x, c(GeomPoint$required_aes, GeomPoint$non_missing_aes))[is_point] - remove[is_line] <- detect_missing(x, c(GeomPath$required_aes, GeomPath$non_missing_aes))[is_line] - remove[is_other] <- detect_missing(x, c(GeomPolygon$required_aes, GeomPolygon$non_missing_aes))[is_other] - if (any(remove)) { - if (!na.rm) { - cli::cli_warn(paste0( - "Removed {sum(remove)} row{?s} containing missing values or values ", - "outside the scale range ({.fn geom_sf})." - )) + handle_na = function(self, data, params) { + remove <- rep(FALSE, nrow(data)) + + types <- sf_types[sf::st_geometry_type(data$geometry)] + types <- split(seq_along(remove), types) + + get_missing <- function(geom) { + detect_missing(data, c(geom$required_aes, geom$non_missing_aes)) } - x <- x[!remove, , drop = FALSE] - type_ind <- type_ind[!remove] - is_collection <- is_collection[!remove] - } - alpha <- x$alpha %||% NA - fill <- fill_alpha(x$fill %||% NA, alpha) - fill[is_line] <- arrow.fill %||% fill[is_line] - col <- x$colour %||% NA - col[is_point | is_line] <- alpha(col[is_point | is_line], alpha[is_point | is_line]) - - size <- x$size %||% 0.5 - linewidth <- x$linewidth %||% 0.5 - point_size <- ifelse( - is_collection, - x$size, - ifelse(is_point, size, linewidth) - ) - stroke <- (x$stroke %||% 0) * .stroke / 2 - fontsize <- point_size * .pt + stroke - lwd <- ifelse(is_point, stroke, linewidth * .pt) - pch <- x$shape - lty <- x$linetype - gp <- gpar( - col = col, fill = fill, fontsize = fontsize, lwd = lwd, lty = lty, - lineend = lineend, linejoin = linejoin, linemitre = linemitre - ) - sf::st_as_grob(x$geometry, pch = pch, gp = gp, arrow = arrow) -} + remove[types$point] <- get_missing(GeomPoint)[types$point] + remove[types$line] <- get_missing(GeomPath)[types$line] + remove[types$other] <- get_missing(GeomPolygon)[types$other] + + remove <- remove | get_missing(self) + + if (any(remove)) { + data <- vec_slice(data, !remove) + if (!isTRUE(params$na.rm)) { + cli::cli_warn( + "Removed {sum(remove)} row{?s} containing missing values or values \\ + outside the scale range ({.fn {snake_class(self)}})." + ) + } + } + + data + } +) #' @export #' @rdname ggsf diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index 666c9799ea..fac4c8b87a 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -151,7 +151,7 @@ test_that("errors are correctly triggered", { ), linewidth = c(1, NA) ) - expect_snapshot_warning(sf_grob(pts, na.rm = FALSE)) + expect_snapshot_warning(GeomSf$handle_na(pts, list(na.rm = FALSE))) }) # Visual tests ------------------------------------------------------------ From 66a4362985e2ac95d15f68793153775cdcfe8162 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 19:52:33 +0200 Subject: [PATCH 069/264] Custom inside-axis position for `coord_radial()` (#5908) * Allow setting custom axis position in `r.axis.inside` * document * add test * add news bullet * fix grid bug when `direction = -1` * fix direction bug for inner axes --- NEWS.md | 6 ++ R/coord-radial.R | 78 ++++++++++++------- man/coord_polar.Rd | 14 +++- ...with-axes-placed-at-90-and-225-degrees.svg | 67 ++++++++++++++++ tests/testthat/test-coord-polar.R | 17 ++++ 5 files changed, 150 insertions(+), 32 deletions(-) create mode 100644 tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg diff --git a/NEWS.md b/NEWS.md index 89f06dfb20..ecb1a4cacd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,11 @@ # ggplot2 (development version) +* `coord_radial(r.axis.inside)` can now take a numeric value to control + placement of internally placed radius axes (@teunbrand, #5805). +* (internal) default labels are derived in `ggplot_build()` rather than + in `ggplot_add.Layer()` (@teunbrand, #5894) +* An attempt is made to use a variable's label attribute as default label + (@teunbrand, #4631) * Themes gain an additional `header_family` argument to easily set the font for headers and titles (#5886). * The `plot.subtitle`, `plot.caption` and `plot.tag` theme elements now inherit diff --git a/R/coord-radial.R b/R/coord-radial.R index b426bc27a8..c47d55bb56 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -7,10 +7,14 @@ #' @param expand If `TRUE`, the default, adds a small expansion factor the #' the limits to prevent overlap between data and axes. If `FALSE`, limits #' are taken directly from the scale. -#' @param r.axis.inside If `TRUE`, places the radius axis inside the -#' panel. If `FALSE`, places the radius axis next to the panel. The default, -#' `NULL`, places the radius axis outside if the `start` and `end` arguments -#' form a full circle. +#' @param r.axis.inside One of the following: +#' * `NULL` (default) places the axis next to the panel if `start` and +#' `end` arguments form a full circle and inside the panel otherwise. +#' * `TRUE` to place the radius axis inside the panel. +#' * `FALSE` to place the radius axis next to the panel. +#' * A numeric value, setting a theta axis value at which +#' the axis should be placed inside the panel. Can be given as a length 2 +#' vector to control primary and secondary axis placement separately. #' @param rotate.angle If `TRUE`, transforms the `angle` aesthetic in data #' in accordance with the computed `theta` position. If `FALSE` (default), #' no such transformation is performed. Can be useful to rotate text geoms in @@ -58,7 +62,10 @@ coord_radial <- function(theta = "x", theta <- arg_match0(theta, c("x", "y")) r <- if (theta == "x") "y" else "x" - check_bool(r.axis.inside, allow_null = TRUE) + if (!is.numeric(r.axis.inside)) { + check_bool(r.axis.inside, allow_null = TRUE) + } + check_bool(expand) check_bool(rotate.angle) check_number_decimal(start, allow_infinite = FALSE) @@ -130,12 +137,29 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, setup_panel_params = function(self, scale_x, scale_y, params = list()) { - c( + + params <- c( view_scales_polar(scale_x, self$theta, expand = self$expand), view_scales_polar(scale_y, self$theta, expand = self$expand), list(bbox = polar_bbox(self$arc, inner_radius = self$inner_radius), arc = self$arc, inner_radius = self$inner_radius) ) + + axis_rotation <- self$r_axis_inside + if (is.numeric(axis_rotation)) { + theta_scale <- switch(self$theta, x = scale_x, y = scale_y) + axis_rotation <- theta_scale$transform(axis_rotation) + axis_rotation <- oob_squish(axis_rotation, params$theta.range) + axis_rotation <- theta_rescale( + axis_rotation, params$theta.range, + params$arc, 1 + ) + params$axis_rotation <- rep_len(axis_rotation, length.out = 2) + } else { + params$axis_rotation <- params$arc + } + + params }, setup_panel_guides = function(self, panel_params, guides, params = list()) { @@ -173,18 +197,17 @@ CoordRadial <- ggproto("CoordRadial", Coord, opposite_r <- isTRUE(scales$r$position %in% c("bottom", "left")) } - if (self$r_axis_inside) { + if (!isFALSE(self$r_axis_inside)) { - arc <- rad2deg(self$arc) r_position <- c("left", "right") # If both opposite direction and opposite position, don't flip if (xor(self$direction == -1, opposite_r)) { - arc <- rev(arc) r_position <- rev(r_position) } - - guide_params[["r"]]$position <- r_position[1] - guide_params[["r.sec"]]$position <- r_position[2] + arc <- rad2deg(panel_params$axis_rotation) * self$direction + if (opposite_r) { + arc <- rev(arc) + } # Set guide text angles guide_params[["r"]]$angle <- guide_params[["r"]]$angle %|W|% arc[1] guide_params[["r.sec"]]$angle <- guide_params[["r.sec"]]$angle %|W|% arc[2] @@ -193,9 +216,9 @@ CoordRadial <- ggproto("CoordRadial", Coord, if (opposite_r) { r_position <- rev(r_position) } - guide_params[["r"]]$position <- r_position[1] - guide_params[["r.sec"]]$position <- r_position[2] } + guide_params[["r"]]$position <- r_position[1] + guide_params[["r.sec"]]$position <- r_position[2] guide_params[drop_guides] <- list(NULL) guides$update_params(guide_params) @@ -223,7 +246,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, gdefs[[t]] <- guides[[t]]$get_layer_key(gdefs[[t]], layers) } - if (self$r_axis_inside) { + if (!isFALSE(self$r_axis_inside)) { # For radial axis, we need to pretend that rotation starts at 0 and # the bounding box is for circles, otherwise tick positions will be # spaced too closely. @@ -273,14 +296,14 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, render_axis_v = function(self, panel_params, theme) { - if (self$r_axis_inside) { + if (!isFALSE(self$r_axis_inside)) { return(list(left = zeroGrob(), right = zeroGrob())) } CoordCartesian$render_axis_v(panel_params, theme) }, render_axis_h = function(self, panel_params, theme) { - if (self$r_axis_inside) { + if (!isFALSE(self$r_axis_inside)) { return(list(top = zeroGrob(), bottom = zeroGrob())) } CoordCartesian$render_axis_h(panel_params, theme) @@ -303,8 +326,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, if (length(theta_min) > 0) { theta_min <- theta_rescale(theta_min, theta_lim, arc, dir) } - theta_fine <- seq(self$arc[1], self$arc[2], length.out = 100) + theta_fine <- theta_rescale(seq(0, 1, length.out = 100), c(0, 1), arc, dir) r_fine <- r_rescale(panel_params$r.major, panel_params$r.range, panel_params$inner_radius) @@ -345,10 +368,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, theta_grid(theta_min, grid_elems[[2]], inner_radius, bbox), element_render( theme, majorr, name = "radius", - x = rescale(rep(r_fine, each = length(theta_fine)) * - rep(sin(theta_fine), length(r_fine)) + 0.5, from = bbox$x), - y = rescale(rep(r_fine, each = length(theta_fine)) * - rep(cos(theta_fine), length(r_fine)) + 0.5, from = bbox$y), + x = rescale(outer(sin(theta_fine), r_fine) + 0.5, from = bbox$x), + y = rescale(outer(cos(theta_fine), r_fine) + 0.5, from = bbox$y), id.lengths = rep(length(theta_fine), length(r_fine)), default.units = "native" ) @@ -359,7 +380,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, border <- element_render(theme, "panel.border", fill = NA) - if (!self$r_axis_inside) { + if (isFALSE(self$r_axis_inside)) { out <- grobTree( panel_guides_grob(panel_params$guides, "theta", theme), panel_guides_grob(panel_params$guides, "theta.sec", theme), @@ -370,14 +391,15 @@ CoordRadial <- ggproto("CoordRadial", Coord, bbox <- panel_params$bbox dir <- self$direction - arc <- if (dir == 1) self$arc else rev(self$arc) - arc <- dir * rad2deg(-arc) + rot <- panel_params$axis_rotation + rot <- if (dir == 1) rot else rev(rot) + rot <- dir * rad2deg(-rot) left <- panel_guides_grob(panel_params$guides, position = "left", theme) - left <- rotate_r_axis(left, arc[1], bbox, "left") + left <- rotate_r_axis(left, rot[1], bbox, "left") right <- panel_guides_grob(panel_params$guides, position = "right", theme) - right <- rotate_r_axis(right, arc[2], bbox, "right") + right <- rotate_r_axis(right, rot[2], bbox, "right") grobTree( panel_guides_grob(panel_params$guides, "theta", theme), @@ -426,7 +448,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, setup_params = function(self, data) { - if (!self$r_axis_inside) { + if (isFALSE(self$r_axis_inside)) { place <- in_arc(c(0, 0.5, 1, 1.5) * pi, self$arc) if (place[1]) { return(list(r_axis = "left", fake_arc = c(0, 2) * pi)) diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index 78265507d6..aadbd9b00f 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -41,10 +41,16 @@ for partial polar coordinates. The default, \code{NULL}, is set to the limits to prevent overlap between data and axes. If \code{FALSE}, limits are taken directly from the scale.} -\item{r.axis.inside}{If \code{TRUE}, places the radius axis inside the -panel. If \code{FALSE}, places the radius axis next to the panel. The default, -\code{NULL}, places the radius axis outside if the \code{start} and \code{end} arguments -form a full circle.} +\item{r.axis.inside}{One of the following: +\itemize{ +\item \code{NULL} (default) places the axis next to the panel if \code{start} and +\code{end} arguments form a full circle and inside the panel otherwise. +\item \code{TRUE} to place the radius axis inside the panel. +\item \code{FALSE} to place the radius axis next to the panel. +\item A numeric value, setting a theta axis value at which +the axis should be placed inside the panel. Can be given as a length 2 +vector to control primary and secondary axis placement separately. +}} \item{rotate.angle}{If \code{TRUE}, transforms the \code{angle} aesthetic in data in accordance with the computed \code{theta} position. If \code{FALSE} (default), diff --git a/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg new file mode 100644 index 0000000000..59e7973b41 --- /dev/null +++ b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +100 +200 +300 + + + + + + +5 +10 + + + + + +5 +10 +x +y +full circle with axes placed at 90 and 225 degrees + + diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index 6e5f435d60..a663a43d98 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -270,3 +270,20 @@ test_that("coord_radial() draws correctly", { theme ) }) + +test_that("coord_radial()'s axis internal placement works", { + + df <- data.frame(x = c(0, 360), y = c(1, 14)) + + expect_doppelganger( + "full circle with axes placed at 90 and 225 degrees", + ggplot(df, aes(x, y)) + + geom_point() + + coord_radial( + expand = FALSE, + r.axis.inside = c(90, 225) + ) + + guides(r.sec = "axis") + + theme(axis.line = element_line()) + ) +}) From e0bb6a3cfbda6e6108b63f5596398d3e9706d434 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:08:21 +0200 Subject: [PATCH 070/264] Strip label accessor (#5924) * new format_strip_labels method * use new method * new accessor function * add test * add news bullet --- NAMESPACE | 1 + NEWS.md | 1 + R/facet-.R | 30 ++++++++++++++++++++++- R/facet-grid-.R | 38 +++++++++++++++++++++++------- R/facet-wrap.R | 33 +++++++++++++++----------- man/get_strip_labels.Rd | 28 ++++++++++++++++++++++ man/render_strips.Rd | 2 +- tests/testthat/test-facet-strips.R | 18 ++++++++++++++ 8 files changed, 127 insertions(+), 24 deletions(-) create mode 100644 man/get_strip_labels.Rd diff --git a/NAMESPACE b/NAMESPACE index d6093fe7e9..6a57c5132d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -427,6 +427,7 @@ export(get_last_plot) export(get_layer_data) export(get_layer_grob) export(get_panel_scales) +export(get_strip_labels) export(get_theme) export(gg_dep) export(gg_par) diff --git a/NEWS.md b/NEWS.md index ecb1a4cacd..708d631e20 100644 --- a/NEWS.md +++ b/NEWS.md @@ -119,6 +119,7 @@ are not of the correct length (#5901). * `geom_hline()` and `geom_vline()` now have `position` argument (@yutannihilation, #4285). +* New function `get_strip_labels()` to retrieve facet labels (@teunbrand, #4979) # ggplot2 3.5.1 diff --git a/R/facet-.R b/R/facet-.R index f985d84afc..96c96dc6fd 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -257,6 +257,9 @@ Facet <- ggproto("Facet", NULL, }, vars = function() { character(0) + }, + format_strip_labels = function(layout, params) { + return() } ) @@ -321,6 +324,31 @@ vars <- function(...) { quos(...) } +#' Accessing a plot's facet strip labels +#' +#' This functions retrieves labels from facet strips with the labeller applied. +#' +#' @param plot A ggplot or build ggplot object. +#' +#' @return `NULL` if there are no labels, otherwise a list of data.frames +#' containing the labels. +#' @export +#' @keywords internal +#' +#' @examples +#' # Basic plot +#' p <- ggplot(mpg, aes(displ, hwy)) + +#' geom_point() +#' +#' get_strip_labels(p) # empty facets +#' get_strip_labels(p + facet_wrap(year ~ cyl)) +#' get_strip_labels(p + facet_grid(year ~ cyl)) +get_strip_labels <- function(plot = get_last_plot()) { + plot <- ggplot_build(plot) + layout <- plot$layout$layout + params <- plot$layout$facet_params + plot$plot$facet$format_strip_labels(layout, params) +} #' Is this object a faceting specification? #' @@ -779,7 +807,7 @@ render_axes <- function(x = NULL, y = NULL, coord, theme, transpose = FALSE) { #' #' @keywords internal #' @export -render_strips <- function(x = NULL, y = NULL, labeller, theme) { +render_strips <- function(x = NULL, y = NULL, labeller = identity, theme) { list( x = build_strip(x, labeller, theme, TRUE), y = build_strip(y, labeller, theme, FALSE) diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 4d4f12f345..f7783f8985 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -380,16 +380,11 @@ FacetGrid <- ggproto("FacetGrid", Facet, table }, - attach_strips = function(table, layout, params, theme) { + attach_strips = function(self, table, layout, params, theme) { - col_vars <- unique0(layout[names(params$cols)]) - row_vars <- unique0(layout[names(params$rows)]) - attr(col_vars, "type") <- "cols" - attr(row_vars, "type") <- "rows" - attr(col_vars, "facet") <- "grid" - attr(row_vars, "facet") <- "grid" + strips <- self$format_strip_labels(layout, params) + strips <- render_strips(strips$cols, strips$rows, theme = theme) - strips <- render_strips(col_vars, row_vars, params$labeller, theme) padding <- convertUnit(calc_element("strip.switch.pad.grid", theme), "cm") switch_x <- !is.null(params$switch) && params$switch %in% c("both", "x") @@ -432,6 +427,33 @@ FacetGrid <- ggproto("FacetGrid", Facet, vars = function(self) { names(c(self$params$rows, self$params$cols)) + }, + + format_strip_labels = function(layout, params) { + + labeller <- match.fun(params$labeller) + + cols <- intersect(names(layout), names(params$cols)) + if (length(cols) > 0) { + col_vars <- unique0(layout[cols]) + attr(col_vars, "type") <- "cols" + attr(col_vars, "facet") <- "grid" + cols <- data_frame0(!!!labeller(col_vars)) + } else { + cols <- NULL + } + + rows <- intersect(names(layout), names(params$rows)) + if (length(rows) > 0) { + row_vars <- unique0(layout[rows]) + attr(row_vars, "type") <- "rows" + attr(row_vars, "facet") <- "grid" + rows <- data_frame0(!!!labeller(row_vars)) + } else { + rows <- NULL + } + + list(cols = cols, rows = rows) } ) diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 4f07736f7d..68c02f0b21 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -371,22 +371,11 @@ FacetWrap <- ggproto("FacetWrap", Facet, weave_axes(table, axes, empty) }, - attach_strips = function(table, layout, params, theme) { + attach_strips = function(self, table, layout, params, theme) { # Format labels - if (length(params$facets) == 0) { - labels <- data_frame0("(all)" = "(all)", .size = 1) - } else { - labels <- layout[names(params$facets)] - } - attr(labels, "facet") <- "wrap" - - # Render individual strips - strips <- render_strips( - x = structure(labels, type = "rows"), - y = structure(labels, type = "cols"), - params$labeller, theme - ) + strips <- self$format_strip_labels(layout, params) + strips <- render_strips(strips$facets, strips$facets, theme = theme) # Set position invariant parameters padding <- convertUnit(calc_element("strip.switch.pad.wrap", theme), "cm") @@ -457,6 +446,22 @@ FacetWrap <- ggproto("FacetWrap", Facet, }, vars = function(self) { names(self$params$facets) + }, + + format_strip_labels = function(layout, params) { + if (length(params$facets) == 0) { + labels <- data_frame0("(all)" = "(all)", .size = 1) + } else { + labels <- layout[intersect(names(params$facets), names(layout))] + } + if (empty(labels)) { + return(NULL) + } + attr(labels, "facet") <- "wrap" + attr(labels, "type") <- switch(params$strip.position, left = , right = "rows", "cols") + + labeller <- match.fun(params$labeller) + list(facets = data_frame0(!!!labeller(labels))) } ) diff --git a/man/get_strip_labels.Rd b/man/get_strip_labels.Rd new file mode 100644 index 0000000000..10c3c3c01b --- /dev/null +++ b/man/get_strip_labels.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/facet-.R +\name{get_strip_labels} +\alias{get_strip_labels} +\title{Accessing a plot's facet strip labels} +\usage{ +get_strip_labels(plot = get_last_plot()) +} +\arguments{ +\item{plot}{A ggplot or build ggplot object.} +} +\value{ +\code{NULL} if there are no labels, otherwise a list of data.frames +containing the labels. +} +\description{ +This functions retrieves labels from facet strips with the labeller applied. +} +\examples{ +# Basic plot +p <- ggplot(mpg, aes(displ, hwy)) + + geom_point() + +get_strip_labels(p) # empty facets +get_strip_labels(p + facet_wrap(year ~ cyl)) +get_strip_labels(p + facet_grid(year ~ cyl)) +} +\keyword{internal} diff --git a/man/render_strips.Rd b/man/render_strips.Rd index b62a836c8d..468caf6899 100644 --- a/man/render_strips.Rd +++ b/man/render_strips.Rd @@ -4,7 +4,7 @@ \alias{render_strips} \title{Render panel strips} \usage{ -render_strips(x = NULL, y = NULL, labeller, theme) +render_strips(x = NULL, y = NULL, labeller = identity, theme) } \arguments{ \item{x, y}{A data.frame with a column for each variable and a row for each diff --git a/tests/testthat/test-facet-strips.R b/tests/testthat/test-facet-strips.R index ece67935a4..c2f131191e 100644 --- a/tests/testthat/test-facet-strips.R +++ b/tests/testthat/test-facet-strips.R @@ -209,3 +209,21 @@ test_that("strip clipping can be set from the theme", { expect_equal(strip$x$top[[1]]$layout$clip, "off") }) +test_that("strip labels can be accessed", { + + expect_null(get_strip_labels(ggplot())) + + expect_equal( + get_strip_labels(ggplot() + facet_wrap(vars("X", "Y"))), + list(facets = data_frame0(`"X"` = "X", `"Y"` = "Y")) + ) + + expect_equal( + get_strip_labels(ggplot() + facet_grid(vars("X"), vars("Y"))), + list( + cols = data_frame0(`"Y"` = "Y"), + rows = data_frame0(`"X"` = "X") + ) + ) +}) + From 1c1cdc3734ee7fc881c8260fa93c398ae52bb88a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:17:25 +0200 Subject: [PATCH 071/264] Reverse dodging (#5923) * `reverse` plumbing for `position_dodge() * `reverse` plumbing in `position_jitterdodge()` * do not internally sort groups in `position_dodge()` * add test * add news bullet * Align interpretation with `position_dodge2()` * document --- NEWS.md | 2 ++ R/position-dodge.R | 18 +++++++++++++----- R/position-dodge2.R | 2 -- R/position-jitterdodge.R | 20 ++++++++++++++++---- man/position_dodge.Rd | 13 +++++++++---- man/position_jitterdodge.Rd | 4 ++++ tests/testthat/test-position_dodge.R | 14 ++++++++++++++ 7 files changed, 58 insertions(+), 15 deletions(-) diff --git a/NEWS.md b/NEWS.md index 708d631e20..6b6cc439ff 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `position_dodge()` and `position_jitterdodge()` now have a `reverse` argument + (@teunbrand, #3610) * `coord_radial(r.axis.inside)` can now take a numeric value to control placement of internally placed radius axes (@teunbrand, #5805). * (internal) default labels are derived in `ggplot_build()` rather than diff --git a/R/position-dodge.R b/R/position-dodge.R index c2d0dc1eca..b3818cf08c 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -16,6 +16,8 @@ #' @param orientation Fallback orientation when the layer or the data does not #' indicate an explicit orientation, like `geom_point()`. Can be `"x"` #' (default) or `"y"`. +#' @param reverse If `TRUE`, will reverse the default stacking order. +#' This is useful if you're rotating both the plot and legend. #' @family position adjustments #' @export #' @examples @@ -82,11 +84,14 @@ #' #' ggplot(mtcars, aes(factor(cyl), fill = factor(vs))) + #' geom_bar(position = position_dodge2(preserve = "total")) -position_dodge <- function(width = NULL, preserve = "total", orientation = "x") { +position_dodge <- function(width = NULL, preserve = "total", orientation = "x", + reverse = FALSE) { + check_bool(reverse) ggproto(NULL, PositionDodge, width = width, preserve = arg_match0(preserve, c("total", "single")), - orientation = arg_match0(orientation, c("x", "y")) + orientation = arg_match0(orientation, c("x", "y")), + reverse = reverse ) } @@ -98,6 +103,7 @@ PositionDodge <- ggproto("PositionDodge", Position, width = NULL, preserve = "total", orientation = "x", + reverse = NULL, setup_params = function(self, data) { flipped_aes <- has_flipped_aes(data, default = self$orientation == "y") data <- flip_data(data, flipped_aes) @@ -119,7 +125,8 @@ PositionDodge <- ggproto("PositionDodge", Position, list( width = self$width, n = n, - flipped_aes = flipped_aes + flipped_aes = flipped_aes, + reverse = self$reverse %||% FALSE ) }, @@ -139,7 +146,8 @@ PositionDodge <- ggproto("PositionDodge", Position, name = "position_dodge", strategy = pos_dodge, n = params$n, - check.width = FALSE + check.width = FALSE, + reverse = !params$reverse # for consistency with `position_dodge2()` ) flip_data(collided, params$flipped_aes) } @@ -164,7 +172,7 @@ pos_dodge <- function(df, width, n = NULL) { # Have a new group index from 1 to number of groups. # This might be needed if the group numbers in this set don't include all of 1:n - groupidx <- match(df$group, sort(unique0(df$group))) + groupidx <- match(df$group, unique0(df$group)) # Find the center for each group, then use that to calculate xmin and xmax df$x <- df$x + width * ((groupidx - 0.5) / n - .5) diff --git a/R/position-dodge2.R b/R/position-dodge2.R index a4c5fdc8ba..bf5f18c56d 100644 --- a/R/position-dodge2.R +++ b/R/position-dodge2.R @@ -2,8 +2,6 @@ #' @rdname position_dodge #' @param padding Padding between elements at the same position. Elements are #' shrunk by this proportion to allow space between them. Defaults to 0.1. -#' @param reverse If `TRUE`, will reverse the default stacking order. -#' This is useful if you're rotating both the plot and legend. position_dodge2 <- function(width = NULL, preserve = "total", padding = 0.1, reverse = FALSE) { ggproto(NULL, PositionDodge2, diff --git a/R/position-jitterdodge.R b/R/position-jitterdodge.R index 768f3d8385..71feb597c2 100644 --- a/R/position-jitterdodge.R +++ b/R/position-jitterdodge.R @@ -11,6 +11,7 @@ #' @param dodge.width the amount to dodge in the x direction. Defaults to 0.75, #' the default `position_dodge()` width. #' @inheritParams position_jitter +#' @inheritParams position_dodge #' @export #' @examples #' set.seed(596) @@ -19,15 +20,18 @@ #' geom_boxplot(outlier.size = 0) + #' geom_point(pch = 21, position = position_jitterdodge()) position_jitterdodge <- function(jitter.width = NULL, jitter.height = 0, - dodge.width = 0.75, seed = NA) { + dodge.width = 0.75, reverse = FALSE, + seed = NA) { if (!is.null(seed) && is.na(seed)) { seed <- sample.int(.Machine$integer.max, 1L) } + check_bool(reverse) ggproto(NULL, PositionJitterdodge, jitter.width = jitter.width, jitter.height = jitter.height, dodge.width = dodge.width, + reverse = reverse, seed = seed ) } @@ -40,6 +44,7 @@ PositionJitterdodge <- ggproto("PositionJitterdodge", Position, jitter.width = NULL, jitter.height = NULL, dodge.width = NULL, + reverse = NULL, required_aes = c("x", "y"), @@ -57,14 +62,21 @@ PositionJitterdodge <- ggproto("PositionJitterdodge", Position, jitter.height = self$jitter.height %||% 0, jitter.width = width / (ndodge + 2), seed = self$seed, - flipped_aes = flipped_aes + flipped_aes = flipped_aes, + reverse = self$reverse %||% FALSE ) }, compute_panel = function(data, params, scales) { data <- flip_data(data, params$flipped_aes) - data <- collide(data, params$dodge.width, "position_jitterdodge", pos_dodge, - check.width = FALSE) + data <- collide( + data, + params$dodge.width, + "position_jitterdodge", + strategy = pos_dodge, + check.width = FALSE, + reverse = !params$reverse # for consistency with `position_dodge2()` + ) trans_x <- if (params$jitter.width > 0) function(x) jitter(x, amount = params$jitter.width) trans_y <- if (params$jitter.height > 0) function(x) jitter(x, amount = params$jitter.height) diff --git a/man/position_dodge.Rd b/man/position_dodge.Rd index 3efb462168..e4f9211110 100644 --- a/man/position_dodge.Rd +++ b/man/position_dodge.Rd @@ -5,7 +5,12 @@ \alias{position_dodge2} \title{Dodge overlapping objects side-to-side} \usage{ -position_dodge(width = NULL, preserve = "total", orientation = "x") +position_dodge( + width = NULL, + preserve = "total", + orientation = "x", + reverse = FALSE +) position_dodge2( width = NULL, @@ -26,11 +31,11 @@ at a position, or the width of a \code{"single"} element?} indicate an explicit orientation, like \code{geom_point()}. Can be \code{"x"} (default) or \code{"y"}.} -\item{padding}{Padding between elements at the same position. Elements are -shrunk by this proportion to allow space between them. Defaults to 0.1.} - \item{reverse}{If \code{TRUE}, will reverse the default stacking order. This is useful if you're rotating both the plot and legend.} + +\item{padding}{Padding between elements at the same position. Elements are +shrunk by this proportion to allow space between them. Defaults to 0.1.} } \description{ Dodging preserves the vertical position of an geom while adjusting the diff --git a/man/position_jitterdodge.Rd b/man/position_jitterdodge.Rd index d158162211..ca5bb8e30c 100644 --- a/man/position_jitterdodge.Rd +++ b/man/position_jitterdodge.Rd @@ -8,6 +8,7 @@ position_jitterdodge( jitter.width = NULL, jitter.height = 0, dodge.width = 0.75, + reverse = FALSE, seed = NA ) } @@ -20,6 +21,9 @@ resolution of the data.} \item{dodge.width}{the amount to dodge in the x direction. Defaults to 0.75, the default \code{position_dodge()} width.} +\item{reverse}{If \code{TRUE}, will reverse the default stacking order. +This is useful if you're rotating both the plot and legend.} + \item{seed}{A random seed to make the jitter reproducible. Useful if you need to apply the same jitter twice, e.g., for a point and a corresponding label. diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index 51d7b54cce..1d7127a239 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -23,3 +23,17 @@ test_that("position_dodge() can dodge points vertically", { expect_equal(layer_data(vertical)$y, c(0.75, 1.25, 1.75, 2.25), ignore_attr = "class") }) + +test_that("position_dodge() can reverse the dodge order", { + + df <- data.frame(x = c(1, 2, 2, 3, 3), group = c("A", "A", "B", "B", "C")) + + # Use label as easy to track identifier + p <- ggplot(df, aes(x, y = 1, fill = group, label = group)) + + ld <- get_layer_data(p + geom_col(position = position_dodge(reverse = TRUE))) + expect_equal(ld$label[order(ld$x)], c("A", "B", "A", "C", "B")) + + ld <- get_layer_data(p + geom_col(position = position_dodge(reverse = FALSE))) + expect_equal(ld$label[order(ld$x)], c("A", "A", "B", "B", "C")) +}) From 257ffaff6a2e4bb7551704532913ee0b0047336c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:18:08 +0200 Subject: [PATCH 072/264] Guard against old discrete scales with identity palettes (#5933) * rescue old palettes * Revert "rescue old palettes" This reverts commit 8031a33029836a62b3bdb803a93bc1d8a70b3c73. * rescue in construction * fix typo --- R/scale-.R | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/R/scale-.R b/R/scale-.R index 9eaa153590..432bd6c7d5 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -231,9 +231,13 @@ discrete_scale <- function(aesthetics, scale_name = deprecated(), palette, name position <- arg_match0(position, c("left", "right", "top", "bottom")) # If the scale is non-positional, break = NULL means removing the guide - if (is.null(breaks) && all(!is_position_aes(aesthetics))) { + is_position <- any(is_position_aes(aesthetics)) + if (is.null(breaks) && !is_position) { guide <- "none" } + if (is_position && identical(palette, identity)) { + palette <- seq_len + } ggproto(NULL, super, call = call, From 52bdbc56a90ab019e9e4f13abcf9e86661130d4f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:20:54 +0200 Subject: [PATCH 073/264] setup sides parameter in `geom_rug()` (#5943) --- R/geom-rug.R | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/R/geom-rug.R b/R/geom-rug.R index a1273e3e08..eca79951d8 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -159,6 +159,11 @@ GeomRug <- ggproto("GeomRug", Geom, rename_size = TRUE, + setup_params = function(data, params) { + params$sides <- params$sides %||% "bl" + params + }, + handle_na = function(self, data, params) { sides_aes <- character() From b11d574cba19268b11f563118224da8034995b54 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:29:57 +0200 Subject: [PATCH 074/264] Pass missing arguments in `guide_coloursteps()` (#5931) * pass missing arguments * document * add news bullet --- NEWS.md | 2 ++ R/guide-colorsteps.R | 3 +++ man/guide_coloursteps.Rd | 5 +++++ 3 files changed, 10 insertions(+) diff --git a/NEWS.md b/NEWS.md index 6b6cc439ff..7c8a921832 100644 --- a/NEWS.md +++ b/NEWS.md @@ -119,6 +119,8 @@ the `nbin` argument (@teunbrand, #5882, #5036) * `after_stat()` and `after_scale()` throw warnings when the computed aesthetics are not of the correct length (#5901). +* `guide_colourbar()` now correctly hands off `position` and `available_aes` + parameters downstream (@teunbrand, #5930) * `geom_hline()` and `geom_vline()` now have `position` argument (@yutannihilation, #4285). * New function `get_strip_labels()` to retrieve facet labels (@teunbrand, #4979) diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index de10b51a04..52b6e1809d 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -52,6 +52,7 @@ guide_coloursteps <- function( even.steps = TRUE, show.limits = NULL, direction = NULL, + position = NULL, reverse = FALSE, order = 0, available_aes = c("colour", "color", "fill"), @@ -67,9 +68,11 @@ guide_coloursteps <- function( alpha = alpha, even.steps = even.steps, show.limits = show.limits, + position = position, direction = direction, reverse = reverse, order = order, + available_aes = available_aes, super = GuideColoursteps ) } diff --git a/man/guide_coloursteps.Rd b/man/guide_coloursteps.Rd index 97e66d6207..a2938df745 100644 --- a/man/guide_coloursteps.Rd +++ b/man/guide_coloursteps.Rd @@ -12,6 +12,7 @@ guide_coloursteps( even.steps = TRUE, show.limits = NULL, direction = NULL, + position = NULL, reverse = FALSE, order = 0, available_aes = c("colour", "color", "fill"), @@ -25,6 +26,7 @@ guide_colorsteps( even.steps = TRUE, show.limits = NULL, direction = NULL, + position = NULL, reverse = FALSE, order = 0, available_aes = c("colour", "color", "fill"), @@ -57,6 +59,9 @@ shown irrespective of the value of \code{show.limits}.} \item{direction}{A character string indicating the direction of the guide. One of "horizontal" or "vertical."} +\item{position}{A character string indicating where the legend should be +placed relative to the plot panels.} + \item{reverse}{logical. If \code{TRUE} the colourbar is reversed. By default, the highest value is on the top and the lowest value is on the bottom} From 01eff23537a21a33ede0e65f42146f65e9a8506a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 20:49:42 +0200 Subject: [PATCH 075/264] Add `geom_step(orientation)` argument (#5937) * add `orientiation` to `geom_step()` * add news bullet * document --- NEWS.md | 1 + R/geom-path.R | 16 ++++++++++++++-- man/geom_path.Rd | 1 + 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 7c8a921832..683d40dbcb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* `geom_step()` now supports the `orientation` argument (@teunbrand, #5936). * `position_dodge()` and `position_jitterdodge()` now have a `reverse` argument (@teunbrand, #3610) * `coord_radial(r.axis.inside)` can now take a numeric value to control diff --git a/R/geom-path.R b/R/geom-path.R index fe4359fb08..9b737267ca 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -305,7 +305,8 @@ GeomLine <- ggproto("GeomLine", GeomPath, #' @rdname geom_path geom_step <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity", direction = "hv", - na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...) { + na.rm = FALSE, orientation = NA, show.legend = NA, + inherit.aes = TRUE, ...) { layer( data = data, mapping = mapping, @@ -316,6 +317,7 @@ geom_step <- function(mapping = NULL, data = NULL, stat = "identity", inherit.aes = inherit.aes, params = list2( direction = direction, + orientation = orientation, na.rm = na.rm, ... ) @@ -328,11 +330,21 @@ geom_step <- function(mapping = NULL, data = NULL, stat = "identity", #' @export #' @include geom-path.R GeomStep <- ggproto("GeomStep", GeomPath, + setup_params = function(data, params) { + params$flipped_aes <- has_flipped_aes(data, params, ambiguous = TRUE) + params + }, + extra_params = c("na.rm", "orientation"), draw_panel = function(data, panel_params, coord, lineend = "butt", linejoin = "round", linemitre = 10, arrow = NULL, arrow.fill = NULL, - direction = "hv") { + direction = "hv", flipped_aes = FALSE) { + data <- flip_data(data, flipped_aes) + if (isTRUE(flipped_aes)) { + direction <- switch(direction, hv = "vh", vh = "hv", direction) + } data <- dapply(data, "group", stairstep, direction = direction) + data <- flip_data(data, flipped_aes) GeomPath$draw_panel( data, panel_params, coord, lineend = lineend, linejoin = linejoin, linemitre = linemitre, diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 00a3ef8e5a..239b7dc0c6 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -41,6 +41,7 @@ geom_step( position = "identity", direction = "hv", na.rm = FALSE, + orientation = NA, show.legend = NA, inherit.aes = TRUE, ... From 6298aecfe503e1667a0abbef0bd6eb723c2cf594 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 11 Jul 2024 21:00:46 +0200 Subject: [PATCH 076/264] Fix overlap identification in `position_dodge2()` (#5939) * fix and vectorise `find_x_overlaps()` * add news bullet * add test * deal with `NA`s more properly * pass `end` correctly --- NEWS.md | 2 ++ R/position-dodge2.R | 23 ++++++++++++++--------- tests/testthat/test-position-dodge2.R | 8 ++++++++ 3 files changed, 24 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index 683d40dbcb..1a887f95ba 100644 --- a/NEWS.md +++ b/NEWS.md @@ -125,6 +125,8 @@ * `geom_hline()` and `geom_vline()` now have `position` argument (@yutannihilation, #4285). * New function `get_strip_labels()` to retrieve facet labels (@teunbrand, #4979) +* Fixed bug in `position_dodge2()`'s identification of range overlaps + (@teunbrand, #5938, #4327). # ggplot2 3.5.1 diff --git a/R/position-dodge2.R b/R/position-dodge2.R index bf5f18c56d..e8e291c62c 100644 --- a/R/position-dodge2.R +++ b/R/position-dodge2.R @@ -132,14 +132,19 @@ pos_dodge2 <- function(df, width, n = NULL, padding = 0.1) { # Find groups of overlapping elements that need to be dodged from one another find_x_overlaps <- function(df) { - overlaps <- numeric(nrow(df)) - overlaps[1] <- counter <- 1 - for (i in seq_asc(2, nrow(df))) { - if (is.na(df$xmin[i]) || is.na(df$xmax[i - 1]) || df$xmin[i] >= df$xmax[i - 1]) { - counter <- counter + 1 - } - overlaps[i] <- counter - } - overlaps + start <- df$xmin + nonzero <- df$xmax != df$xmin + missing <- is.na(df$xmin) | is.na(df$xmax) + start <- vec_fill_missing(start, "downup") + end <- vec_fill_missing(df$xmax, "downup") + + # For end we take largest end seen so far of previous observation + end <- cummax(c(end[1], end[-nrow(df)])) + # Start new group when 'start >= end' for non zero-width ranges + # For zero-width ranges, start must be strictly larger than end + overlaps <- cumsum(start > end | (start == end & nonzero)) + # Missing ranges always get separate group + overlaps[missing] <- seq_len(sum(missing)) + max(overlaps, na.rm = TRUE) + match(overlaps, unique0(overlaps)) } diff --git a/tests/testthat/test-position-dodge2.R b/tests/testthat/test-position-dodge2.R index d1e54a37fc..5377f14b2d 100644 --- a/tests/testthat/test-position-dodge2.R +++ b/tests/testthat/test-position-dodge2.R @@ -118,3 +118,11 @@ test_that("groups are different when two blocks have externall touching point",{ ) expect_equal(find_x_overlaps(df1), seq_len(2)) }) + +test_that("overlaps are identified correctly", { + df <- data.frame( + xmin = c(1, 2, 3, 5), + xmax = c(4, 3, 4, 6) + ) + expect_equal(find_x_overlaps(df), c(1, 1, 1, 2)) +}) From 98f5e12955f776c820cece1da00dde05766fa706 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:58:17 +0200 Subject: [PATCH 077/264] Recognise empty scale with `limits = ` as empty (#5948) * discrete scale is also empty when limits is a function * add news bullet --- NEWS.md | 2 ++ R/scale-discrete-.R | 4 +++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 1a887f95ba..92f111dbb0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -127,6 +127,8 @@ * New function `get_strip_labels()` to retrieve facet labels (@teunbrand, #4979) * Fixed bug in `position_dodge2()`'s identification of range overlaps (@teunbrand, #5938, #4327). +* Fixed bug where empty discrete scales weren't recognised as such + (@teunbrand, #5945). # ggplot2 3.5.1 diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index 82bb8eb8fe..8fea10caf2 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -130,7 +130,9 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, }, is_empty = function(self) { - is.null(self$range$range) && is.null(self$limits) && is.null(self$range_c$range) + is.null(self$range$range) && + (is.null(self$limits) || is.function(self$limits)) && + is.null(self$range_c$range) }, reset = function(self) { From f5782ff1d63b2c1cbdff618a02f471cdeb4a7994 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:58:29 +0200 Subject: [PATCH 078/264] `facet_grid()` evaluates facets before adding margins (#5944) * evaluate facets before adding margins * add test * add news bullet --- NEWS.md | 2 ++ R/facet-grid-.R | 19 ++++++++++++++----- tests/testthat/test-facet-map.R | 4 ++++ 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index 92f111dbb0..d0f10aadc4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug in `facet_grid(margins = TRUE)` when using expresssions + (@teunbrand, #1864). * `geom_step()` now supports the `orientation` argument (@teunbrand, #5936). * `position_dodge()` and `position_jitterdodge()` now have a `reverse` argument (@teunbrand, #3610) diff --git a/R/facet-grid-.R b/R/facet-grid-.R index f7783f8985..7bfb30dd6e 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -297,12 +297,21 @@ FacetGrid <- ggproto("FacetGrid", Facet, return(data) } - # Compute faceting values and add margins - margin_vars <- list(intersect(names(rows), names(data)), - intersect(names(cols), names(data))) - data <- reshape_add_margins(data, margin_vars, params$margins) - + # Compute faceting values facet_vals <- eval_facets(c(rows, cols), data, params$.possible_columns) + if (nrow(facet_vals) == nrow(data)) { + # Margins are computed on evaluated faceting values (#1864). + facet_vals <- reshape_add_margins( + # We add an index column to track data recycling + vec_cbind(facet_vals, .index = seq_len(nrow(facet_vals))), + list(intersect(names(rows), names(facet_vals)), + intersect(names(cols), names(facet_vals))), + params$margins + ) + # Apply recycling on original data to fit margins + data <- vec_slice(data, facet_vals$.index) + facet_vals$.index <- NULL + } # If any faceting variables are missing, add them in by # duplicating the data diff --git a/tests/testthat/test-facet-map.R b/tests/testthat/test-facet-map.R index 35e3256958..de2bf20af2 100644 --- a/tests/testthat/test-facet-map.R +++ b/tests/testthat/test-facet-map.R @@ -22,6 +22,10 @@ test_that("margins add extra data", { loc <- panel_map_one(facet_grid(a~b, margins = "b"), df) expect_equal(nrow(loc), nrow(df) * 2) + + # For variables including computation (#1864) + loc <- panel_map_one(facet_grid(a ~ I(b + 1), margins = TRUE), df) + expect_equal(nrow(loc), nrow(df) * 4) }) test_that("grid: missing facet columns are duplicated", { From c679d4303f1f8bc4cae1e3eda7e89be78125628b Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 12 Jul 2024 10:27:15 +0200 Subject: [PATCH 079/264] Preserve `NA`s in discrete palettes (#5949) * choose `na.value` when unmatched * add test * add news bullet --- NEWS.md | 2 ++ R/scale-.R | 24 ++++++++++++------------ tests/testthat/test-scale-manual.R | 24 ++++++++++++++++++++++++ 3 files changed, 38 insertions(+), 12 deletions(-) diff --git a/NEWS.md b/NEWS.md index d0f10aadc4..4c0ea1e891 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Missing values from discrete palettes are no longer translated + (@teunbrand, #5929). * Fixed bug in `facet_grid(margins = TRUE)` when using expresssions (@teunbrand, #1864). * `geom_step()` now supports the `orientation` argument (@teunbrand, #5936). diff --git a/R/scale-.R b/R/scale-.R index 432bd6c7d5..1773f15142 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -973,23 +973,23 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, self$n.breaks.cache <- n } - if (!is_null(names(pal))) { + na_value <- if (self$na.translate) self$na.value else NA + pal_names <- names(pal) + + if (!is_null(pal_names)) { # if pal is named, limit the pal by the names first, # then limit the values by the pal - idx_nomatch <- is.na(match(names(pal), limits)) - pal[idx_nomatch] <- NA - pal_match <- pal[match(as.character(x), names(pal))] - pal_match <- unname(pal_match) - } else { - # if pal is not named, limit the values directly - pal_match <- pal[match(as.character(x), limits)] + pal[is.na(match(pal_names, limits))] <- na_value + pal <- unname(pal) + limits <- pal_names } + pal <- c(pal, na_value) + pal_match <- pal[match(as.character(x), limits, nomatch = length(pal))] - if (self$na.translate) { - ifelse(is.na(x) | is.na(pal_match), self$na.value, pal_match) - } else { - pal_match + if (!is.na(na_value)) { + pal_match[is.na(x)] <- na_value } + pal_match }, rescale = function(self, x, limits = self$get_limits(), range = c(1, length(limits))) { diff --git a/tests/testthat/test-scale-manual.R b/tests/testthat/test-scale-manual.R index 4e45b65557..3d87268c41 100644 --- a/tests/testthat/test-scale-manual.R +++ b/tests/testthat/test-scale-manual.R @@ -152,3 +152,27 @@ test_that("limits and breaks (#4619)", { expect_equal(s3$map(c("4", "6", "8")), c("a", "b", "c")) expect_equal(s3$break_positions(), c("a", "c")) }) + +test_that("NAs from palette are not translated (#5929)", { + + s1 <- scale_colour_manual( + values = c("4" = "a", "6" = NA, "8" = "c"), + na.translate = TRUE, na.value = "x" + ) + s1$train(c("8", "6", "4")) + expect_equal(s1$map(c("4", "6", "8", "10")), c("a", NA, "c", "x")) + + s2 <- scale_colour_manual( + values = c("4" = "a", "6" = NA, "8" = "c"), + na.translate = TRUE, na.value = NA + ) + s2$train(c("8", "6", "4")) + expect_equal(s2$map(c("4", "6", "8", "10")), c("a", NA, "c", NA)) + + s3 <- scale_colour_manual( + values = c("4" = "a", "6" = NA, "8" = "c"), + na.translate = FALSE, na.value = "x" + ) + s3$train(c("8", "6", "4")) + expect_equal(s3$map(c("4", "6", "8", "10")), c("a", NA, "c", NA)) +}) From 25ad0b17865c1280c464ccfbee38c3d7eb5df95d Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 15 Jul 2024 23:01:14 +0200 Subject: [PATCH 080/264] exclude `palette` as dot param (#5992) --- R/scale-gradient.R | 2 +- R/scale-grey.R | 2 +- R/scale-hue.R | 2 +- R/scale-linetype.R | 2 +- R/scale-shape.R | 2 +- man/scale_gradient.Rd | 3 --- man/scale_grey.Rd | 3 --- man/scale_hue.Rd | 3 --- man/scale_linetype.Rd | 3 --- man/scale_shape.Rd | 3 --- 10 files changed, 5 insertions(+), 20 deletions(-) diff --git a/R/scale-gradient.R b/R/scale-gradient.R index 788ee3e9f0..32f61a2e8e 100644 --- a/R/scale-gradient.R +++ b/R/scale-gradient.R @@ -16,7 +16,7 @@ #' @param low,high Colours for low and high ends of the gradient. #' @param guide Type of legend. Use `"colourbar"` for continuous #' colour bar, or `"legend"` for discrete colour legend. -#' @inheritDotParams continuous_scale -na.value -guide -aesthetics -expand -position +#' @inheritDotParams continuous_scale -na.value -guide -aesthetics -expand -position -palette #' @seealso [scales::pal_seq_gradient()] for details on underlying #' palette, [scale_colour_steps()] for binned variants of these scales. #' diff --git a/R/scale-grey.R b/R/scale-grey.R index b3683295f7..cc6a88033e 100644 --- a/R/scale-grey.R +++ b/R/scale-grey.R @@ -5,7 +5,7 @@ #' #' @inheritParams scales::pal_grey #' @inheritParams scale_colour_hue -#' @inheritDotParams discrete_scale -expand -position -scale_name +#' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @family colour scales #' @seealso #' The documentation on [colour aesthetics][aes_colour_fill_alpha]. diff --git a/R/scale-hue.R b/R/scale-hue.R index ba50f81dc2..db743612ed 100644 --- a/R/scale-hue.R +++ b/R/scale-hue.R @@ -4,7 +4,7 @@ #' It does not generate colour-blind safe palettes. #' #' @param na.value Colour to use for missing values -#' @inheritDotParams discrete_scale -aesthetics -expand -position -scale_name +#' @inheritDotParams discrete_scale -aesthetics -expand -position -scale_name -palette #' @param aesthetics Character string or vector of character strings listing the #' name(s) of the aesthetic(s) that this scale works with. This can be useful, for #' example, to apply colour settings to the `colour` and `fill` aesthetics at the diff --git a/R/scale-linetype.R b/R/scale-linetype.R index a1b983b23d..bc4fa0ce71 100644 --- a/R/scale-linetype.R +++ b/R/scale-linetype.R @@ -6,7 +6,7 @@ #' no inherent order, this use is not advised. #' #' @inheritParams scale_x_discrete -#' @inheritDotParams discrete_scale -expand -position -na.value -scale_name +#' @inheritDotParams discrete_scale -expand -position -na.value -scale_name -palette #' @param na.value The linetype to use for `NA` values. #' @rdname scale_linetype #' @seealso diff --git a/R/scale-shape.R b/R/scale-shape.R index 7c4c750519..ecb8a2a2a1 100644 --- a/R/scale-shape.R +++ b/R/scale-shape.R @@ -10,7 +10,7 @@ #' @param solid Should the shapes be solid, `TRUE`, or hollow, #' `FALSE`? #' @inheritParams scale_x_discrete -#' @inheritDotParams discrete_scale -expand -position -scale_name +#' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @rdname scale_shape #' @seealso #' The documentation for [differentiation related aesthetics][aes_linetype_size_shape]. diff --git a/man/scale_gradient.Rd b/man/scale_gradient.Rd index f861378c0c..619e71f3ef 100644 --- a/man/scale_gradient.Rd +++ b/man/scale_gradient.Rd @@ -103,9 +103,6 @@ omitted.} \describe{ \item{\code{scale_name}}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} The name of the scale that should be used for error messages associated with this scale.} - \item{\code{palette}}{A palette function that when called with a numeric vector with -values between 0 and 1 returns the corresponding output values -(e.g., \code{\link[scales:pal_area]{scales::pal_area()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_grey.Rd b/man/scale_grey.Rd index 6b04f40688..0ee97a15de 100644 --- a/man/scale_grey.Rd +++ b/man/scale_grey.Rd @@ -33,9 +33,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_hue.Rd b/man/scale_hue.Rd index 99776d95d3..1280e741bb 100644 --- a/man/scale_hue.Rd +++ b/man/scale_hue.Rd @@ -39,9 +39,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index da4cf2b7c3..9b57b40978 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -24,9 +24,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index ffbb381481..8c8b8320fc 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -21,9 +21,6 @@ omitted.} \item{...}{ Arguments passed on to \code{\link[=discrete_scale]{discrete_scale}} \describe{ - \item{\code{palette}}{A palette function that when called with a single integer -argument (the number of levels in the scale) returns the values that -they should take (e.g., \code{\link[scales:pal_hue]{scales::pal_hue()}}).} \item{\code{breaks}}{One of: \itemize{ \item \code{NULL} for no breaks From 7fb4c382f9ea332844d469663a8047355a88dd7a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 17 Jul 2024 17:55:28 +0200 Subject: [PATCH 081/264] Exclude labels from `aes_params` field (#6004) * exclude labels from `aes_params` * add test --- R/labels.R | 2 ++ tests/testthat/test-labels.R | 15 +++++++++++++++ 2 files changed, 17 insertions(+) diff --git a/R/labels.R b/R/labels.R index 3012868874..2bc5551034 100644 --- a/R/labels.R +++ b/R/labels.R @@ -24,9 +24,11 @@ setup_plot_labels <- function(plot, layers, data) { # Find labels from every layer for (i in seq_along(layers)) { layer <- layers[[i]] + exclude <- names(layer$aes_params) mapping <- layer$computed_mapping mapping <- strip_stage(mapping) mapping <- strip_dots(mapping, strip_pronoun = TRUE) + mapping <- mapping[setdiff(names(mapping), exclude)] # Acquire default labels mapping_default <- make_labels(mapping) diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index e338226bd4..c659e39cf5 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -74,6 +74,21 @@ test_that("Labels can be extracted from attributes", { expect_equal(labels$y, "disp") }) +test_that("Labels from static aesthetics are ignored (#6003)", { + + df <- data.frame(x = 1, y = 1, f = 1) + + p <- ggplot(df, aes(x, y, colour = f)) + geom_point() + labels <- ggplot_build(p)$plot$labels + + expect_equal(labels$colour, "f") + + p <- ggplot(df, aes(x, y, colour = f)) + geom_point(colour = "blue") + labels <- ggplot_build(p)$plot$labels + + expect_null(labels$colour) +}) + test_that("alt text is returned", { p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() From 8895ec2d4dcb7000737fec249d3a93d5879aa823 Mon Sep 17 00:00:00 2001 From: olivroy <52606734+olivroy@users.noreply.github.com> Date: Tue, 6 Aug 2024 03:31:49 -0400 Subject: [PATCH 082/264] Update CONTRIBUTING.md (#6030) --- CONTRIBUTING.md | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8796efb5d8..77553769db 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -61,20 +61,19 @@ Each of these steps are described in more detail below. This might feel overwhelming the first time you get set up, but it gets easier with practice. If you get stuck at any point, please reach out for help on the [ggplot2-dev](https://groups.google.com/forum/#!forum/ggplot2-dev) mailing list. -If you're not familiar with git or github, please start by reading +If you're not familiar with git or github, please start by reading Pull requests will be evaluated against a seven point checklist: @@ -100,20 +99,16 @@ Pull requests will be evaluated against a seven point checklist: and don't submit any others until the first one has been processed. 1. __Use ggplot2 coding style__. Please follow the - [official tidyverse style](http://style.tidyverse.org). Maintaining + [official tidyverse style](https://style.tidyverse.org). Maintaining a consistent style across the whole code base makes it much easier to jump into the code. If you're modifying existing ggplot2 code that doesn't follow the style guide, a separate pull request to fix the style would be greatly appreciated. 1. If you're adding new parameters or a new function, you'll also need - to document them with [roxygen](https://github.com/klutometis/roxygen). + to document them with [roxygen2](https://github.com/r-lib/roxygen2). Make sure to re-run `devtools::document()` on the code before submitting. - Currently, ggplot2 uses the development version of roxygen2, which you - can get with `install_github("klutometis/roxygen")`. This will be - available on CRAN in the near future. - 1. If fixing a bug or adding a new feature to a non-graphical function, please add a [testthat](https://github.com/r-lib/testthat) unit test. From 09d5c35f24d8df43be9236f5e2a8ef3faf5c828f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Cs=C3=A1rdi?= Date: Wed, 7 Aug 2024 13:52:51 +0200 Subject: [PATCH 083/264] Use latest GHA workflows (#6028) --- .github/workflows/R-CMD-check.yaml | 25 ++++++++++++++----------- .github/workflows/pkgdown.yaml | 10 +++++++--- .github/workflows/pr-commands.yaml | 12 +++++++++--- .github/workflows/test-coverage.yaml | 25 ++++++++++++++++++------- 4 files changed, 48 insertions(+), 24 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index cfdefdb714..2e6d40ab70 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -10,7 +10,9 @@ on: pull_request: branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -25,15 +27,15 @@ jobs: - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - # use 4.1 to check with rtools40's older compiler - - {os: windows-latest, r: '4.1'} + # use 4.0 or 4.1 to check with rtools40's older compiler + - {os: windows-latest, r: 'oldrel-4'} - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - - {os: ubuntu-latest, r: 'oldrel-2'} - - {os: ubuntu-latest, r: 'oldrel-3'} - - {os: ubuntu-latest, r: 'oldrel-4'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: ubuntu-latest, r: 'oldrel-2'} + - {os: ubuntu-latest, r: 'oldrel-3'} + - {os: ubuntu-latest, r: 'oldrel-4'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -46,7 +48,7 @@ jobs: VDIFFR_LOG_PATH: "../vdiffr.Rout.fail" steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -62,9 +64,10 @@ jobs: extra-packages: > any::rcmdcheck, Hmisc=?ignore-before-r=4.1.0, - quantreg=?ignore-before-r=4.3.0, + quantreg=?ignore-before-r=4.3.0 needs: check - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b05fc..4bbce75080 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -9,7 +9,9 @@ on: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -19,8 +21,10 @@ jobs: group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index 71f335b3ea..2edd93f27e 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -4,7 +4,9 @@ on: issue_comment: types: [created] -name: Commands +name: pr-commands.yaml + +permissions: read-all jobs: document: @@ -13,8 +15,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: @@ -50,8 +54,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb50294..988226098e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -15,7 +17,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +25,37 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( quiet = FALSE, clean = FALSE, - install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") ) + covr::to_cobertura(cov) shell: Rscript {0} + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + - name: Show testthat output if: always() run: | ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package From b1a7a58bc932f66424072bc464270533c6c404f7 Mon Sep 17 00:00:00 2001 From: agmurray Date: Thu, 15 Aug 2024 10:31:32 -0700 Subject: [PATCH 084/264] Adding the option `seed = 0` into the jitter argument (#6035) Fixes #5875 --- DESCRIPTION | 2 +- R/position-jitter.R | 2 +- man/position_jitter.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3f34454b36..d97ce7e689 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -78,7 +78,7 @@ Config/testthat/edition: 3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Collate: 'ggproto.R' 'ggplot-global.R' diff --git a/R/position-jitter.R b/R/position-jitter.R index 99d807fbe3..ddf59d090b 100644 --- a/R/position-jitter.R +++ b/R/position-jitter.R @@ -41,7 +41,7 @@ #' geom_jitter(position = position_jitter(width = 0.1, height = 0.1)) #' #' # Create a jitter object for reproducible jitter: -#' jitter <- position_jitter(width = 0.1, height = 0.1) +#' jitter <- position_jitter(width = 0.1, height = 0.1, seed = 0) #' ggplot(mtcars, aes(am, vs)) + #' geom_point(position = jitter) + #' geom_point(position = jitter, color = "red", aes(am + 0.2, vs + 0.2)) diff --git a/man/position_jitter.Rd b/man/position_jitter.Rd index d0531116d6..b43f4ade40 100644 --- a/man/position_jitter.Rd +++ b/man/position_jitter.Rd @@ -49,7 +49,7 @@ ggplot(mtcars, aes(am, vs)) + geom_jitter(position = position_jitter(width = 0.1, height = 0.1)) # Create a jitter object for reproducible jitter: -jitter <- position_jitter(width = 0.1, height = 0.1) +jitter <- position_jitter(width = 0.1, height = 0.1, seed = 0) ggplot(mtcars, aes(am, vs)) + geom_point(position = jitter) + geom_point(position = jitter, color = "red", aes(am + 0.2, vs + 0.2)) From c1b62755a390bb4d707a42a87131a0c5318aadb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Catalina=20Ca=C3=B1izares?= <88352293+ccani007@users.noreply.github.com> Date: Thu, 15 Aug 2024 10:45:26 -0700 Subject: [PATCH 085/264] Fixes # 5960 (#6036) Changed "unscaled x" because the function takes transformed values. --- R/stat-bin.R | 7 +++---- man/geom_histogram.Rd | 7 +++---- man/stat_summary.Rd | 7 +++---- 3 files changed, 9 insertions(+), 12 deletions(-) diff --git a/R/stat-bin.R b/R/stat-bin.R index 4c00b2e3ab..c085f818a2 100644 --- a/R/stat-bin.R +++ b/R/stat-bin.R @@ -1,8 +1,7 @@ #' @param binwidth The width of the bins. Can be specified as a numeric value -#' or as a function that calculates width from unscaled x. Here, "unscaled x" -#' refers to the original x values in the data, before application of any -#' scale transformation. When specifying a function along with a grouping -#' structure, the function will be called once per group. +#' or as a function that takes x after scale transformation as input and +#' returns a single numeric value. When specifying a function along with a +#' grouping structure, the function will be called once per group. #' The default is to use the number of bins in `bins`, #' covering the range of the data. You should always override #' this value, exploring multiple widths to find the best to illustrate the diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index f60ec4b1f5..a4a95c503f 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -128,10 +128,9 @@ that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. \code{\link[=borders]{borders()}}.} \item{binwidth}{The width of the bins. Can be specified as a numeric value -or as a function that calculates width from unscaled x. Here, "unscaled x" -refers to the original x values in the data, before application of any -scale transformation. When specifying a function along with a grouping -structure, the function will be called once per group. +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. The default is to use the number of bins in \code{bins}, covering the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the diff --git a/man/stat_summary.Rd b/man/stat_summary.Rd index 034e11afdb..83cbe4c9a7 100644 --- a/man/stat_summary.Rd +++ b/man/stat_summary.Rd @@ -135,10 +135,9 @@ single number.} \item{bins}{Number of bins. Overridden by \code{binwidth}. Defaults to 30.} \item{binwidth}{The width of the bins. Can be specified as a numeric value -or as a function that calculates width from unscaled x. Here, "unscaled x" -refers to the original x values in the data, before application of any -scale transformation. When specifying a function along with a grouping -structure, the function will be called once per group. +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. The default is to use the number of bins in \code{bins}, covering the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the From c706a01a62d96678f98dfef7eee3fde94e54ae34 Mon Sep 17 00:00:00 2001 From: Sierra Johnson <80361498+sierrajohnson@users.noreply.github.com> Date: Thu, 15 Aug 2024 14:30:55 -0600 Subject: [PATCH 086/264] Add labeller example for optional argument. Fixes #5916 (#6038) --- R/labeller.R | 3 +++ man/labellers.Rd | 3 +++ 2 files changed, 6 insertions(+) diff --git a/R/labeller.R b/R/labeller.R index 442f05d496..3dbb9b63ac 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -83,6 +83,9 @@ #' # Interpreting the labels as plotmath expressions #' p + facet_grid(. ~ cyl2) #' p + facet_grid(. ~ cyl2, labeller = label_parsed) +#' +#' # Include optional argument in label function +#' p + facet_grid(. ~ cyl, labeller = function(x) label_both(x, sep = "=")) #' } #' @name labellers NULL diff --git a/man/labellers.Rd b/man/labellers.Rd index 63a4980eb7..09f160bf40 100644 --- a/man/labellers.Rd +++ b/man/labellers.Rd @@ -108,6 +108,9 @@ p + facet_grid(am ~ vs+cyl, labeller = label_context) # Interpreting the labels as plotmath expressions p + facet_grid(. ~ cyl2) p + facet_grid(. ~ cyl2, labeller = label_parsed) + +# Include optional argument in label function +p + facet_grid(. ~ cyl, labeller = function(x) label_both(x, sep = "=")) } } \seealso{ From c4c826a3979f16e1dd19c42f508ab0b018de9b02 Mon Sep 17 00:00:00 2001 From: Sierra Johnson <80361498+sierrajohnson@users.noreply.github.com> Date: Thu, 15 Aug 2024 14:52:33 -0600 Subject: [PATCH 087/264] Making bw argument in stat_density case insensitive. Fixes #5941 (#6041) --- R/stat-density.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/stat-density.R b/R/stat-density.R index 27cafd4b6d..add18570fc 100644 --- a/R/stat-density.R +++ b/R/stat-density.R @@ -242,6 +242,7 @@ reflect_density <- function(dens, bounds, from, to) { precompute_bw = function(x, bw = "nrd0") { bw <- bw[1] if (is.character(bw)) { + bw <- to_lower_ascii(bw) bw <- arg_match0(bw, c("nrd0", "nrd", "ucv", "bcv", "sj", "sj-ste", "sj-dpi")) bw <- switch( to_lower_ascii(bw), From 7572d09cbb54f52ff0963d1a71f6f11d7c9b149d Mon Sep 17 00:00:00 2001 From: Stephen Uong <47620395+phispu@users.noreply.github.com> Date: Thu, 15 Aug 2024 13:57:46 -0700 Subject: [PATCH 088/264] Updated documentation: confidence intervals to confidence bands. Fixes #6025 (#6040) --- R/geom-smooth.R | 2 +- R/stat-smooth.R | 8 ++++---- man/geom_smooth.Rd | 10 +++++----- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/R/geom-smooth.R b/R/geom-smooth.R index 0c3432620c..2247bf2a5b 100644 --- a/R/geom-smooth.R +++ b/R/geom-smooth.R @@ -9,7 +9,7 @@ #' `predictdf()` generic and its methods. For most methods the standard #' error bounds are computed using the [predict()] method -- the #' exceptions are `loess()`, which uses a t-based approximation, and -#' `glm()`, where the normal confidence interval is constructed on the link +#' `glm()`, where the normal confidence band is constructed on the link #' scale and then back-transformed to the response scale. #' #' @eval rd_orientation() diff --git a/R/stat-smooth.R b/R/stat-smooth.R index 864e229edf..9c72d3570c 100644 --- a/R/stat-smooth.R +++ b/R/stat-smooth.R @@ -18,7 +18,7 @@ #' `y ~ poly(x, 2)`, `y ~ log(x)`. `NULL` by default, in which case #' `method = NULL` implies `formula = y ~ x` when there are fewer than 1,000 #' observations and `formula = y ~ s(x, bs = "cs")` otherwise. -#' @param se Display confidence interval around smooth? (`TRUE` by default, see +#' @param se Display confidence band around smooth? (`TRUE` by default, see #' `level` to control.) #' @param fullrange If `TRUE`, the smoothing line gets expanded to the range of the plot, #' potentially beyond the data. This does not extend the line into any additional padding @@ -26,7 +26,7 @@ #' @param xseq A numeric vector of values at which the smoother is evaluated. #' When `NULL` (default), `xseq` is internally evaluated as a sequence of `n` #' equally spaced points for continuous data. -#' @param level Level of confidence interval to use (0.95 by default). +#' @param level Level of confidence band to use (0.95 by default). #' @param span Controls the amount of smoothing for the default loess smoother. #' Smaller numbers produce wigglier lines, larger numbers produce smoother #' lines. Only used with loess, i.e. when `method = "loess"`, @@ -40,8 +40,8 @@ #' .details = "`stat_smooth()` provides the following variables, some of #' which depend on the orientation:", #' "y|x" = "Predicted value.", -#' "ymin|xmin" = "Lower pointwise confidence interval around the mean.", -#' "ymax|xmax" = "Upper pointwise confidence interval around the mean.", +#' "ymin|xmin" = "Lower pointwise confidence band around the mean.", +#' "ymax|xmax" = "Upper pointwise confidence band around the mean.", #' "se" = "Standard error." #' ) #' @export diff --git a/man/geom_smooth.Rd b/man/geom_smooth.Rd index ece17611a4..67c0c3e0c7 100644 --- a/man/geom_smooth.Rd +++ b/man/geom_smooth.Rd @@ -125,7 +125,7 @@ model that \code{method = NULL} would use, then set \code{method = NULL} implies \code{formula = y ~ x} when there are fewer than 1,000 observations and \code{formula = y ~ s(x, bs = "cs")} otherwise.} -\item{se}{Display confidence interval around smooth? (\code{TRUE} by default, see +\item{se}{Display confidence band around smooth? (\code{TRUE} by default, see \code{level} to control.)} \item{na.rm}{If \code{FALSE}, the default, missing values are removed with @@ -168,7 +168,7 @@ created by \code{expansion}.} When \code{NULL} (default), \code{xseq} is internally evaluated as a sequence of \code{n} equally spaced points for continuous data.} -\item{level}{Level of confidence interval to use (0.95 by default).} +\item{level}{Level of confidence band to use (0.95 by default).} \item{method.args}{List of additional arguments passed on to the modelling function defined by \code{method}.} @@ -184,7 +184,7 @@ Calculation is performed by the (currently undocumented) \code{predictdf()} generic and its methods. For most methods the standard error bounds are computed using the \code{\link[=predict]{predict()}} method -- the exceptions are \code{loess()}, which uses a t-based approximation, and -\code{glm()}, where the normal confidence interval is constructed on the link +\code{glm()}, where the normal confidence band is constructed on the link scale and then back-transformed to the response scale. } \section{Orientation}{ @@ -216,8 +216,8 @@ Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. These are calculated by the 'stat' part of layers and can be accessed with \link[=aes_eval]{delayed evaluation}. \code{stat_smooth()} provides the following variables, some of which depend on the orientation: \itemize{ \item \code{after_stat(y)} \emph{or} \code{after_stat(x)}\cr Predicted value. -\item \code{after_stat(ymin)} \emph{or} \code{after_stat(xmin)}\cr Lower pointwise confidence interval around the mean. -\item \code{after_stat(ymax)} \emph{or} \code{after_stat(xmax)}\cr Upper pointwise confidence interval around the mean. +\item \code{after_stat(ymin)} \emph{or} \code{after_stat(xmin)}\cr Lower pointwise confidence band around the mean. +\item \code{after_stat(ymax)} \emph{or} \code{after_stat(xmax)}\cr Upper pointwise confidence band around the mean. \item \code{after_stat(se)}\cr Standard error. } } From 11244c52a202f6e672cb6fc8a943805eb4ba850a Mon Sep 17 00:00:00 2001 From: agmurray Date: Thu, 15 Aug 2024 14:13:34 -0700 Subject: [PATCH 089/264] `show.legend` for factor data for all levels, even when not observed (#6037) * Added text to show how to add color to legends for all levels, even when no data for some levels exists. Fixes #5869 * Update R/layer.R edits from Tuen Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * Includes edits from Teun to clarify language and ran `devtools::document()` --------- Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> --- R/layer.R | 4 +++- man/borders.Rd | 4 +++- man/geom_abline.Rd | 4 +++- man/geom_bar.Rd | 4 +++- man/geom_bin_2d.Rd | 4 +++- man/geom_blank.Rd | 4 +++- man/geom_boxplot.Rd | 4 +++- man/geom_contour.Rd | 4 +++- man/geom_count.Rd | 4 +++- man/geom_density.Rd | 4 +++- man/geom_density_2d.Rd | 4 +++- man/geom_dotplot.Rd | 4 +++- man/geom_errorbarh.Rd | 4 +++- man/geom_function.Rd | 4 +++- man/geom_hex.Rd | 4 +++- man/geom_histogram.Rd | 4 +++- man/geom_jitter.Rd | 4 +++- man/geom_linerange.Rd | 4 +++- man/geom_map.Rd | 4 +++- man/geom_path.Rd | 4 +++- man/geom_point.Rd | 4 +++- man/geom_polygon.Rd | 4 +++- man/geom_qq.Rd | 4 +++- man/geom_quantile.Rd | 4 +++- man/geom_ribbon.Rd | 4 +++- man/geom_rug.Rd | 4 +++- man/geom_segment.Rd | 4 +++- man/geom_smooth.Rd | 4 +++- man/geom_spoke.Rd | 4 +++- man/geom_text.Rd | 4 +++- man/geom_tile.Rd | 4 +++- man/geom_violin.Rd | 4 +++- man/layer.Rd | 4 +++- man/layer_sf.Rd | 4 +++- man/stat_ecdf.Rd | 4 +++- man/stat_ellipse.Rd | 4 +++- man/stat_identity.Rd | 4 +++- man/stat_sf_coordinates.Rd | 4 +++- man/stat_summary.Rd | 4 +++- man/stat_summary_2d.Rd | 4 +++- man/stat_unique.Rd | 4 +++- 41 files changed, 123 insertions(+), 41 deletions(-) diff --git a/R/layer.R b/R/layer.R index 8b4621bde2..7fc53571ef 100644 --- a/R/layer.R +++ b/R/layer.R @@ -58,7 +58,9 @@ #' `NA`, the default, includes if any aesthetics are mapped. #' `FALSE` never includes, and `TRUE` always includes. #' It can also be a named logical vector to finely select the aesthetics to -#' display. +#' display. To include legend keys for all levels, even +#' when no data exists, use `TRUE`. If `NA`, all levels are shown in legend, +#' but unobserved levels are omitted. #' @param inherit.aes If `FALSE`, overrides the default aesthetics, #' rather than combining with them. This is most useful for helper functions #' that define both data and aesthetics and shouldn't inherit behaviour from diff --git a/man/borders.Rd b/man/borders.Rd index 1fcb3f2630..2fa16916e9 100644 --- a/man/borders.Rd +++ b/man/borders.Rd @@ -79,7 +79,9 @@ to use \code{position_jitter()}, give the position as \code{"jitter"}. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{\code{inherit.aes}}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from diff --git a/man/geom_abline.Rd b/man/geom_abline.Rd index 8fd63ae8e0..0c3bd12b24 100644 --- a/man/geom_abline.Rd +++ b/man/geom_abline.Rd @@ -89,7 +89,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{position}{A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and diff --git a/man/geom_bar.Rd b/man/geom_bar.Rd index 4f8196b4c1..6c8c67cc19 100644 --- a/man/geom_bar.Rd +++ b/man/geom_bar.Rd @@ -122,7 +122,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_bin_2d.Rd b/man/geom_bin_2d.Rd index 38341bf063..fa3b32b4ce 100644 --- a/man/geom_bin_2d.Rd +++ b/man/geom_bin_2d.Rd @@ -101,7 +101,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_blank.Rd b/man/geom_blank.Rd index c547845953..1f02b9cbc6 100644 --- a/man/geom_blank.Rd +++ b/man/geom_blank.Rd @@ -93,7 +93,9 @@ lists which parameters it can accept. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_boxplot.Rd b/man/geom_boxplot.Rd index e995aa6635..918b082d4b 100644 --- a/man/geom_boxplot.Rd +++ b/man/geom_boxplot.Rd @@ -145,7 +145,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_contour.Rd b/man/geom_contour.Rd index d53e300a79..72114072e2 100644 --- a/man/geom_contour.Rd +++ b/man/geom_contour.Rd @@ -169,7 +169,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_count.Rd b/man/geom_count.Rd index 370db388ed..1b925e7450 100644 --- a/man/geom_count.Rd +++ b/man/geom_count.Rd @@ -96,7 +96,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_density.Rd b/man/geom_density.Rd index 86bf57d6e9..58f6dae9e2 100644 --- a/man/geom_density.Rd +++ b/man/geom_density.Rd @@ -110,7 +110,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_density_2d.Rd b/man/geom_density_2d.Rd index 68f1353262..f063cfdd4a 100644 --- a/man/geom_density_2d.Rd +++ b/man/geom_density_2d.Rd @@ -138,7 +138,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_dotplot.Rd b/man/geom_dotplot.Rd index 1a57df3233..ff7f30a4fc 100644 --- a/man/geom_dotplot.Rd +++ b/man/geom_dotplot.Rd @@ -131,7 +131,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_errorbarh.Rd b/man/geom_errorbarh.Rd index f72ccd5a2a..21a4c79f5c 100644 --- a/man/geom_errorbarh.Rd +++ b/man/geom_errorbarh.Rd @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_function.Rd b/man/geom_function.Rd index 529f552d11..451c779003 100644 --- a/man/geom_function.Rd +++ b/man/geom_function.Rd @@ -100,7 +100,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_hex.Rd b/man/geom_hex.Rd index 1876bf19fe..11dbdb1f87 100644 --- a/man/geom_hex.Rd +++ b/man/geom_hex.Rd @@ -99,7 +99,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index a4a95c503f..1f290dbcdc 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -120,7 +120,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_jitter.Rd b/man/geom_jitter.Rd index 4ca3577792..2fa8acf555 100644 --- a/man/geom_jitter.Rd +++ b/man/geom_jitter.Rd @@ -108,7 +108,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index 03eb82f896..0d70775f6d 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -149,7 +149,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_map.Rd b/man/geom_map.Rd index f6aaf69dca..6a634702e9 100644 --- a/man/geom_map.Rd +++ b/man/geom_map.Rd @@ -89,7 +89,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 239b7dc0c6..8c530e4d33 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -140,7 +140,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_point.Rd b/man/geom_point.Rd index b7e6a0d5d2..762d4a1f80 100644 --- a/man/geom_point.Rd +++ b/man/geom_point.Rd @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_polygon.Rd b/man/geom_polygon.Rd index 5e69742056..22670cbb8b 100644 --- a/man/geom_polygon.Rd +++ b/man/geom_polygon.Rd @@ -103,7 +103,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_qq.Rd b/man/geom_qq.Rd index 62ff813561..d450b3d948 100644 --- a/man/geom_qq.Rd +++ b/man/geom_qq.Rd @@ -156,7 +156,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_quantile.Rd b/man/geom_quantile.Rd index a3aa6ac3c0..568c33e970 100644 --- a/man/geom_quantile.Rd +++ b/man/geom_quantile.Rd @@ -109,7 +109,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_ribbon.Rd b/man/geom_ribbon.Rd index 418c759f8c..2c7e805fc7 100644 --- a/man/geom_ribbon.Rd +++ b/man/geom_ribbon.Rd @@ -130,7 +130,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_rug.Rd b/man/geom_rug.Rd index db5b200b76..6e84a4d985 100644 --- a/man/geom_rug.Rd +++ b/man/geom_rug.Rd @@ -108,7 +108,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_segment.Rd b/man/geom_segment.Rd index 05ecf827e8..fc3adbbd8c 100644 --- a/man/geom_segment.Rd +++ b/man/geom_segment.Rd @@ -128,7 +128,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_smooth.Rd b/man/geom_smooth.Rd index 67c0c3e0c7..6d89a61782 100644 --- a/man/geom_smooth.Rd +++ b/man/geom_smooth.Rd @@ -140,7 +140,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_spoke.Rd b/man/geom_spoke.Rd index 216686f8ec..7fe6a9d9ee 100644 --- a/man/geom_spoke.Rd +++ b/man/geom_spoke.Rd @@ -98,7 +98,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 9c64a258d5..5f5dabe2d0 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -138,7 +138,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_tile.Rd b/man/geom_tile.Rd index ac32298ee7..326f36a2f4 100644 --- a/man/geom_tile.Rd +++ b/man/geom_tile.Rd @@ -133,7 +133,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/geom_violin.Rd b/man/geom_violin.Rd index 4041d770c7..974d1c5bdc 100644 --- a/man/geom_violin.Rd +++ b/man/geom_violin.Rd @@ -130,7 +130,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/layer.Rd b/man/layer.Rd index 8ce4e49715..b4070fbe2a 100644 --- a/man/layer.Rd +++ b/man/layer.Rd @@ -94,7 +94,9 @@ supplied parameters and aesthetics are understood by the \code{geom} or \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{key_glyph}{A legend key drawing function or a string providing the function name minus the \code{draw_key_} prefix. See \link{draw_key} for details.} diff --git a/man/layer_sf.Rd b/man/layer_sf.Rd index 8da9547aed..cda8db1d2e 100644 --- a/man/layer_sf.Rd +++ b/man/layer_sf.Rd @@ -92,7 +92,9 @@ supplied parameters and aesthetics are understood by the \code{geom} or \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} } \description{ The \code{layer_sf()} function is a variant of \code{\link[=layer]{layer()}} meant to be used by diff --git a/man/stat_ecdf.Rd b/man/stat_ecdf.Rd index d0941b2b56..8d92c51743 100644 --- a/man/stat_ecdf.Rd +++ b/man/stat_ecdf.Rd @@ -105,7 +105,9 @@ a warning. If \code{TRUE} silently removes missing values.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_ellipse.Rd b/man/stat_ellipse.Rd index bed871d361..138bda2e65 100644 --- a/man/stat_ellipse.Rd +++ b/man/stat_ellipse.Rd @@ -112,7 +112,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_identity.Rd b/man/stat_identity.Rd index 945eaafd87..f5dd6e1a5d 100644 --- a/man/stat_identity.Rd +++ b/man/stat_identity.Rd @@ -93,7 +93,9 @@ lists which parameters it can accept. \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_sf_coordinates.Rd b/man/stat_sf_coordinates.Rd index 35ce136a6c..1a8aef4440 100644 --- a/man/stat_sf_coordinates.Rd +++ b/man/stat_sf_coordinates.Rd @@ -72,7 +72,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_summary.Rd b/man/stat_summary.Rd index 83cbe4c9a7..3ebf979e54 100644 --- a/man/stat_summary.Rd +++ b/man/stat_summary.Rd @@ -161,7 +161,9 @@ to either \code{"x"} or \code{"y"}. See the \emph{Orientation} section for more \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_summary_2d.Rd b/man/stat_summary_2d.Rd index 464cdeacc3..9ee4604b65 100644 --- a/man/stat_summary_2d.Rd +++ b/man/stat_summary_2d.Rd @@ -132,7 +132,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions diff --git a/man/stat_unique.Rd b/man/stat_unique.Rd index 89a7e728b5..137c99f180 100644 --- a/man/stat_unique.Rd +++ b/man/stat_unique.Rd @@ -97,7 +97,9 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions From 19d45502557533fa03a645e34b9306e87a096b2b Mon Sep 17 00:00:00 2001 From: catalamarti Date: Thu, 15 Aug 2024 14:31:59 -0700 Subject: [PATCH 090/264] correct misleading error (#6043) --- R/utilities-break.R | 3 +++ tests/testthat/_snaps/utilities-break.md | 4 ++++ tests/testthat/test-utilities-break.R | 3 +++ 3 files changed, 10 insertions(+) create mode 100644 tests/testthat/_snaps/utilities-break.md create mode 100644 tests/testthat/test-utilities-break.R diff --git a/R/utilities-break.R b/R/utilities-break.R index 1bcce62ec3..0ed711ad7a 100644 --- a/R/utilities-break.R +++ b/R/utilities-break.R @@ -24,6 +24,9 @@ #' table(cut_width(runif(1000), 0.1, center = 0)) #' table(cut_width(runif(1000), 0.1, labels = FALSE)) cut_interval <- function(x, n = NULL, length = NULL, ...) { + if ((!is.null(n) && !is.null(length)) || (is.null(n) && is.null(length))) { + cli::cli_abort("Specify exactly one of {.var n} and {.var length}.") + } cut(x, breaks(x, "width", n, length), include.lowest = TRUE, ...) } diff --git a/tests/testthat/_snaps/utilities-break.md b/tests/testthat/_snaps/utilities-break.md new file mode 100644 index 0000000000..c8115c4c48 --- /dev/null +++ b/tests/testthat/_snaps/utilities-break.md @@ -0,0 +1,4 @@ +# cut_interval gives the correct + + Specify exactly one of `n` and `length`. + diff --git a/tests/testthat/test-utilities-break.R b/tests/testthat/test-utilities-break.R new file mode 100644 index 0000000000..23bc143a45 --- /dev/null +++ b/tests/testthat/test-utilities-break.R @@ -0,0 +1,3 @@ +test_that("cut_interval throws the correct error message", { + expect_snapshot_error(cut_interval(x = 1:10, width = 10)) +}) From 73811607903a40831d20dd239cb81c040790633f Mon Sep 17 00:00:00 2001 From: Matt Russell Date: Thu, 15 Aug 2024 22:40:46 +0100 Subject: [PATCH 091/264] Fix typo in `labeller` docs (#6034) --- R/labeller.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/labeller.R b/R/labeller.R index 3dbb9b63ac..f23f22b459 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -323,7 +323,7 @@ as_labeller <- function(x, default = label_value, multi_line = TRUE) { #' #' This function makes it easy to assign different labellers to #' different factors. The labeller can be a function or it can be a -#' named character vectors that will serve as a lookup table. +#' named character vector that will serve as a lookup table. #' #' In case of functions, if the labeller has class `labeller`, it #' is directly applied on the data frame of labels. Otherwise, it is From 308d4c32394b59009e58aef3cce1f2dd560be722 Mon Sep 17 00:00:00 2001 From: Stephen Uong <47620395+phispu@users.noreply.github.com> Date: Thu, 15 Aug 2024 15:12:51 -0700 Subject: [PATCH 092/264] `labs()`: Added `gg` class (#6045) --- NEWS.md | 1 + R/labels.R | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 4c0ea1e891..285399407e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Added `gg` class to `labs()` (@phispu, #5553). * Missing values from discrete palettes are no longer translated (@teunbrand, #5929). * Fixed bug in `facet_grid(margins = TRUE)` when using expresssions diff --git a/R/labels.R b/R/labels.R index 2bc5551034..7662153e91 100644 --- a/R/labels.R +++ b/R/labels.R @@ -139,7 +139,7 @@ labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), args <- args[!duplicated(names(args))] args <- rename_aes(args) - structure(args, class = "labels") + structure(args, class = c("labels", "gg")) } #' @rdname labs From ee5c9e5b4f0ef551b00a80f3bb10060d878202bc Mon Sep 17 00:00:00 2001 From: Sierra Johnson <80361498+sierrajohnson@users.noreply.github.com> Date: Thu, 15 Aug 2024 16:16:07 -0600 Subject: [PATCH 093/264] Add translate_string_shape to GeomSf (#6039) --- NEWS.md | 1 + R/geom-sf.R | 3 +++ 2 files changed, 4 insertions(+) diff --git a/NEWS.md b/NEWS.md index 285399407e..28ecb99196 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* geom_sf now accepts shape names (@sierrajohnson, #5808) * Added `gg` class to `labs()` (@phispu, #5553). * Missing values from discrete palettes are no longer translated (@teunbrand, #5929). diff --git a/R/geom-sf.R b/R/geom-sf.R index c6298e4b3a..457b8c272d 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -200,6 +200,9 @@ GeomSf <- ggproto("GeomSf", Geom, if (!inherits(coord, "CoordSf")) { cli::cli_abort("{.fn {snake_class(self)}} can only be used with {.fn coord_sf}.") } + if (is.character(data$shape)) { + data$shape <- translate_shape_string(data$shape) + } data <- coord$transform(data, panel_params) From 633e350f3416037432a981a345e3aa9ba25f2349 Mon Sep 17 00:00:00 2001 From: Stephen Uong <47620395+phispu@users.noreply.github.com> Date: Thu, 15 Aug 2024 15:26:02 -0700 Subject: [PATCH 094/264] `geom_function()`: x-axis title produced automatically where no data is added (#6047) --- NEWS.md | 2 ++ R/stat-function.R | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 28ecb99196..f9bdc996e0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug in `stat_function()` so x-axis title now produced automatically + when no data added. (@phispu, #5647). * geom_sf now accepts shape names (@sierrajohnson, #5808) * Added `gg` class to `labs()` (@phispu, #5553). * Missing values from discrete palettes are no longer translated diff --git a/R/stat-function.R b/R/stat-function.R index 8f31b8daba..bf6d2e4b74 100644 --- a/R/stat-function.R +++ b/R/stat-function.R @@ -50,7 +50,7 @@ stat_function <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export StatFunction <- ggproto("StatFunction", Stat, - default_aes = aes(y = after_scale(y)), + default_aes = aes(x = NULL, y = after_scale(y)), compute_group = function(data, scales, fun, xlim = NULL, n = 101, args = list()) { if (is.null(scales$x)) { From d8eb945ba2b5de9d76fd137fd76101a23a0e87e1 Mon Sep 17 00:00:00 2001 From: Etienne Bacher <52219252+etiennebacher@users.noreply.github.com> Date: Tue, 20 Aug 2024 14:19:01 +0200 Subject: [PATCH 095/264] fix some lints (#6050) --- R/annotation-logticks.R | 6 +++--- R/bin.R | 2 +- R/compat-plyr.R | 4 ++-- R/coord-polar.R | 2 +- R/coord-sf.R | 4 ++-- R/facet-.R | 2 +- R/facet-grid-.R | 4 ++-- R/facet-wrap.R | 4 ++-- R/fortify-spatial.R | 8 ++++---- R/geom-dotplot.R | 20 ++++++++++---------- R/geom-label.R | 2 +- R/geom-segment.R | 2 +- R/geom-smooth.R | 4 ++-- R/guide-.R | 4 ++-- R/guide-axis-stack.R | 4 ++-- R/guide-axis.R | 16 ++++++++-------- R/guide-bins.R | 2 +- R/guide-colorbar.R | 4 ++-- R/guide-legend.R | 2 +- R/guides-.R | 4 ++-- R/legend-draw.R | 2 +- R/limits.R | 2 +- R/margins.R | 2 +- R/plot-build.R | 16 ++++++++-------- R/position-dodge.R | 2 +- R/position-dodge2.R | 2 +- R/save.R | 2 +- R/scale-.R | 2 +- R/scale-binned.R | 2 +- R/scale-expansion.R | 2 +- R/scale-manual.R | 2 +- R/stat-bindot.R | 4 ++-- R/stat-density.R | 2 +- R/stat-ecdf.R | 2 +- R/stat-qq-line.R | 4 ++-- R/stat-smooth-methods.R | 4 ++-- R/stat-summary-bin.R | 6 +++--- R/stat-summary.R | 6 +++--- R/summarise-plot.R | 4 ++-- R/utilities-checks.R | 2 +- 40 files changed, 85 insertions(+), 85 deletions(-) diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R index 33f0a952a4..13c8f609f5 100644 --- a/R/annotation-logticks.R +++ b/R/annotation-logticks.R @@ -165,7 +165,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, names(xticks)[names(xticks) == "value"] <- x_name # Rename to 'x' for coordinates$transform xticks <- coord$transform(xticks, panel_params) - xticks = xticks[xticks$x <= 1 & xticks$x >= 0,] + xticks <- xticks[xticks$x <= 1 & xticks$x >= 0,] if (outside) xticks$end = -xticks$end @@ -203,7 +203,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, names(yticks)[names(yticks) == "value"] <- y_name # Rename to 'y' for coordinates$transform yticks <- coord$transform(yticks, panel_params) - yticks = yticks[yticks$y <= 1 & yticks$y >= 0,] + yticks <- yticks[yticks$y <= 1 & yticks$y >= 0,] if (outside) yticks$end = -yticks$end @@ -238,7 +238,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, # - start: on the other axis, start position of the line (usually 0) # - end: on the other axis, end position of the line (for example, .1, .2, or .3) calc_logticks <- function(base = 10, ticks_per_base = base - 1, - minpow = 0, maxpow = minpow + 1, start = 0, shortend = .1, midend = .2, longend = .3) { + minpow = 0, maxpow = minpow + 1, start = 0, shortend = 0.1, midend = 0.2, longend = 0.3) { # Number of blocks of tick marks reps <- maxpow - minpow diff --git a/R/bin.R b/R/bin.R index 856568f08c..a7784d02e5 100644 --- a/R/bin.R +++ b/R/bin.R @@ -165,7 +165,7 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) { } # Add row for missings - if (any(is.na(bins))) { + if (anyNA(bins)) { bin_count <- c(bin_count, sum(is.na(bins))) bin_widths <- c(bin_widths, NA) bin_x <- c(bin_x, NA) diff --git a/R/compat-plyr.R b/R/compat-plyr.R index 95c317a02c..efc2865a0c 100644 --- a/R/compat-plyr.R +++ b/R/compat-plyr.R @@ -54,13 +54,13 @@ rename <- function(x, replace) { id_var <- function(x, drop = FALSE) { if (length(x) == 0) { id <- integer() - n = 0L + n <- 0L } else if (!is.null(attr(x, "n")) && !drop) { return(x) } else if (is.factor(x) && !drop) { x <- addNA(x, ifany = TRUE) id <- as.integer(x) - n <- length(levels(x)) + n <- nlevels(x) } else { levels <- sort(unique0(x), na.last = TRUE) id <- match(x, levels) diff --git a/R/coord-polar.R b/R/coord-polar.R index e0712760fb..f1c8108ddf 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -137,7 +137,7 @@ CoordPolar <- ggproto("CoordPolar", Coord, ret[[n]]$sec.labels <- out$sec.labels } - details = list( + details <- list( x.range = ret$x$range, y.range = ret$y$range, x.major = ret$x$major, y.major = ret$y$major, x.minor = ret$x$minor, y.minor = ret$y$minor, diff --git a/R/coord-sf.R b/R/coord-sf.R index f861ae2d28..a14b3c718c 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -416,7 +416,7 @@ sf_rescale01 <- function(x, x_range, y_range) { # different limits methods calc_limits_bbox <- function(method, xlim, ylim, crs, default_crs) { - if (any(!is.finite(c(xlim, ylim))) && method != "geometry_bbox") { + if (!all(is.finite(c(xlim, ylim))) && method != "geometry_bbox") { cli::cli_abort(c( "Scale limits cannot be mapped onto spatial coordinates in {.fn coord_sf}.", "i" = "Consider setting {.code lims_method = \"geometry_bbox\"} or {.code default_crs = NULL}." @@ -585,7 +585,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, } parse_axes_labeling <- function(x) { - labs = unlist(strsplit(x, "")) + labs <- unlist(strsplit(x, "")) list(top = labs[1], right = labs[2], bottom = labs[3], left = labs[4]) } diff --git a/R/facet-.R b/R/facet-.R index 96c96dc6fd..359c19a248 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -678,7 +678,7 @@ find_panel <- function(table) { } #' @rdname find_panel #' @export -panel_cols = function(table) { +panel_cols <- function(table) { panels <- table$layout[grepl("^panel", table$layout$name), , drop = FALSE] unique0(panels[, c('l', 'r')]) } diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 7bfb30dd6e..c51df5c138 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -319,8 +319,8 @@ FacetGrid <- ggproto("FacetGrid", Facet, if (length(missing_facets) > 0) { to_add <- unique0(layout[missing_facets]) - data_rep <- rep.int(1:nrow(data), nrow(to_add)) - facet_rep <- rep(1:nrow(to_add), each = nrow(data)) + data_rep <- rep.int(seq_len(nrow(data)), nrow(to_add)) + facet_rep <- rep(seq_len(nrow(to_add)), each = nrow(data)) data <- unrowname(data[data_rep, , drop = FALSE]) facet_vals <- unrowname(vec_cbind( diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 68c02f0b21..93ae19da91 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -242,8 +242,8 @@ FacetWrap <- ggproto("FacetWrap", Facet, to_add <- unique0(layout[missing_facets]) - data_rep <- rep.int(1:nrow(data), nrow(to_add)) - facet_rep <- rep(1:nrow(to_add), each = nrow(data)) + data_rep <- rep.int(seq_len(nrow(data)), nrow(to_add)) + facet_rep <- rep(seq_len(nrow(to_add)), each = nrow(data)) data <- data[data_rep, , drop = FALSE] facet_vals <- vec_cbind( diff --git a/R/fortify-spatial.R b/R/fortify-spatial.R index 6fe7392a37..0e9f37d046 100644 --- a/R/fortify-spatial.R +++ b/R/fortify-spatial.R @@ -71,7 +71,7 @@ fortify.Polygons <- function(model, data, ...) { }) pieces <- vec_rbind0(!!!pieces) - pieces$order <- 1:nrow(pieces) + pieces$order <- seq_len(nrow(pieces)) pieces$id <- model@ID pieces$piece <- factor(pieces$piece) pieces$group <- interaction(pieces$id, pieces$piece) @@ -89,7 +89,7 @@ fortify.Polygon <- function(model, data, ...) { df <- as.data.frame(model@coords) names(df) <- c("long", "lat") - df$order <- 1:nrow(df) + df$order <- seq_len(nrow(df)) df$hole <- model@hole df } @@ -124,7 +124,7 @@ fortify.Lines <- function(model, data, ...) { }) pieces <- vec_rbind0(!!!pieces) - pieces$order <- 1:nrow(pieces) + pieces$order <- seq_len(nrow(pieces)) pieces$id <- model@ID pieces$piece <- factor(pieces$piece) pieces$group <- interaction(pieces$id, pieces$piece) @@ -142,7 +142,7 @@ fortify.Line <- function(model, data, ...) { df <- as.data.frame(model@coords) names(df) <- c("long", "lat") - df$order <- 1:nrow(df) + df$order <- seq_len(nrow(df)) df } diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index e163fb272b..7a0f9a5e08 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -197,25 +197,25 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, # Set up the stacking function and range if (is.null(params$stackdir) || params$stackdir == "up") { - stackdots <- function(a) a - .5 + stackdots <- function(a) a - 0.5 stackaxismin <- 0 stackaxismax <- 1 } else if (params$stackdir == "down") { - stackdots <- function(a) -a + .5 + stackdots <- function(a) -a + 0.5 stackaxismin <- -1 stackaxismax <- 0 } else if (params$stackdir == "center") { stackdots <- function(a) a - 1 - max(a - 1) / 2 - stackaxismin <- -.5 - stackaxismax <- .5 + stackaxismin <- -0.5 + stackaxismax <- 0.5 } else if (params$stackdir == "centerwhole") { stackdots <- function(a) a - 1 - floor(max(a - 1) / 2) - stackaxismin <- -.5 - stackaxismax <- .5 + stackaxismin <- -0.5 + stackaxismax <- 0.5 } # Fill the bins: at a given x (or y), if count=3, make 3 entries at that x - data <- data[rep(1:nrow(data), data$count), ] + data <- data[rep(seq_len(nrow(data)), data$count), ] # Next part will set the position of each dot within each stack # If stackgroups=TRUE, split only on x (or y) and panel; if not stacking, also split by group @@ -231,7 +231,7 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, # Within each x, or x+group, set countidx=1,2,3, and set stackpos according to stack function data <- dapply(data, plyvars, function(xx) { - xx$countidx <- 1:nrow(xx) + xx$countidx <- seq_len(nrow(xx)) xx$stackpos <- stackdots(xx$countidx) xx }) @@ -281,11 +281,11 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, binaxis <- ifelse(binaxis == "x", "y", "x") if (binaxis == "x") { - stackaxis = "y" + stackaxis <- "y" dotdianpc <- dotsize * tdata$binwidth[1] / (max(panel_params$x.range) - min(panel_params$x.range)) } else if (binaxis == "y") { - stackaxis = "x" + stackaxis <- "x" dotdianpc <- dotsize * tdata$binwidth[1] / (max(panel_params$y.range) - min(panel_params$y.range)) } diff --git a/R/geom-label.R b/R/geom-label.R index e8a4605b54..a265850f91 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -81,7 +81,7 @@ GeomLabel <- ggproto("GeomLabel", Geom, size.unit <- resolve_text_unit(size.unit) - grobs <- lapply(1:nrow(data), function(i) { + grobs <- lapply(seq_len(nrow(data)), function(i) { row <- data[i, , drop = FALSE] labelGrob(lab[i], x = unit(row$x, "native"), diff --git a/R/geom-segment.R b/R/geom-segment.R index be3492bb56..303a040337 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -134,7 +134,7 @@ GeomSegment <- ggproto("GeomSegment", Geom, )) } - data$group <- 1:nrow(data) + data$group <- seq_len(nrow(data)) starts <- subset(data, select = c(-xend, -yend)) ends <- rename(subset(data, select = c(-x, -y)), c("xend" = "x", "yend" = "y")) diff --git a/R/geom-smooth.R b/R/geom-smooth.R index 2247bf2a5b..8874ef491c 100644 --- a/R/geom-smooth.R +++ b/R/geom-smooth.R @@ -153,8 +153,8 @@ GeomSmooth <- ggproto("GeomSmooth", Geom, ribbon <- transform(data, colour = NA) path <- transform(data, alpha = NA) - ymin = flipped_names(flipped_aes)$ymin - ymax = flipped_names(flipped_aes)$ymax + ymin <- flipped_names(flipped_aes)$ymin + ymax <- flipped_names(flipped_aes)$ymax has_ribbon <- se && !is.null(data[[ymax]]) && !is.null(data[[ymin]]) gList( diff --git a/R/guide-.R b/R/guide-.R index 0a334c4580..1856394ee3 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -487,7 +487,7 @@ Guide <- ggproto( # Helper function that may facilitate flipping theme elements by # swapping x/y related arguments to `element_grob()` -flip_element_grob = function(..., flip = FALSE) { +flip_element_grob <- function(..., flip = FALSE) { if (!flip) { ans <- element_grob(...) return(ans) @@ -499,7 +499,7 @@ flip_element_grob = function(..., flip = FALSE) { } # The flippable arguments for `flip_element_grob()`. -flip_names = c( +flip_names <- c( "x" = "y", "y" = "x", "width" = "height", diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R index c645c29d99..b11a969b8f 100644 --- a/R/guide-axis-stack.R +++ b/R/guide-axis-stack.R @@ -41,7 +41,7 @@ guide_axis_stack <- function(first = "axis", ..., title = waiver(), theme = NULL # Check available aesthetics available <- lapply(axes, `[[`, name = "available_aes") available <- vapply(available, function(x) all(c("x", "y") %in% x), logical(1)) - if (all(!available)) { + if (!any(available)) { cli::cli_abort(paste0( "{.fn guide_axis_stack} can only use guides that handle {.field x} and ", "{.field y} aesthetics." @@ -49,7 +49,7 @@ guide_axis_stack <- function(first = "axis", ..., title = waiver(), theme = NULL } # Remove guides that don't support x/y aesthetics - if (any(!available)) { + if (!all(available)) { remove <- which(!available) removed <- vapply(axes[remove], snake_class, character(1)) axes[remove] <- NULL diff --git a/R/guide-axis.R b/R/guide-axis.R index dc57ffd23e..a0f1fb5ce3 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -592,23 +592,23 @@ axis_label_element_overrides <- function(axis_position, angle = NULL) { if (axis_position == "bottom") { - hjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - vjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 + hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 + vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 } else if (axis_position == "left") { - hjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - vjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 + hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 + vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 } else if (axis_position == "top") { - hjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - vjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 + hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 + vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 } else if (axis_position == "right") { - hjust = if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - vjust = if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 + hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 + vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 } diff --git a/R/guide-bins.R b/R/guide-bins.R index e2bd0db428..518655cbba 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -326,7 +326,7 @@ GuideBins <- ggproto( } ) -parse_binned_breaks = function(scale, breaks = scale$get_breaks()) { +parse_binned_breaks <- function(scale, breaks = scale$get_breaks()) { breaks <- breaks[!is.na(breaks)] if (length(breaks) == 0) { diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index ca63f29b54..5154c67c07 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -366,12 +366,12 @@ GuideColourbar <- ggproto( if (params$direction == "horizontal") { width <- 1 / nrow(decor) height <- 1 - x <- (seq(nrow(decor)) - 1) * width + x <- (seq_len(nrow(decor)) - 1) * width y <- 0 } else { width <- 1 height <- 1 / nrow(decor) - y <- (seq(nrow(decor)) - 1) * height + y <- (seq_len(nrow(decor)) - 1) * height x <- 0 } grob <- rectGrob( diff --git a/R/guide-legend.R b/R/guide-legend.R index 95dba1cfa0..6e3524b5bd 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -631,7 +631,7 @@ keep_key_data <- function(key, data, aes, show) { if (isTRUE(any(show)) || length(show) == 0) { return(TRUE) } - if (isTRUE(all(!show))) { + if (isTRUE(!any(show))) { return(FALSE) } # Second, we go find if the value is actually present in the data. diff --git a/R/guides-.R b/R/guides-.R index fc9d6e2b3c..d45f55e892 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -194,7 +194,7 @@ Guides <- ggproto( if (is.character(index)) { index <- match(index, self$aesthetics) } - if (any(is.na(index)) || length(index) == 0) { + if (anyNA(index) || length(index) == 0) { return(NULL) } if (length(index) == 1) { @@ -209,7 +209,7 @@ Guides <- ggproto( if (is.character(index)) { index <- match(index, self$aesthetics) } - if (any(is.na(index)) || length(index) == 0) { + if (anyNA(index) || length(index) == 0) { return(NULL) } if (length(index) == 1) { diff --git a/R/legend-draw.R b/R/legend-draw.R index 9bfd1d9d93..ccfb035872 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -207,7 +207,7 @@ draw_key_vpath <- function(data, params, size) { #' @export #' @rdname draw_key draw_key_dotplot <- function(data, params, size) { - pointsGrob(0.5, 0.5, size = unit(.5, "npc"), + pointsGrob(0.5, 0.5, size = unit(0.5, "npc"), pch = 21, gp = gg_par( col = alpha(data$colour %||% "black", data$alpha), diff --git a/R/limits.R b/R/limits.R index 26528ee7ff..087c4c11d0 100644 --- a/R/limits.R +++ b/R/limits.R @@ -116,7 +116,7 @@ limits.numeric <- function(lims, var, call = caller_env()) { if (length(lims) != 2) { cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) } - if (!any(is.na(lims)) && lims[1] > lims[2]) { + if (!anyNA(lims) && lims[1] > lims[2]) { trans <- "reverse" } else { trans <- "identity" diff --git a/R/margins.R b/R/margins.R index 0fee3ca0ab..176072b4de 100644 --- a/R/margins.R +++ b/R/margins.R @@ -198,7 +198,7 @@ justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, ) } else { - children = gList(grobs) + children <- gList(grobs) } diff --git a/R/plot-build.R b/R/plot-build.R index 2a68dd550f..23d2a11b0f 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -250,18 +250,18 @@ ggplot_gtable.ggplot_built <- function(data) { pans <- plot_table$layout[grepl("^panel", plot_table$layout$name), , drop = FALSE] if (title_pos == "panel") { - title_l = min(pans$l) - title_r = max(pans$r) + title_l <- min(pans$l) + title_r <- max(pans$r) } else { - title_l = 1 - title_r = ncol(plot_table) + title_l <- 1 + title_r <- ncol(plot_table) } if (caption_pos == "panel") { - caption_l = min(pans$l) - caption_r = max(pans$r) + caption_l <- min(pans$l) + caption_r <- max(pans$r) } else { - caption_l = 1 - caption_r = ncol(plot_table) + caption_l <- 1 + caption_r <- ncol(plot_table) } plot_table <- gtable_add_rows(plot_table, subtitle_height, pos = 0) diff --git a/R/position-dodge.R b/R/position-dodge.R index b3818cf08c..ec4b64cdad 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -175,7 +175,7 @@ pos_dodge <- function(df, width, n = NULL) { groupidx <- match(df$group, unique0(df$group)) # Find the center for each group, then use that to calculate xmin and xmax - df$x <- df$x + width * ((groupidx - 0.5) / n - .5) + df$x <- df$x + width * ((groupidx - 0.5) / n - 0.5) df$xmin <- df$x - d_width / n / 2 df$xmax <- df$x + d_width / n / 2 diff --git a/R/position-dodge2.R b/R/position-dodge2.R index e8e291c62c..a670ffc349 100644 --- a/R/position-dodge2.R +++ b/R/position-dodge2.R @@ -113,7 +113,7 @@ pos_dodge2 <- function(df, width, n = NULL, padding = 0.1) { df$x <- (df$xmin + df$xmax) / 2 # If no elements occupy the same position, there is no need to add padding - if (!any(duplicated(df$xid))) { + if (!anyDuplicated(df$xid) > 0) { return(df) } diff --git a/R/save.R b/R/save.R index 2f28c49418..acc4176162 100644 --- a/R/save.R +++ b/R/save.R @@ -197,7 +197,7 @@ plot_dim <- function(dim = c(NA, NA), scale = 1, units = "in", dim <- to_inches(dim) * scale - if (any(is.na(dim))) { + if (anyNA(dim)) { if (length(grDevices::dev.list()) == 0) { default_dim <- c(7, 7) } else { diff --git a/R/scale-.R b/R/scale-.R index 1773f15142..fd0bbd444f 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -123,7 +123,7 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam position <- arg_match0(position, c("left", "right", "top", "bottom")) # If the scale is non-positional, break = NULL means removing the guide - if (is.null(breaks) && all(!is_position_aes(aesthetics))) { + if (is.null(breaks) && !any(is_position_aes(aesthetics))) { guide <- "none" } diff --git a/R/scale-binned.R b/R/scale-binned.R index d84080fdef..4db4f1a916 100644 --- a/R/scale-binned.R +++ b/R/scale-binned.R @@ -92,7 +92,7 @@ ScaleBinnedPosition <- ggproto("ScaleBinnedPosition", ScaleBinned, include.lowest = TRUE, right = self$right ) - (x - x_binned + .5) * diff(all_breaks)[x_binned] + all_breaks[x_binned] + (x - x_binned + 0.5) * diff(all_breaks)[x_binned] + all_breaks[x_binned] } else { x <- as.numeric(self$oob(x, limits)) x <- ifelse(!is.na(x), x, self$na.value) diff --git a/R/scale-expansion.R b/R/scale-expansion.R index 8ec72c2a78..e3392fc5bf 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -69,7 +69,7 @@ expand_range4 <- function(limits, expand) { cli::cli_abort("{.arg expand} must be a numeric vector with 2 or 4 elements.") } - if (all(!is.finite(limits))) { + if (!any(is.finite(limits))) { return(c(-Inf, Inf)) } diff --git a/R/scale-manual.R b/R/scale-manual.R index 6e96a54c3b..bcd0624094 100644 --- a/R/scale-manual.R +++ b/R/scale-manual.R @@ -176,7 +176,7 @@ manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), if (length(breaks) <= length(values)) { names(values) <- breaks } else { - names(values) <- breaks[1:length(values)] + names(values) <- breaks[seq_along(values)] } } diff --git a/R/stat-bindot.R b/R/stat-bindot.R index 66e40ce6cb..85eecc4d54 100644 --- a/R/stat-bindot.R +++ b/R/stat-bindot.R @@ -143,14 +143,14 @@ densitybin <- function(x, weight = NULL, binwidth = NULL, method = method, range # Sort weight and x, by x weight <- weight[order(x)] - x <- x[order(x)] + x <- sort(x, na.last = TRUE) cbin <- 0 # Current bin ID bin <- rep.int(NA, length(x)) # The bin ID for each observation binend <- -Inf # End position of current bin (scan left to right) # Scan list and put dots in bins - for (i in 1:length(x)) { + for (i in seq_along(x)) { # If past end of bin, start a new bin at this point if (x[i] >= binend) { binend <- x[i] + binwidth diff --git a/R/stat-density.R b/R/stat-density.R index add18570fc..5b948f5d88 100644 --- a/R/stat-density.R +++ b/R/stat-density.R @@ -239,7 +239,7 @@ reflect_density <- function(dens, bounds, from, to) { # Similar to stats::density.default # Once R4.3.0 is the lowest supported version, this function can be replaced by # using `density(..., warnWbw = FALSE)`. -precompute_bw = function(x, bw = "nrd0") { +precompute_bw <- function(x, bw = "nrd0") { bw <- bw[1] if (is.character(bw)) { bw <- to_lower_ascii(bw) diff --git a/R/stat-ecdf.R b/R/stat-ecdf.R index 85287b9130..96430b1e32 100644 --- a/R/stat-ecdf.R +++ b/R/stat-ecdf.R @@ -147,7 +147,7 @@ wecdf <- function(x, weights = NULL) { x <- x[ord] weights <- weights[ord] - if (any(!is.finite(weights))) { + if (!all(is.finite(weights))) { cli::cli_warn(c(paste0( "The {.field weight} aesthetic does not support non-finite or ", "{.code NA} values." diff --git a/R/stat-qq-line.R b/R/stat-qq-line.R index 67b0da407d..8133216779 100644 --- a/R/stat-qq-line.R +++ b/R/stat-qq-line.R @@ -11,7 +11,7 @@ geom_qq_line <- function(mapping = NULL, ..., distribution = stats::qnorm, dparams = list(), - line.p = c(.25, .75), + line.p = c(0.25, 0.75), fullrange = FALSE, na.rm = FALSE, show.legend = NA, @@ -56,7 +56,7 @@ StatQqLine <- ggproto("StatQqLine", Stat, distribution = stats::qnorm, dparams = list(), na.rm = FALSE, - line.p = c(.25, .75), + line.p = c(0.25, 0.75), fullrange = FALSE) { sample <- sort(data$sample) diff --git a/R/stat-smooth-methods.R b/R/stat-smooth-methods.R index 77d50cdff3..dc90e3c457 100644 --- a/R/stat-smooth-methods.R +++ b/R/stat-smooth-methods.R @@ -60,7 +60,7 @@ predictdf.loess <- function(model, xseq, se, level) { if (se) { y <- pred$fit - ci <- pred$se.fit * stats::qt(level / 2 + .5, pred$df) + ci <- pred$se.fit * stats::qt(level / 2 + 0.5, pred$df) ymin <- y - ci ymax <- y + ci base::data.frame(x = xseq, y, ymin, ymax, se = pred$se.fit) @@ -79,7 +79,7 @@ predictdf.locfit <- function(model, xseq, se, level) { if (se) { y <- pred$fit - ci <- pred$se.fit * stats::qt(level / 2 + .5, model$dp["df2"]) + ci <- pred$se.fit * stats::qt(level / 2 + 0.5, model$dp["df2"]) ymin <- y - ci ymax <- y + ci base::data.frame(x = xseq, y, ymin, ymax, se = pred$se.fit) diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index ce57b6def9..e9cd675e09 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -23,15 +23,15 @@ stat_summary_bin <- function(mapping = NULL, data = NULL, fun.ymax = deprecated()) { if (lifecycle::is_present(fun.y)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.y)", "stat_summary_bin(fun)") - fun = fun %||% fun.y + fun <- fun %||% fun.y } if (lifecycle::is_present(fun.ymin)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.ymin)", "stat_summary_bin(fun.min)") - fun.min = fun.min %||% fun.ymin + fun.min <- fun.min %||% fun.ymin } if (lifecycle::is_present(fun.ymax)) { deprecate_warn0("3.3.0", "stat_summary_bin(fun.ymax)", "stat_summary_bin(fun.max)") - fun.max = fun.max %||% fun.ymax + fun.max <- fun.max %||% fun.ymax } layer( data = data, diff --git a/R/stat-summary.R b/R/stat-summary.R index ddcb7b5ae3..cf2e2ef4c7 100644 --- a/R/stat-summary.R +++ b/R/stat-summary.R @@ -143,15 +143,15 @@ stat_summary <- function(mapping = NULL, data = NULL, fun.ymax = deprecated()) { if (lifecycle::is_present(fun.y)) { deprecate_warn0("3.3.0", "stat_summary(fun.y)", "stat_summary(fun)") - fun = fun %||% fun.y + fun <- fun %||% fun.y } if (lifecycle::is_present(fun.ymin)) { deprecate_warn0("3.3.0", "stat_summary(fun.ymin)", "stat_summary(fun.min)") - fun.min = fun.min %||% fun.ymin + fun.min <- fun.min %||% fun.ymin } if (lifecycle::is_present(fun.ymax)) { deprecate_warn0("3.3.0", "stat_summary(fun.ymax)", "stat_summary(fun.max)") - fun.max = fun.max %||% fun.ymax + fun.max <- fun.max %||% fun.ymax } layer( data = data, diff --git a/R/summarise-plot.R b/R/summarise-plot.R index 9411c1c586..bdb7cc7af4 100644 --- a/R/summarise-plot.R +++ b/R/summarise-plot.R @@ -61,7 +61,7 @@ NULL #' @rdname summarise_plot #' @export -summarise_layout = function(p) { +summarise_layout <- function(p) { check_inherits(p, "ggplot_built") l <- p$layout @@ -98,7 +98,7 @@ summarise_layout = function(p) { #' @rdname summarise_plot #' @export -summarise_coord = function(p) { +summarise_coord <- function(p) { check_inherits(p, "ggplot_built") # Given a transform object, find the log base; if the transform object is diff --git a/R/utilities-checks.R b/R/utilities-checks.R index db5fee2353..a1ed1b5091 100644 --- a/R/utilities-checks.R +++ b/R/utilities-checks.R @@ -182,7 +182,7 @@ check_inherits <- function(x, #' #' # Possibly throw an error #' try(check_device("glyphs", action = "abort")) -check_device = function(feature, action = "warn", op = NULL, maybe = FALSE, +check_device <- function(feature, action = "warn", op = NULL, maybe = FALSE, call = caller_env()) { check_bool(maybe, allow_na = TRUE) From 1a6e4958d9730f1d71bdd1261dde0aa52a6b90b2 Mon Sep 17 00:00:00 2001 From: Etienne Bacher <52219252+etiennebacher@users.noreply.github.com> Date: Tue, 20 Aug 2024 14:53:00 +0200 Subject: [PATCH 096/264] Fix some lints in the `tests` folder (#6051) * fix more lints * revert any(duplicated()) changes --- tests/testthat/test-aes-calculated.R | 2 +- tests/testthat/test-aes-grouping.R | 2 +- tests/testthat/test-coord-.R | 3 +- tests/testthat/test-coord-polar.R | 4 +- tests/testthat/test-coord-train.R | 6 +- tests/testthat/test-coord_sf.R | 4 +- tests/testthat/test-empty-data.R | 6 +- tests/testthat/test-facet-strips.R | 18 ++--- tests/testthat/test-fortify.R | 2 +- tests/testthat/test-geom-dotplot.R | 86 +++++++++++----------- tests/testthat/test-geom-path.R | 8 +- tests/testthat/test-geom-rug.R | 18 ++--- tests/testthat/test-geom-sf.R | 12 +-- tests/testthat/test-geom-violin.R | 10 +-- tests/testthat/test-guides.R | 8 +- tests/testthat/test-layer.R | 2 +- tests/testthat/test-scale-type.R | 4 +- tests/testthat/test-scales-breaks-labels.R | 52 ++++++------- tests/testthat/test-scales.R | 4 +- tests/testthat/test-sec-axis.R | 8 +- tests/testthat/test-stat-density.R | 2 +- tests/testthat/test-stat-function.R | 4 +- tests/testthat/test-stat-ydensity.R | 4 +- tests/testthat/test-stats.R | 4 +- tests/testthat/test-theme.R | 14 ++-- tests/testthat/test-utilities.R | 16 ++-- 26 files changed, 151 insertions(+), 152 deletions(-) diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index 62d25697d3..b453af02f5 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -6,7 +6,7 @@ test_that("names surrounded by .. is calculated", { expect_equal(is_calculated_aes(aes(..x.., ..x, x..)), c(TRUE, FALSE, FALSE)) # even when nested - expect_equal(is_calculated_aes(aes(f(..x..))), TRUE) + expect_true(is_calculated_aes(aes(f(..x..)))) }) test_that("call to stat() is calculated", { diff --git a/tests/testthat/test-aes-grouping.R b/tests/testthat/test-aes-grouping.R index bea15e2630..d5536cc417 100644 --- a/tests/testthat/test-aes-grouping.R +++ b/tests/testthat/test-aes-grouping.R @@ -26,7 +26,7 @@ test_that("no error for aes(groupS)", { g <- add_group(df2) expect_equal(nrow(g), nrow(df2)) - expect_equal(names(g), c("x", "y", "groupS", "group")) + expect_named(g, c("x", "y", "groupS", "group")) }) test_that("label is not used as a grouping var", { diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index b372478981..76a174454c 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -37,8 +37,7 @@ test_that("guide names are not removed by `train_panel_guides()`", { layout$setup_panel_guides(guides_list(NULL), plot$layers) # Line showing change in outcome - expect_equal(names(layout$panel_params[[1]]$guides$aesthetics), - c("x", "y", "x.sec", "y.sec")) + expect_named(layout$panel_params[[1]]$guides$aesthetics, c("x", "y", "x.sec", "y.sec")) }) test_that("check coord limits errors only on bad inputs", { diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index a663a43d98..e9cdcc4813 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -1,7 +1,7 @@ test_that("polar distance is calculated correctly", { dat <- data_frame( theta = c(0, 2*pi, 2, 6, 6, 1, 1, 0), - r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, .5)) + r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, 0.5)) scales <- list( x = scale_x_continuous(limits = c(0, 2*pi)), @@ -176,7 +176,7 @@ test_that("polar coordinates draw correctly", { dat <- data_frame( theta = c(0, 2*pi, 2, 6, 6, 1, 1, 0), - r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, .5), + r = c(0, 0, 0.5, 0.5, 1, 1, 0.75, 0.5), g = 1:8 ) expect_doppelganger("Rays, circular arcs, and spiral arcs", diff --git a/tests/testthat/test-coord-train.R b/tests/testthat/test-coord-train.R index b326fc6fe1..9d42ec3c79 100644 --- a/tests/testthat/test-coord-train.R +++ b/tests/testthat/test-coord-train.R @@ -5,7 +5,7 @@ test_that("NA's don't appear in breaks", { ns <- names(trained)[grepl("(\\.major)|(\\.minor)$", names(trained))] for (n in ns) { - if (!is.null(trained[n]) && any(is.na(trained[n]))) + if (!is.null(trained[n]) && anyNA(trained[n])) return(TRUE) } @@ -19,8 +19,8 @@ test_that("NA's don't appear in breaks", { # This is a test to make sure the later tests will be useful! # It's possible that changes to the way that breaks are calculated will # make it so that scale_break_positions will no longer give NA for range 1, 12 - expect_true(any(is.na(scale_x$break_positions()))) - expect_true(any(is.na(scale_y$break_positions()))) + expect_true(anyNA(scale_x$break_positions())) + expect_true(anyNA(scale_y$break_positions())) # Check the various types of coords to make sure they don't have NA breaks expect_false(any_NA_major_minor(coord_polar()$setup_panel_params(scale_x, scale_y))) diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index c668b3ec79..12a667be5b 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -309,8 +309,8 @@ test_that("sf_transform_xy() works", { # transform back out2 <- sf_transform_xy(out, 4326, 3347) expect_identical(data$city, out2$city) - expect_true(all(abs(out2$x - data$x) < .01)) - expect_true(all(abs(out2$y - data$y) < .01)) + expect_true(all(abs(out2$x - data$x) < 0.01)) + expect_true(all(abs(out2$y - data$y) < 0.01)) }) diff --git a/tests/testthat/test-empty-data.R b/tests/testthat/test-empty-data.R index 3d7c27c52d..bdcc02003c 100644 --- a/tests/testthat/test-empty-data.R +++ b/tests/testthat/test-empty-data.R @@ -88,13 +88,13 @@ test_that("empty layers still generate one grob per panel", { geom_point() + facet_wrap(~y) - expect_equal(length(get_layer_grob(d)), 3) + expect_length(get_layer_grob(d), 3) }) test_that("missing layers generate one grob per panel", { df <- data_frame(x = 1:4, y = rep(1:2, 2), g = rep(1:2, 2)) base <- ggplot(df, aes(x, y)) + geom_point(shape = NA, na.rm = TRUE) - expect_equal(length(get_layer_grob(base)), 1) - expect_equal(length(get_layer_grob(base + facet_wrap(~ g))), 2) + expect_length(get_layer_grob(base), 1) + expect_length(get_layer_grob(base + facet_wrap(~ g)), 2) }) diff --git a/tests/testthat/test-facet-strips.R b/tests/testthat/test-facet-strips.R index c2f131191e..d13f8d500c 100644 --- a/tests/testthat/test-facet-strips.R +++ b/tests/testthat/test-facet-strips.R @@ -143,16 +143,16 @@ test_that("padding is only added if axis is present", { strip.switch.pad.grid = unit(10, "mm") ) pg <- ggplotGrob(p) - expect_equal(length(pg$heights), 19) - expect_equal(length(pg$widths), 18) + expect_length(pg$heights, 19) + expect_length(pg$widths, 18) pg <- ggplotGrob( p + scale_x_continuous(position = "top") + scale_y_continuous(position = "right") ) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[9]), "1cm") - expect_equal(length(pg$widths), 19) + expect_length(pg$widths, 19) expect_equal(as.character(pg$widths[13]), "1cm") # Also add padding with negative ticks and no text (#5251) @@ -160,7 +160,7 @@ test_that("padding is only added if axis is present", { p + scale_x_continuous(labels = NULL, position = "top") + theme(axis.ticks.length.x.top = unit(-2, "mm")) ) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[9]), "1cm") # Inverse should be true when strips are switched @@ -172,17 +172,17 @@ test_that("padding is only added if axis is present", { ) pg <- ggplotGrob(p) - expect_equal(length(pg$heights), 20) + expect_length(pg$heights, 20) expect_equal(as.character(pg$heights[13]), "1cm") - expect_equal(length(pg$widths), 19) + expect_length(pg$widths, 19) expect_equal(as.character(pg$widths[7]), "1cm") pg <- ggplotGrob( p + scale_x_continuous(position = "top") + scale_y_continuous(position = "right") ) - expect_equal(length(pg$heights), 19) - expect_equal(length(pg$widths), 18) + expect_length(pg$heights, 19) + expect_length(pg$widths, 18) }) test_that("y strip labels are rotated when strips are switched", { diff --git a/tests/testthat/test-fortify.R b/tests/testthat/test-fortify.R index 03980c19c1..3a48c76ba0 100644 --- a/tests/testthat/test-fortify.R +++ b/tests/testthat/test-fortify.R @@ -11,7 +11,7 @@ test_that("spatial polygons have correct ordering", { y - dely,y - dely,y + dely,y + dely,y - dely), ncol = 2)) } - make_hole <- function(x = 0, y = 0, height = .5, width = .5){ + make_hole <- function(x = 0, y = 0, height = 0.5, width = 0.5){ p <- make_square(x = x, y = y, height = height, width = width) p@hole <- TRUE p diff --git a/tests/testthat/test-geom-dotplot.R b/tests/testthat/test-geom-dotplot.R index 3cf61d4216..648c52f926 100644 --- a/tests/testthat/test-geom-dotplot.R +++ b/tests/testthat/test-geom-dotplot.R @@ -17,7 +17,7 @@ test_that("dodging works", { ndodge <- 3 # The amount of space allocated within each dodge group - dwidth <- .9 / ndodge + dwidth <- 0.9 / ndodge # This should be the x position for each before dodging xbase <- ceiling(df$group / ndodge) @@ -36,20 +36,20 @@ test_that("dodging works", { test_that("binning works", { bp <- ggplot(dat, aes(y)) + - geom_dotplot(binwidth = .4, method = "histodot") + geom_dotplot(binwidth = 0.4, method = "histodot") x <- get_layer_data(bp)$x # Need ugly hack to make sure mod function doesn't give values like -3.99999 # due to floating point error - expect_true(all(abs((x - min(x) + 1e-7) %% .4) < 1e-6)) + expect_true(all(abs((x - min(x) + 1e-7) %% 0.4) < 1e-6)) bp <- ggplot(dat, aes(x = y)) + - geom_dotplot(binwidth = .4, method = "dotdensity") + geom_dotplot(binwidth = 0.4, method = "dotdensity") x <- get_layer_data(bp)$x # This one doesn't ensure that dotdensity works, but it does check that it's not # doing fixed bin sizes - expect_false(all(abs((x - min(x) + 1e-7) %% .4) < 1e-6)) + expect_false(all(abs((x - min(x) + 1e-7) %% 0.4) < 1e-6)) }) test_that("NA's result in warning from stat_bindot", { @@ -58,7 +58,7 @@ test_that("NA's result in warning from stat_bindot", { dat$x[c(2,10)] <- NA # Need to assign it to a var here so that it doesn't automatically print - expect_snapshot_warning(ggplot_build(ggplot(dat, aes(x)) + geom_dotplot(binwidth = .2))) + expect_snapshot_warning(ggplot_build(ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.2))) }) test_that("when binning on y-axis, limits depend on the panel", { @@ -92,99 +92,99 @@ test_that("geom_dotplot draws correctly", { # Basic dotplot with binning along x axis expect_doppelganger("basic dotplot with dot-density binning, binwidth = .4", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4) + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4) ) expect_doppelganger("histodot binning (equal bin spacing)", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, method = "histodot") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, method = "histodot") ) expect_doppelganger("dots stacked closer: stackratio=.5, fill=white", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackratio = .5, fill = "white") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackratio = 0.5, fill = "white") ) expect_doppelganger("larger dots: dotsize=1.5, fill=white", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, dotsize = 1.4, fill = "white") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, dotsize = 1.4, fill = "white") ) # Stacking methods expect_doppelganger("stack up", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "up") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "up") ) expect_doppelganger("stack down", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "down") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "down") ) expect_doppelganger("stack center", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "center") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "center") ) expect_doppelganger("stack centerwhole", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "centerwhole") + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "centerwhole") ) # Stacking methods with coord_flip expect_doppelganger("stack up with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "up") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "up") + coord_flip() ) expect_doppelganger("stack down with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "down") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "down") + coord_flip() ) expect_doppelganger("stack center with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "center") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "center") + coord_flip() ) expect_doppelganger("stack centerwhole with coord_flip", - ggplot(dat, aes(x)) + geom_dotplot(binwidth = .4, stackdir = "centerwhole") + coord_flip() + ggplot(dat, aes(x)) + geom_dotplot(binwidth = 0.4, stackdir = "centerwhole") + coord_flip() ) # Binning along x, with groups expect_doppelganger("multiple groups, bins not aligned", - ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = .4, alpha = .4) + ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = 0.4, alpha = 0.4) ) expect_doppelganger("multiple groups, bins aligned", - ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = .4, alpha = .4, binpositions = "all") + ggplot(dat, aes(x, fill = g)) + geom_dotplot(binwidth = 0.4, alpha = 0.4, binpositions = "all") ) # Binning along y axis expect_doppelganger("bin along y, stack center", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "center") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "center") ) expect_doppelganger("bin along y, stack centerwhole", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "centerwhole") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "centerwhole") ) expect_doppelganger("bin along y, stack centerwhole, histodot", - ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "centerwhole", method = "histodot") + ggplot(dat, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "centerwhole", method = "histodot") ) # Binning along y, with multiple grouping factors dat2 <- data_frame(x = rep(factor(LETTERS[1:3]), 30), y = rnorm(90), g = rep(factor(LETTERS[1:2]), 45)) expect_doppelganger("bin x, three y groups, stack centerwhole", - ggplot(dat2, aes(y, x)) + geom_dotplot(binwidth = .25, binaxis = "x", stackdir = "centerwhole") + ggplot(dat2, aes(y, x)) + geom_dotplot(binwidth = 0.25, binaxis = "x", stackdir = "centerwhole") ) expect_doppelganger("bin y, three x groups, stack centerwhole", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "centerwhole") + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "centerwhole") ) expect_doppelganger("bin y, three x groups, bins aligned across groups", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "center", binpositions = "all") + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "center", binpositions = "all") ) expect_doppelganger("bin y, three x groups, bins aligned, coord_flip", - ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = .25, binaxis = "y", stackdir = "center", binpositions = "all") + + ggplot(dat2, aes(x, y)) + geom_dotplot(binwidth = 0.25, binaxis = "y", stackdir = "center", binpositions = "all") + coord_flip() ) expect_doppelganger("bin y, dodged", - ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, .4)) + - geom_dotplot(binwidth = .25, position = "dodge", binaxis = "y", stackdir = "center") + ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, 0.4)) + + geom_dotplot(binwidth = 0.25, position = "dodge", binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, dodged, coord_flip", - ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, .4)) + - geom_dotplot(binwidth = .25, position = "dodge", binaxis = "y", stackdir = "center") + + ggplot(dat2, aes("foo", y, fill = x)) + scale_y_continuous(breaks = seq(-4, 4, 0.4)) + + geom_dotplot(binwidth = 0.25, position = "dodge", binaxis = "y", stackdir = "center") + coord_flip() ) expect_doppelganger("bin y, three x groups, fill and dodge", - ggplot(dat2, aes(x, y, fill = g)) + scale_y_continuous(breaks = seq(-4 ,4, .4)) + - geom_dotplot(binwidth = .2, position = "dodge", binaxis = "y", stackdir = "center") + ggplot(dat2, aes(x, y, fill = g)) + scale_y_continuous(breaks = seq(-4 ,4, 0.4)) + + geom_dotplot(binwidth = 0.2, position = "dodge", binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, continous x-axis, grouping by x", - ggplot(dat2, aes(as.numeric(x), y, group = x)) + geom_dotplot(binwidth = .2, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(as.numeric(x), y, group = x)) + geom_dotplot(binwidth = 0.2, binaxis = "y", stackdir = "center") ) expect_doppelganger("bin y, continous x-axis, single x group", - ggplot(dat2, aes(as.numeric(x), y)) + geom_dotplot(binwidth = .2, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(as.numeric(x), y)) + geom_dotplot(binwidth = 0.2, binaxis = "y", stackdir = "center") ) # border width and size @@ -198,31 +198,31 @@ test_that("geom_dotplot draws correctly", { stroke = rep(c(1, 2), length.out = nrow(dat)) ) ) + - geom_dotplot(binwidth = .4, fill = "red", col = "blue") + + geom_dotplot(binwidth = 0.4, fill = "red", col = "blue") + continuous_scale("stroke", palette = function(x) scales::rescale(x, to = c(1, 6))) + guides(linetype = guide_legend(order = 1)) ) # Stacking groups expect_doppelganger("3 stackgroups, dot-density with aligned bins", - ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, binpositions = "all", alpha = 0.5) + ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, binpositions = "all", alpha = 0.5) ) expect_doppelganger("3 stackgroups, histodot", - ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + ggplot(dat2, aes(y, fill = x)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) ) expect_doppelganger("3 stackgroups, bin y, histodot", - ggplot(dat2, aes(1, y, fill = x)) + geom_dotplot(binaxis = "y", binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + ggplot(dat2, aes(1, y, fill = x)) + geom_dotplot(binaxis = "y", binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) ) # This one is currently broken but it would be a really rare case, and it # probably requires a really ugly hack to fix expect_doppelganger("bin y, dodging, 3 stackgroups, histodot", ggplot(dat2, aes(x, y, fill = g)) + - geom_dotplot(binaxis = "y", binwidth = .25, stackgroups = TRUE, method = "histodot", + geom_dotplot(binaxis = "y", binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5, stackdir = "centerwhole") ) expect_doppelganger("facets, 3 groups, histodot, stackgroups", - ggplot(dat2, aes(y, fill = g)) + geom_dotplot(binwidth = .25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + + ggplot(dat2, aes(y, fill = g)) + geom_dotplot(binwidth = 0.25, stackgroups = TRUE, method = "histodot", alpha = 0.5) + facet_grid(x ~ .) ) @@ -231,10 +231,10 @@ test_that("geom_dotplot draws correctly", { dat2$x[c(1, 10)] <- NA expect_warning(expect_doppelganger("2 NA values, dot-density binning, binwidth = .4", - ggplot(dat2, aes(x)) + geom_dotplot(binwidth = .4) + ggplot(dat2, aes(x)) + geom_dotplot(binwidth = 0.4) )) expect_warning(expect_doppelganger("2 NA values, bin along y, stack center", - ggplot(dat2, aes(0, x)) + geom_dotplot(binwidth = .4, binaxis = "y", stackdir = "center") + ggplot(dat2, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "center") )) }) diff --git a/tests/testthat/test-geom-path.R b/tests/testthat/test-geom-path.R index 6cf55aece9..3255a2f4cb 100644 --- a/tests/testthat/test-geom-path.R +++ b/tests/testthat/test-geom-path.R @@ -1,8 +1,8 @@ test_that("keep_mid_true drops leading/trailing FALSE", { - expect_equal(keep_mid_true(c(F, F)), c(F, F)) - expect_equal(keep_mid_true(c(F, T, F, T, F)), c(F, T, T, T, F)) - expect_equal(keep_mid_true(c(T, T, F, T, F)), c(T, T, T, T, F)) - expect_equal(keep_mid_true(c(F, T, F, T, T)), c(F, T, T, T, T)) + expect_equal(keep_mid_true(c(FALSE, FALSE)), c(FALSE, FALSE)) + expect_equal(keep_mid_true(c(FALSE, TRUE, FALSE, TRUE, FALSE)), c(FALSE, TRUE, TRUE, TRUE, FALSE)) + expect_equal(keep_mid_true(c(TRUE, TRUE, FALSE, TRUE, FALSE)), c(TRUE, TRUE, TRUE, TRUE, FALSE)) + expect_equal(keep_mid_true(c(FALSE, TRUE, FALSE, TRUE, TRUE)), c(FALSE, TRUE, TRUE, TRUE, TRUE)) }) test_that("geom_path() throws meaningful error on bad combination of varying aesthetics", { diff --git a/tests/testthat/test-geom-rug.R b/tests/testthat/test-geom-rug.R index 28aa17efcb..7539a494a6 100644 --- a/tests/testthat/test-geom-rug.R +++ b/tests/testthat/test-geom-rug.R @@ -1,4 +1,4 @@ -n = 10 +n <- 10 df <- data_frame(x = 1:n, y = (1:n)^3) p <- ggplot(df, aes(x, y)) + geom_point() + geom_rug(sides = 'l') @@ -7,16 +7,16 @@ test_that("coord_flip flips the rugs", { b <- get_layer_grob(p + coord_flip(), 2) # Rugs along y-axis, all x coordinates are the same - expect_equal(length(a[[1]]$children[[1]]$x0), 1) - expect_equal(length(a[[1]]$children[[1]]$x1), 1) - expect_equal(length(a[[1]]$children[[1]]$y0), n) - expect_equal(length(a[[1]]$children[[1]]$y1), n) + expect_length(a[[1]]$children[[1]]$x0, 1) + expect_length(a[[1]]$children[[1]]$x1, 1) + expect_length(a[[1]]$children[[1]]$y0, n) + expect_length(a[[1]]$children[[1]]$y1, n) # Rugs along x-axis, all y coordinates are the same - expect_equal(length(b[[1]]$children[[1]]$x0), n) - expect_equal(length(b[[1]]$children[[1]]$x1), n) - expect_equal(length(b[[1]]$children[[1]]$y0), 1) - expect_equal(length(b[[1]]$children[[1]]$y1), 1) + expect_length(b[[1]]$children[[1]]$x0, n) + expect_length(b[[1]]$children[[1]]$x1, n) + expect_length(b[[1]]$children[[1]]$y0, 1) + expect_length(b[[1]]$children[[1]]$y1, 1) }) test_that("Rug length needs unit object", { diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index fac4c8b87a..e52a13e917 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -30,23 +30,23 @@ test_that("geom_sf() determines the legend type automatically", { } # test the automatic choice - expect_identical(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mp, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mls, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "line") - expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mpol, TRUE)$plot$layers[[1]]$computed_geom_params$legend, "other") # test that automatic choice can be overridden manually - expect_identical(fun_geom_sf(mp, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mp, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mp, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mls, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mls, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mls, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") - expect_identical(fun_geom_sf(mpol, "point")$plot$layers[[1]]$show.legend, TRUE) + expect_true(fun_geom_sf(mpol, "point")$plot$layers[[1]]$show.legend) expect_identical(fun_geom_sf(mpol, "point")$plot$layers[[1]]$computed_geom_params$legend, "point") }) diff --git a/tests/testthat/test-geom-violin.R b/tests/testthat/test-geom-violin.R index eabbc5c95c..7d73c04e94 100644 --- a/tests/testthat/test-geom-violin.R +++ b/tests/testthat/test-geom-violin.R @@ -43,7 +43,7 @@ test_that("quantiles do not fail on zero-range data", { p <- ggplot(zero.range.data) + geom_violin(aes(1, y), draw_quantiles = 0.5) # This should return without error and have length one - expect_equal(length(get_layer_grob(p)), 1) + expect_length(get_layer_grob(p), 1) }) test_that("quantiles fails outside 0-1 bound", { @@ -81,7 +81,7 @@ test_that("quantiles do not issue warning", { test_that("geom_violin draws correctly", { set.seed(111) dat <- data_frame(x = rep(factor(LETTERS[1:3]), 30), y = rnorm(90)) - dat <- dat[dat$x != "C" | c(T, F),] # Keep half the C's + dat <- dat[dat$x != "C" | c(TRUE, FALSE),] # Keep half the C's expect_doppelganger("basic", ggplot(dat, aes(x = x, y = y)) + geom_violin() @@ -90,13 +90,13 @@ test_that("geom_violin draws correctly", { ggplot(dat, aes(x = x, y = y)) + geom_violin(scale = "count"), ) expect_doppelganger("narrower (width=.5)", - ggplot(dat, aes(x = x, y = y)) + geom_violin(width = .5) + ggplot(dat, aes(x = x, y = y)) + geom_violin(width = 0.5) ) expect_doppelganger("with tails and points", ggplot(dat, aes(x = x, y = y)) + geom_violin(trim = FALSE) + geom_point(shape = 21) ) expect_doppelganger("with smaller bandwidth and points", - ggplot(dat, aes(x = x, y = y)) + geom_violin(adjust = .3) + geom_point(shape = 21) + ggplot(dat, aes(x = x, y = y)) + geom_violin(adjust = 0.3) + geom_point(shape = 21) ) expect_doppelganger("dodging", ggplot(dat, aes(x = "foo", y = y, fill = x)) + geom_violin() @@ -126,6 +126,6 @@ test_that("geom_violin draws correctly", { ) expect_doppelganger("grouping on x and fill, dodge width = 0.5", ggplot(dat2, aes(x = x, y = y, fill = g)) + - geom_violin(position = position_dodge(width = .5)) + geom_violin(position = position_dodge(width = 0.5)) ) }) diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index a2e5ae918d..f0057a7452 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -44,7 +44,7 @@ test_that("colourbar trains without labels", { sc <- scale_colour_continuous(limits = c(0, 4), labels = NULL) out <- g$train(scale = sc) - expect_equal(names(out$key), c("colour", ".value")) + expect_named(out$key, c("colour", ".value")) }) test_that("Colorbar respects show.legend in layer", { @@ -213,7 +213,7 @@ test_that("guide merging for guide_legend() works as expected", { }) test_that("size = NA doesn't throw rendering errors", { - df = data.frame( + df <- data.frame( x = c(1, 2), group = c("a","b") ) @@ -903,7 +903,7 @@ test_that("guides are positioned correctly", { p2 <- p2 + theme(legend.position = "inside") # Placement of legend inside expect_doppelganger("legend inside plot, centered", - p2 + theme(legend.position.inside = c(.5, .5)) + p2 + theme(legend.position.inside = c(0.5, 0.5)) ) expect_doppelganger("legend inside plot, bottom left", p2 + theme(legend.justification = c(0,0), legend.position.inside = c(0,0)) @@ -912,7 +912,7 @@ test_that("guides are positioned correctly", { p2 + theme(legend.justification = c(1,1), legend.position.inside = c(1,1)) ) expect_doppelganger("legend inside plot, bottom left of legend at center", - p2 + theme(legend.justification = c(0,0), legend.position.inside = c(.5,.5)) + p2 + theme(legend.justification = c(0,0), legend.position.inside = c(0.5,0.5)) ) }) diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 0a89af1da8..ea7f9c8c60 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -80,7 +80,7 @@ test_that("if an aes is mapped to a function that returns NULL, it is removed", df <- data_frame(x = 1:10) null <- function(...) NULL p <- cdata(ggplot(df, aes(x, null()))) - expect_identical(names(p[[1]]), c("x", "PANEL", "group")) + expect_named(p[[1]], c("x", "PANEL", "group")) }) test_that("layers are stateless except for the computed params", { diff --git a/tests/testthat/test-scale-type.R b/tests/testthat/test-scale-type.R index 4be2fe9ebf..3ca1f06637 100644 --- a/tests/testthat/test-scale-type.R +++ b/tests/testthat/test-scale-type.R @@ -1,9 +1,9 @@ test_that("no scale for NULL aesthetic", { - expect_equal(find_scale("colour", NULL), NULL) + expect_null(find_scale("colour", NULL)) }) test_that("no scale for Inf aesthetic", { - expect_equal(find_scale("colour", Inf), NULL) + expect_null(find_scale("colour", Inf)) }) test_that("message + continuous for unknown type", { diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index d24e0ab638..c3a314cacc 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -47,9 +47,9 @@ test_that("out-of-range breaks are dropped", { # Limits are specified, and all breaks are out of range sc <- scale_x_continuous(breaks = c(1,5), labels = letters[c(1,5)], limits = c(2, 4)) bi <- sc$break_info() - expect_equal(length(bi$labels), 0) - expect_equal(length(bi$major), 0) - expect_equal(length(bi$major_source), 0) + expect_length(bi$labels, 0) + expect_length(bi$major, 0) + expect_length(bi$major_source, 0) # limits aren't specified, automatic labels # limits are set by the data @@ -72,36 +72,36 @@ test_that("out-of-range breaks are dropped", { sc <- scale_x_continuous(breaks = c(1,5), labels = letters[c(1,5)]) sc$train_df(data_frame(x = 2:4)) bi <- sc$break_info() - expect_equal(length(bi$labels), 0) - expect_equal(length(bi$major), 0) - expect_equal(length(bi$major_source), 0) + expect_length(bi$labels, 0) + expect_length(bi$major, 0) + expect_length(bi$major_source, 0) }) test_that("no minor breaks when only one break", { sc1 <- scale_x_discrete(limits = "a") sc2 <- scale_x_continuous(limits = 1) - expect_equal(length(sc1$get_breaks_minor()), 0) - expect_equal(length(sc2$get_breaks_minor()), 0) + expect_length(sc1$get_breaks_minor(), 0) + expect_length(sc2$get_breaks_minor(), 0) }) init_scale <- function(...) { sc <- scale_x_discrete(...) sc$train(factor(1:100)) - expect_equal(length(sc$get_limits()), 100) + expect_length(sc$get_limits(), 100) sc } test_that("discrete labels match breaks", { sc <- init_scale(breaks = 0:5 * 10) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) expect_equal(sc$get_labels(), sc$get_breaks(), ignore_attr = TRUE) sc <- init_scale(breaks = 0:5 * 10, labels = letters[1:6]) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) expect_equal(sc$get_labels(), letters[2:6]) sc <- init_scale(breaks = 0:5 * 10, labels = @@ -110,8 +110,8 @@ test_that("discrete labels match breaks", { pick_5 <- function(x) sample(x, 5) sc <- init_scale(breaks = pick_5) - expect_equal(length(sc$get_breaks()), 5) - expect_equal(length(sc$get_labels()), 5) + expect_length(sc$get_breaks(), 5) + expect_length(sc$get_labels(), 5) }) test_that("scale breaks work with numeric log transformation", { @@ -141,30 +141,30 @@ test_that("passing continuous limits to a discrete scale generates a warning", { }) test_that("suppressing breaks, minor_breask, and labels works", { - expect_equal(scale_x_continuous(breaks = NULL, limits = c(1, 3))$get_breaks(), NULL) - expect_equal(scale_x_discrete(breaks = NULL, limits = c("one", "three"))$get_breaks(), NULL) - expect_equal(scale_x_continuous(minor_breaks = NULL, limits = c(1, 3))$get_breaks_minor(), NULL) + expect_null(scale_x_continuous(breaks = NULL, limits = c(1, 3))$get_breaks()) + expect_null(scale_x_discrete(breaks = NULL, limits = c("one", "three"))$get_breaks()) + expect_null(scale_x_continuous(minor_breaks = NULL, limits = c(1, 3))$get_breaks_minor()) - expect_equal(scale_x_continuous(labels = NULL, limits = c(1, 3))$get_labels(), NULL) - expect_equal(scale_x_discrete(labels = NULL, limits = c("one", "three"))$get_labels(), NULL) + expect_null(scale_x_continuous(labels = NULL, limits = c(1, 3))$get_labels()) + expect_null(scale_x_discrete(labels = NULL, limits = c("one", "three"))$get_labels()) # date, datetime lims <- as.Date(c("2000/1/1", "2000/2/1")) - expect_equal(scale_x_date(breaks = NULL, limits = lims)$get_breaks(), NULL) + expect_null(scale_x_date(breaks = NULL, limits = lims)$get_breaks()) # NA is defunct, should throw error expect_error(scale_x_date(breaks = NA, limits = lims)$get_breaks()) - expect_equal(scale_x_date(labels = NULL, limits = lims)$get_labels(), NULL) + expect_null(scale_x_date(labels = NULL, limits = lims)$get_labels()) expect_error(scale_x_date(labels = NA, limits = lims)$get_labels()) - expect_equal(scale_x_date(minor_breaks = NULL, limits = lims)$get_breaks_minor(), NULL) + expect_null(scale_x_date(minor_breaks = NULL, limits = lims)$get_breaks_minor()) expect_error(scale_x_date(minor_breaks = NA, limits = lims)$get_breaks_minor()) # date, datetime lims <- as.POSIXct(c("2000/1/1 0:0:0", "2010/1/1 0:0:0")) - expect_equal(scale_x_datetime(breaks = NULL, limits = lims)$get_breaks(), NULL) + expect_null(scale_x_datetime(breaks = NULL, limits = lims)$get_breaks()) expect_error(scale_x_datetime(breaks = NA, limits = lims)$get_breaks()) - expect_equal(scale_x_datetime(labels = NULL, limits = lims)$get_labels(), NULL) + expect_null(scale_x_datetime(labels = NULL, limits = lims)$get_labels()) expect_error(scale_x_datetime(labels = NA, limits = lims)$get_labels()) - expect_equal(scale_x_datetime(minor_breaks = NULL, limits = lims)$get_breaks_minor(), NULL) + expect_null(scale_x_datetime(minor_breaks = NULL, limits = lims)$get_breaks_minor()) expect_error(scale_x_datetime(minor_breaks = NA, limits = lims)$get_breaks_minor()) }) diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 4e104f9024..0ba2989e39 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -2,10 +2,10 @@ test_that("building a plot does not affect its scales", { dat <- data_frame(x = rnorm(20), y = rnorm(20)) p <- ggplot(dat, aes(x, y)) + geom_point() - expect_equal(length(p$scales$scales), 0) + expect_length(p$scales$scales, 0) ggplot_build(p) - expect_equal(length(p$scales$scales), 0) + expect_length(p$scales$scales, 0) }) test_that("ranges update only for variables listed in aesthetics", { diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index 2b8fde0d94..56a788b469 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -242,7 +242,7 @@ test_that("sec_axis() respects custom transformations", { expect_doppelganger( "sec_axis, custom transform", ggplot(dat, aes(x = x, y = y)) + - geom_line(linewidth = 1, na.rm = T) + + geom_line(linewidth = 1, na.rm = TRUE) + scale_y_continuous( transform = magnify_trans_log(interval_low = 0.5, interval_high = 1, reducer = 0.5, reducer2 = 8), breaks = @@ -364,21 +364,21 @@ test_that("sec_axis() works for power transformations (monotonicity test doesn't scale_y_continuous(sec.axis = sec_axis(transform = ~ .^0.5)) scale <- get_panel_scales(p)$y breaks <- scale$break_info() - expect_equal(breaks$major, sqrt(breaks$sec.major), tolerance = .005) + expect_equal(breaks$major, sqrt(breaks$sec.major), tolerance = 0.005) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = dup_axis()) scale <- get_panel_scales(p)$x breaks <- scale$break_info() - expect_equal(breaks$major, breaks$sec.major, tolerance = .001) + expect_equal(breaks$major, breaks$sec.major, tolerance = 0.001) p <- ggplot(foo, aes(x, y)) + geom_point() + scale_x_sqrt(sec.axis = sec_axis(~ . * 100)) scale <- get_panel_scales(p)$x breaks <- scale$break_info() - expect_equal(breaks$major, breaks$sec.major, tolerance = .001) + expect_equal(breaks$major, breaks$sec.major, tolerance = 0.001) }) test_that("discrete scales can have secondary axes", { diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 5f2ec3adb8..0894fc2944 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -123,7 +123,7 @@ test_that("compute_density returns useful df and throws warning when <2 values", expect_warning(dens <- compute_density(1, NULL, from = 0, to = 0)) expect_equal(nrow(dens), 1) - expect_equal(names(dens), c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) + expect_named(dens, c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) expect_type(dens$x, "double") }) diff --git a/tests/testthat/test-stat-function.R b/tests/testthat/test-stat-function.R index 4025dcca96..483578d97f 100644 --- a/tests/testthat/test-stat-function.R +++ b/tests/testthat/test-stat-function.R @@ -18,8 +18,8 @@ test_that("uses scale limits, not data limits", { expect_equal(ret$y[c(1, 101)], ret_log$y[c(1, 101)]) expect_equal(range(ret$x), c(0.1, 100)) expect_equal(range(ret_log$x), c(-1, 2)) - expect_false(any(is.na(ret$y))) - expect_false(any(is.na(ret_log$y))) + expect_false(anyNA(ret$y)) + expect_false(anyNA(ret_log$y)) }) test_that("works in plots without any data", { diff --git a/tests/testthat/test-stat-ydensity.R b/tests/testthat/test-stat-ydensity.R index d9f39b4708..3b70fc7673 100644 --- a/tests/testthat/test-stat-ydensity.R +++ b/tests/testthat/test-stat-ydensity.R @@ -17,13 +17,13 @@ test_that("`drop = FALSE` preserves groups with 1 observations", { ld <- get_layer_data(p + geom_violin(drop = TRUE)), "Groups with fewer than two datapoints have been dropped" ) - expect_equal(length(unique(ld$x)), 3) + expect_length(unique(ld$x), 3) expect_warning( ld <- get_layer_data(p + geom_violin(drop = FALSE)), "Cannot compute density for groups with fewer than two datapoints" ) - expect_equal(length(unique(ld$x)), 4) + expect_length(unique(ld$x), 4) }) test_that("mapped_discrete class is preserved", { diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index b1acda601e..0739f78a6d 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -3,12 +3,12 @@ test_that("plot succeeds even if some computation fails", { p1 <- ggplot(df, aes(x, y)) + geom_point() b1 <- ggplot_build(p1) - expect_equal(length(b1$data), 1) + expect_length(b1$data, 1) p2 <- p1 + stat_summary(fun = function(x) stop("Failed computation")) expect_warning(b2 <- ggplot_build(p2), "Computation failed") - expect_equal(length(b2$data), 2) + expect_length(b2$data, 2) }) test_that("error message is thrown when aesthetics are missing", { diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index a9568cfd72..03f2a11d48 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -412,7 +412,7 @@ test_that("current theme can be updated with new elements", { ) # theme calculation for nonexisting element returns NULL - expect_identical(calc_element("abcde", plot_theme(b1)), NULL) + expect_null(calc_element("abcde", plot_theme(b1))) # element tree gets merged properly register_theme_elements( @@ -730,12 +730,12 @@ test_that("axes ticks can have independent lengths", { scale_x_continuous(sec.axis = dup_axis()) + scale_y_continuous(sec.axis = dup_axis()) + theme( - axis.ticks.length.x.top = unit(-.5, "cm"), - axis.ticks.length.x.bottom = unit(-.25, "cm"), - axis.ticks.length.y.left = unit(.25, "cm"), - axis.ticks.length.y.right = unit(.5, "cm"), - axis.text.x.bottom = element_text(margin = margin(t = .25, unit = "cm")), - axis.text.x.top = element_text(margin = margin(b = .25, unit = "cm")) + axis.ticks.length.x.top = unit(-0.5, "cm"), + axis.ticks.length.x.bottom = unit(-0.25, "cm"), + axis.ticks.length.y.left = unit(0.25, "cm"), + axis.ticks.length.y.right = unit(0.5, "cm"), + axis.text.x.bottom = element_text(margin = margin(t = 0.25, unit = "cm")), + axis.text.x.top = element_text(margin = margin(b = 0.25, unit = "cm")) ) expect_doppelganger("ticks_length", plot) }) diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index 4537b03210..08e948ca82 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -2,14 +2,14 @@ test_that("finite_cases.data.frame", { finite_cases <- function(x) cases(x, is_finite) # All finite -------------------------------------------------------------- - expect_identical(finite_cases(data_frame(x = 4)), TRUE) # 1x1 - expect_identical(finite_cases(data_frame(x = 4, y = 11)), TRUE) # 1x2 + expect_true(finite_cases(data_frame(x = 4))) # 1x1 + expect_true(finite_cases(data_frame(x = 4, y = 11))) # 1x2 expect_identical(finite_cases(data_frame(x = 4:5)), c(TRUE, TRUE)) # 2x1 expect_identical(finite_cases(data_frame(x = 4:5, y = 11:12)), c(TRUE, TRUE)) # 2x2 # Has one NA -------------------------------------------------------------- - expect_identical(finite_cases(data_frame(x = NA)), FALSE) # 1x1 - expect_identical(finite_cases(data_frame(x = 4, y = NA)), FALSE) # 1x2 + expect_false(finite_cases(data_frame(x = NA))) # 1x1 + expect_false(finite_cases(data_frame(x = 4, y = NA))) # 1x2 expect_identical(finite_cases(data_frame(x = c(4, NA))), c(TRUE, FALSE)) # 2x1 expect_identical(finite_cases(data_frame(x = c(4, NA), y = c(11, NA))), c(TRUE, FALSE)) # 2x2 expect_identical(finite_cases(data_frame(x = c(4, NA), y = c(NA, 12))), c(FALSE, FALSE)) # 2x2 @@ -17,7 +17,7 @@ test_that("finite_cases.data.frame", { # Testing NaN and Inf, using miscellaneous data shapes -------------------- expect_identical(finite_cases(data_frame(x = c(4, NaN))), c(TRUE, FALSE)) - expect_identical(finite_cases(data_frame(x = Inf)), FALSE) + expect_false(finite_cases(data_frame(x = Inf))) expect_identical(finite_cases(data_frame(x = c(4, 5), y = c(-Inf, 12))), c(FALSE, TRUE)) }) @@ -87,7 +87,7 @@ test_that("parse_safe works with multi expressions", { }) test_that("x and y aesthetics have the same length", { - expect_equal(length(ggplot_global$x_aes), length(ggplot_global$y_aes)) + expect_length(ggplot_global$x_aes, length(ggplot_global$y_aes)) }) test_that("check_required_aesthetics() errors on missing", { @@ -189,8 +189,8 @@ test_that("expose/ignore_data() can round-trip a data.frame", { # data.frame with ignored columns df <- data_frame0(a = 1:3, b = I(4:6), c = LETTERS[1:3], d = I(LETTERS[4:6])) test <- .ignore_data(df)[[1]] - expect_equal(names(test), c("a", "c", ".ignored")) - expect_equal(names(test$.ignored), c("b", "d")) + expect_named(test, c("a", "c", ".ignored")) + expect_named(test$.ignored, c("b", "d")) test <- .expose_data(test)[[1]] expect_equal(test, df[, c("a", "c", "b", "d")]) From 2071c97098104379e10504fafc04117713bda96c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 20 Aug 2024 15:00:16 +0200 Subject: [PATCH 097/264] Axis alignment over multiple panels (#5826) * Don't fix viewport size * add null padding * Fix viewport size, but flexibly * add test * add news bullet --- NEWS.md | 1 + R/guide-axis.R | 18 ++- .../facet-labels/outside-justified-labels.svg | 144 ++++++++++++++++++ tests/testthat/test-facet-labels.R | 27 ++++ 4 files changed, 189 insertions(+), 1 deletion(-) create mode 100644 tests/testthat/_snaps/facet-labels/outside-justified-labels.svg diff --git a/NEWS.md b/NEWS.md index f9bdc996e0..807e9a00fd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Axis labels are now justified across facet panels (@teunbrand, #5820) * Fixed bug in `stat_function()` so x-axis title now produced automatically when no data added. (@phispu, #5647). * geom_sf now accepts shape names (@sierrajohnson, #5808) diff --git a/R/guide-axis.R b/R/guide-axis.R index a0f1fb5ce3..8280219f3d 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -424,6 +424,7 @@ GuideAxis <- ggproto( # Unlist the 'label' grobs z <- if (params$position == "left") c(2, 1, 3) else 1:3 z <- rep(z, c(1, length(grobs$labels), 1)) + has_labels <- !is.zero(grobs$labels[[1]]) grobs <- c(list(grobs$ticks), grobs$labels, list(grobs$title)) # Initialise empty gtable @@ -445,10 +446,25 @@ GuideAxis <- ggproto( vp <- exec( viewport, !!params$orth_aes := unit(params$orth_side, "npc"), - !!params$orth_size := params$measure_gtable(gt), + !!params$orth_size := max(params$measure_gtable(gt), unit(1, "npc")), just = params$opposite ) + # Add null-unit padding to justify based on eventual gtable cell shape + # rather than dimensions of this axis alone. + if (has_labels && params$position %in% c("left", "right")) { + where <- layout$l[-c(1, length(layout$l))] + just <- with(elements$text, rotate_just(angle, hjust, vjust))$hjust %||% 0.5 + gt <- gtable_add_cols(gt, unit(just, "null"), pos = min(where) - 1) + gt <- gtable_add_cols(gt, unit(1 - just, "null"), pos = max(where) + 1) + } + if (has_labels && params$position %in% c("top", "bottom")) { + where <- layout$t[-c(1, length(layout$t))] + just <- with(elements$text, rotate_just(angle, hjust, vjust))$vjust %||% 0.5 + gt <- gtable_add_rows(gt, unit(1 - just, "null"), pos = min(where) - 1) + gt <- gtable_add_rows(gt, unit(just, "null"), pos = max(where) + 1) + } + # Assemble with axis line absoluteGrob( gList(axis_line, gt), diff --git a/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg b/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg new file mode 100644 index 0000000000..9b04f0b614 --- /dev/null +++ b/tests/testthat/_snaps/facet-labels/outside-justified-labels.svg @@ -0,0 +1,144 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +C + + + + + + + + + + +D + + + + + + + + + + +A + + + + + + + + + + +B + + + +X +X +X +X +X + +X + +X +X +X +X +X + +X +YYYYY + +Y + + +YYYYY + +Y +x +y +outside-justified labels + + diff --git a/tests/testthat/test-facet-labels.R b/tests/testthat/test-facet-labels.R index 6d086e0b7b..c8613bc978 100644 --- a/tests/testthat/test-facet-labels.R +++ b/tests/testthat/test-facet-labels.R @@ -157,3 +157,30 @@ test_that("parsed labels are rendered correctly", { facet_wrap(~ f, labeller = label_parsed) ) }) + +test_that("outside-justified labels are justified across panels", { + + df <- data.frame( + x = c("X\nX\nX\nX\nX", "X"), + y = c("YYYYY", "Y"), + f1 = c("A", "B"), + f2 = c("C", "D") + ) + + # By default, axis labels are inside-justified so it doesn't matter whether + # justification occurs across panels. This changes for outside-justification. + # See #5820 + + p <- ggplot(df, aes(x, y)) + + geom_point() + + facet_grid(f1 ~ f2, scales = "free") + + guides(x.sec = "axis", y.sec = "axis") + + theme( + axis.text.y.left = element_text(hjust = 0), + axis.text.y.right = element_text(hjust = 1), + axis.text.x.top = element_text(vjust = 1), + axis.text.x.bottom = element_text(vjust = 0) + ) + + expect_doppelganger("outside-justified labels", p) +}) From 995b40cca6d9906acd09748b9bd3da9b0d0cba1f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 20 Aug 2024 15:31:33 +0200 Subject: [PATCH 098/264] Move coord clipping responsibility from facet to coord (#5953) * move panel assembly to coord * move panel clipping responsibility from facets to coords * coord_radial uses clipping path * only apply clipping mask when possibly supported * add news bullet * turn on strip clipping by default * remove superfluous `clip` argument * add another bullet * reminder for the future --- NEWS.md | 7 ++ R/coord-.R | 14 ++++ R/coord-radial.R | 21 +++++ R/facet-.R | 7 +- R/facet-grid-.R | 8 +- R/facet-null.R | 3 +- R/facet-wrap.R | 2 +- R/layout.R | 15 +--- R/theme-defaults.R | 6 +- ...et-wrap-with-omitted-inner-axis-labels.svg | 77 +++++++++++++------ ...sitioned-correctly-in-non-table-layout.svg | 36 --------- tests/testthat/test-coord-polar.R | 3 + 12 files changed, 111 insertions(+), 88 deletions(-) diff --git a/NEWS.md b/NEWS.md index 807e9a00fd..3408f12b44 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,12 @@ # ggplot2 (development version) +* `coord_radial(clip = "on")` clips to the panel area when the graphics device + supports clipping paths (@teunbrand, #5952). +* (internal) Panel clipping responsibility moved from Facet class to Coord + class through new `Coord$draw_panel()` method. +* `theme(strip.clip)` now defaults to `"on"` and is independent of Coord + clipping (@teunbrand, 5952). +* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). * Axis labels are now justified across facet panels (@teunbrand, #5820) * Fixed bug in `stat_function()` so x-axis title now produced automatically when no data added. (@phispu, #5647). diff --git a/R/coord-.R b/R/coord-.R index 6736059fbc..57cf351f92 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -208,6 +208,20 @@ Coord <- ggproto("Coord", # used as a fudge for CoordFlip and CoordPolar modify_scales = function(scales_x, scales_y) { invisible() + }, + + draw_panel = function(self, panel, params, theme) { + fg <- self$render_fg(params, theme) + bg <- self$render_bg(params, theme) + if (isTRUE(theme$panel.ontop)) { + panel <- list2(!!!panel, bg, fg) + } else { + panel <- list2(bg, !!!panel, fg) + } + gTree( + children = inject(gList(!!!panel)), + vp = viewport(clip = self$clip) + ) } ) diff --git a/R/coord-radial.R b/R/coord-radial.R index c47d55bb56..2f44e1ae4b 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -409,6 +409,27 @@ CoordRadial <- ggproto("CoordRadial", Coord, ) }, + + draw_panel = function(self, panel, params, theme) { + clip_support <- check_device("clippingPaths", "test", maybe = TRUE) + if (self$clip == "on" && !isFALSE(clip_support)) { + clip_path <- data_frame0( + x = c(Inf, Inf, -Inf, -Inf), + y = c(Inf, -Inf, -Inf, Inf) + ) + clip_path <- coord_munch(self, clip_path, params, is_closed = TRUE) + clip_path <- polygonGrob(clip_path$x, clip_path$y) + # Note that clipping path is applied to panel without coord + # foreground/background (added in parent method). + # These may contain decorations that needn't be clipped + panel <- list(gTree( + children = inject(gList(!!!panel)), + vp = viewport(clip = clip_path) + )) + } + ggproto_parent(Coord, self)$draw_panel(panel, params, theme) + }, + labels = function(self, labels, panel_params) { # `Layout$resolve_label()` doesn't know to look for theta/r/r.sec guides, # so we'll handle title propagation here. diff --git a/R/facet-.R b/R/facet-.R index 359c19a248..780c8bd184 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -153,8 +153,7 @@ Facet <- ggproto("Facet", NULL, table <- self$init_gtable( panels, layout, theme, ranges, params, - aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]), - clip = coord$clip + aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]) ) table <- self$attach_axes(table, layout, ranges, coord, theme, params) @@ -198,7 +197,7 @@ Facet <- ggproto("Facet", NULL, data }, init_gtable = function(panels, layout, theme, ranges, params, - aspect_ratio = NULL, clip = "on") { + aspect_ratio = NULL) { # Initialise matrix of panels dim <- c(max(layout$ROW), max(layout$COL)) @@ -228,7 +227,7 @@ Facet <- ggproto("Facet", NULL, "layout", table, widths = widths, heights = heights, respect = !is.null(aspect_ratio), - clip = clip, z = matrix(1, dim[1], dim[2]) + clip = "off", z = matrix(1, dim[1], dim[2]) ) # Set panel names diff --git a/R/facet-grid-.R b/R/facet-grid-.R index c51df5c138..a0b6e31931 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -404,13 +404,13 @@ FacetGrid <- ggproto("FacetGrid", Facet, space <- if (!inside_x & table_has_grob(table, "axis-b")) padding table <- seam_table( table, strips$x$bottom, side = "bottom", name = "strip-b", - shift = shift_x, z = 2, clip = "on", spacing = space + shift = shift_x, z = 2, clip = "off", spacing = space ) } else { space <- if (!inside_x & table_has_grob(table, "axis-t")) padding table <- seam_table( table, strips$x$top, side = "top", name = "strip-t", - shift = shift_x, z = 2, clip = "on", spacing = space + shift = shift_x, z = 2, clip = "off", spacing = space ) } @@ -422,13 +422,13 @@ FacetGrid <- ggproto("FacetGrid", Facet, space <- if (!inside_y & table_has_grob(table, "axis-l")) padding table <- seam_table( table, strips$y$left, side = "left", name = "strip-l", - shift = shift_y, z = 2, clip = "on", spacing = space + shift = shift_y, z = 2, clip = "off", spacing = space ) } else { space <- if (!inside_y & table_has_grob(table, "axis-r")) padding table <- seam_table( table, strips$y$right, side = "right", name = "strip-r", - shift = shift_y, z = 2, clip = "on", spacing = space + shift = shift_y, z = 2, clip = "off", spacing = space ) } table diff --git a/R/facet-null.R b/R/facet-null.R index bc95141fde..c66f39fa03 100644 --- a/R/facet-null.R +++ b/R/facet-null.R @@ -63,11 +63,10 @@ FacetNull <- ggproto("FacetNull", Facet, grob_widths <- unit.c(grobWidth(axis_v$left), unit(1, "null"), grobWidth(axis_v$right)) grob_heights <- unit.c(grobHeight(axis_h$top), unit(abs(aspect_ratio), "null"), grobHeight(axis_h$bottom)) grob_names <- c("spacer", "axis-l", "spacer", "axis-t", "panel", "axis-b", "spacer", "axis-r", "spacer") - grob_clip <- c("off", "off", "off", "off", coord$clip, "off", "off", "off", "off") layout <- gtable_matrix("layout", all, widths = grob_widths, heights = grob_heights, - respect = respect, clip = grob_clip, + respect = respect, clip = "off", z = z_matrix ) layout$layout$name <- grob_names diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 93ae19da91..854aacdd80 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -405,7 +405,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, shift <- if (inside) shift[1] else shift[2] size <- unit(size, "cm") - table <- weave(table, mat, shift, size, name = prefix, z = 2, clip = "on") + table <- weave(table, mat, shift, size, name = prefix, z = 2, clip = "off") if (!inside) { axes <- grepl(paste0("axis-", pos), table$layout$name) diff --git a/R/layout.R b/R/layout.R index f6e04f9b9c..1b578111b2 100644 --- a/R/layout.R +++ b/R/layout.R @@ -80,19 +80,8 @@ Layout <- ggproto("Layout", NULL, panels <- lapply(seq_along(panels[[1]]), function(i) { panel <- lapply(panels, `[[`, i) panel <- c(facet_bg[i], panel, facet_fg[i]) - - coord_fg <- self$coord$render_fg(self$panel_params[[i]], theme) - coord_bg <- self$coord$render_bg(self$panel_params[[i]], theme) - if (isTRUE(theme$panel.ontop)) { - panel <- c(panel, list(coord_bg), list(coord_fg)) - } else { - panel <- c(list(coord_bg), panel, list(coord_fg)) - } - - ggname( - paste("panel", i, sep = "-"), - gTree(children = inject(gList(!!!panel))) - ) + panel <- self$coord$draw_panel(panel, self$panel_params[[i]], theme) + ggname(paste("panel", i, sep = "-"), panel) }) plot_table <- self$facet$draw_panels( panels, diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 951f20a01c..9c94e9dce5 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -212,7 +212,7 @@ theme_grey <- function(base_size = 11, base_family = "", panel.ontop = FALSE, strip.background = element_rect(fill = "grey85", colour = NA), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text( colour = "grey10", size = rel(0.8), @@ -511,7 +511,7 @@ theme_void <- function(base_size = 11, base_family = "", legend.box.margin = rel(0), legend.box.spacing = unit(0.2, "cm"), legend.ticks.length = rel(0.2), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text(size = rel(0.8)), strip.switch.pad.grid = rel(0.5), strip.switch.pad.wrap = rel(0.5), @@ -643,7 +643,7 @@ theme_test <- function(base_size = 11, base_family = "", panel.ontop = FALSE, strip.background = element_rect(fill = "grey85", colour = "grey20"), - strip.clip = "inherit", + strip.clip = "on", strip.text = element_text( colour = "grey10", size = rel(0.8), diff --git a/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg b/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg index 66caee5c07..7c936b4768 100644 --- a/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg +++ b/tests/testthat/_snaps/facet-/facet-wrap-with-omitted-inner-axis-labels.svg @@ -108,83 +108,110 @@ - - + + - + + +6 - - + + - - -6 + 1 - - + + - + 8 - -0 - - + + - + + +0 - - + + - + 4 + + + + + + + + + 0 - - + + - + 4 + + + + + + + + + 1 - - + + - + 6 + + + + + + + + + 0 diff --git a/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg b/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg index c3f247ebe5..7d546bcc7e 100644 --- a/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg +++ b/tests/testthat/_snaps/facet-layout/axes-are-positioned-correctly-in-non-table-layout.svg @@ -93,24 +93,6 @@ - - - - - - - - - - - - - - - - - - @@ -349,15 +331,6 @@ - - - - - - - - - @@ -380,15 +353,6 @@ - - - - - - - - - diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index e9cdcc4813..da49368108 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -158,6 +158,9 @@ test_that("bounding box calculations are sensible", { # Visual tests ------------------------------------------------------------ +#TODO: Once {vdiffr} supports non-rectangular clipping paths, we should add a +# test for `coord_radial(clip = "on")`'s ability to clip to the sector + test_that("polar coordinates draw correctly", { theme <- theme_test() + theme( From c8b802211c1bb39fa038fa5b5c76354daf8f409a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 20 Aug 2024 16:13:17 +0200 Subject: [PATCH 099/264] Improve `pal_qualitative()` (#5954) * precompute checks and lengths * don't use loop to select minimal palette * accept change in error message * add news bullet --- NEWS.md | 1 + R/scale-hue.R | 22 +++++++++++----------- tests/testthat/_snaps/scale-hue.md | 2 +- tests/testthat/test-scale-hue.R | 3 +-- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3408f12b44..4e38488231 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* (internal) improvements to `pal_qualitative()` (@teunbrand, #5013) * `coord_radial(clip = "on")` clips to the panel area when the graphics device supports clipping paths (@teunbrand, #5952). * (internal) Panel clipping responsibility moved from Facet class to Coord diff --git a/R/scale-hue.R b/R/scale-hue.R index db743612ed..414f10864e 100644 --- a/R/scale-hue.R +++ b/R/scale-hue.R @@ -205,22 +205,22 @@ scale_fill_qualitative <- function(name = waiver(), ..., type = NULL, #' @param type a character vector or a list of character vectors #' @noRd pal_qualitative <- function(type, h, c, l, h.start, direction) { + type_list <- type + if (!is.list(type_list)) { + type_list <- list(type_list) + } + if (!all(vapply(type_list, is.character, logical(1)))) { + stop_input_type(type, "a character vector or list of character vectors") + } + type_lengths <- lengths(type_list) function(n) { - type_list <- if (!is.list(type)) list(type) else type - if (!all(vapply(type_list, is.character, logical(1)))) { - cli::cli_abort("{.arg type} must be a character vector or a list of character vectors.") - } - type_lengths <- lengths(type_list) # If there are more levels than color codes default to pal_hue() if (max(type_lengths) < n) { return(scales::pal_hue(h, c, l, h.start, direction)(n)) } # Use the minimum length vector that exceeds the number of levels (n) - type_list <- type_list[order(type_lengths)] - i <- 1 - while (length(type_list[[i]]) < n) { - i <- i + 1 - } - type_list[[i]][seq_len(n)] + i <- which(type_lengths >= n) + i <- i[which.min(type_lengths[i])] + type_list[[i]] } } diff --git a/tests/testthat/_snaps/scale-hue.md b/tests/testthat/_snaps/scale-hue.md index bccf63c43a..8221bba045 100644 --- a/tests/testthat/_snaps/scale-hue.md +++ b/tests/testthat/_snaps/scale-hue.md @@ -1,4 +1,4 @@ # scale_hue() checks the type input - `type` must be a character vector or a list of character vectors. + `type` must be a character vector or list of character vectors, not an integer vector. diff --git a/tests/testthat/test-scale-hue.R b/tests/testthat/test-scale-hue.R index 12568590a8..6f0b0c5234 100644 --- a/tests/testthat/test-scale-hue.R +++ b/tests/testthat/test-scale-hue.R @@ -1,6 +1,5 @@ test_that("scale_hue() checks the type input", { - pal <- pal_qualitative(type = 1:4) - expect_snapshot_error(pal(4)) + expect_snapshot_error(pal_qualitative(type = 1:4)) pal <- pal_qualitative(type = colors()) expect_silent(pal(4)) pal <- pal_qualitative(type = list(colors()[1:10], colors()[11:30])) From e5c389252e82b93b82cc93bce6efcd5e9832d479 Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Fri, 23 Aug 2024 11:39:12 +0200 Subject: [PATCH 100/264] Add changes from #4875 (#6049) --- R/geom-path.R | 3 ++- R/geom-text.R | 5 +++-- man/geom_path.Rd | 3 ++- man/geom_text.Rd | 5 +++-- man/labeller.Rd | 2 +- 5 files changed, 11 insertions(+), 7 deletions(-) diff --git a/R/geom-path.R b/R/geom-path.R index 9b737267ca..b63a1a1877 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -36,8 +36,9 @@ #' @examples #' # geom_line() is suitable for time series #' ggplot(economics, aes(date, unemploy)) + geom_line() +#' # separate by colour and use "timeseries" legend key glyph #' ggplot(economics_long, aes(date, value01, colour = variable)) + -#' geom_line() +#' geom_line(key_glyph = "timeseries") #' #' # You can get a timeseries that run vertically by setting the orientation #' ggplot(economics, aes(unemploy, date)) + geom_line(orientation = "y") diff --git a/R/geom-text.R b/R/geom-text.R index d0f33a12ff..22ae141a1c 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -98,10 +98,11 @@ #' scale_colour_discrete(l = 40) #' p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") #' -#' p + geom_text(aes(size = wt)) +#' # Scale size of text, and change legend key glyph from a to point +#' p + geom_text(aes(size = wt), key_glyph = "point") #' # Scale height of text, rather than sqrt(height) #' p + -#' geom_text(aes(size = wt)) + +#' geom_text(aes(size = wt), key_glyph = "point") + #' scale_radius(range = c(3,6)) #' #' # You can display expressions by setting parse = TRUE. The diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 8c530e4d33..833ee757c6 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -205,8 +205,9 @@ the \code{NA} is removed silently, without warning. \examples{ # geom_line() is suitable for time series ggplot(economics, aes(date, unemploy)) + geom_line() +# separate by colour and use "timeseries" legend key glyph ggplot(economics_long, aes(date, value01, colour = variable)) + - geom_line() + geom_line(key_glyph = "timeseries") # You can get a timeseries that run vertically by setting the orientation ggplot(economics, aes(unemploy, date)) + geom_line(orientation = "y") diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 5f5dabe2d0..f50563730c 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -249,10 +249,11 @@ p + geom_text(aes(colour = factor(cyl))) + scale_colour_discrete(l = 40) p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") -p + geom_text(aes(size = wt)) +# Scale size of text, and change legend key glyph from a to point +p + geom_text(aes(size = wt), key_glyph = "point") # Scale height of text, rather than sqrt(height) p + - geom_text(aes(size = wt)) + + geom_text(aes(size = wt), key_glyph = "point") + scale_radius(range = c(3,6)) # You can display expressions by setting parse = TRUE. The diff --git a/man/labeller.Rd b/man/labeller.Rd index 52481179f9..2c863d2aee 100644 --- a/man/labeller.Rd +++ b/man/labeller.Rd @@ -42,7 +42,7 @@ for the argument \code{labeller}. \description{ This function makes it easy to assign different labellers to different factors. The labeller can be a function or it can be a -named character vectors that will serve as a lookup table. +named character vector that will serve as a lookup table. } \details{ In case of functions, if the labeller has class \code{labeller}, it From c9dce8a91a22d895d4318bb180c03021fe89b78b Mon Sep 17 00:00:00 2001 From: "Collin K. Berke, Ph.D." <32435546+collinberke@users.noreply.github.com> Date: Fri, 23 Aug 2024 02:41:50 -0700 Subject: [PATCH 101/264] Fix typos layer and geom_text docs (#6053) --- R/geom-text.R | 2 +- R/layer.R | 2 +- man/borders.Rd | 2 +- man/geom_blank.Rd | 2 +- man/geom_contour.Rd | 2 +- man/geom_errorbarh.Rd | 2 +- man/geom_function.Rd | 2 +- man/geom_jitter.Rd | 2 +- man/geom_linerange.Rd | 2 +- man/geom_map.Rd | 2 +- man/geom_path.Rd | 2 +- man/geom_point.Rd | 2 +- man/geom_polygon.Rd | 2 +- man/geom_ribbon.Rd | 2 +- man/geom_rug.Rd | 2 +- man/geom_segment.Rd | 2 +- man/geom_spoke.Rd | 2 +- man/geom_text.Rd | 4 ++-- man/geom_tile.Rd | 2 +- man/ggsf.Rd | 2 +- man/layer.Rd | 2 +- man/layer_sf.Rd | 2 +- 22 files changed, 23 insertions(+), 23 deletions(-) diff --git a/R/geom-text.R b/R/geom-text.R index 22ae141a1c..a913227e4b 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -49,7 +49,7 @@ #' can be used in various ways, including to prevent overplotting and #' improving the display. The `position` argument accepts the following: #' * The result of calling a position function, such as `position_jitter()`. -#' * A string nameing the position adjustment. To give the position as a +#' * A string naming the position adjustment. To give the position as a #' string, strip the function name of the `position_` prefix. For example, #' to use `position_jitter()`, give the position as `"jitter"`. #' * For more information and other ways to specify the position, see the diff --git a/R/layer.R b/R/layer.R index 7fc53571ef..bcad622d98 100644 --- a/R/layer.R +++ b/R/layer.R @@ -36,7 +36,7 @@ #' [layer geom][layer_geoms] documentation. #' @param stat The statistical transformation to use on the data for this layer. #' When using a `geom_*()` function to construct a layer, the `stat` -#' argument can be used the override the default coupling between geoms and +#' argument can be used to override the default coupling between geoms and #' stats. The `stat` argument accepts the following: #' * A `Stat` ggproto subclass, for example `StatCount`. #' * A string naming the stat. To give the stat as a string, strip the diff --git a/man/borders.Rd b/man/borders.Rd index 2fa16916e9..2f5e9f6841 100644 --- a/man/borders.Rd +++ b/man/borders.Rd @@ -53,7 +53,7 @@ will be used as the layer data. A \code{function} can be created from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{\code{stat}}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_blank.Rd b/man/geom_blank.Rd index 1f02b9cbc6..a8d4a2613d 100644 --- a/man/geom_blank.Rd +++ b/man/geom_blank.Rd @@ -37,7 +37,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_contour.Rd b/man/geom_contour.Rd index 72114072e2..c42aec41c9 100644 --- a/man/geom_contour.Rd +++ b/man/geom_contour.Rd @@ -89,7 +89,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_errorbarh.Rd b/man/geom_errorbarh.Rd index 21a4c79f5c..4e6fb3aae9 100644 --- a/man/geom_errorbarh.Rd +++ b/man/geom_errorbarh.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_function.Rd b/man/geom_function.Rd index 451c779003..faf9d8552e 100644 --- a/man/geom_function.Rd +++ b/man/geom_function.Rd @@ -41,7 +41,7 @@ mapping.} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_jitter.Rd b/man/geom_jitter.Rd index 2fa8acf555..03ad3e8490 100644 --- a/man/geom_jitter.Rd +++ b/man/geom_jitter.Rd @@ -40,7 +40,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index 0d70775f6d..87bc5c8e75 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -81,7 +81,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_map.Rd b/man/geom_map.Rd index 6a634702e9..58e83adad4 100644 --- a/man/geom_map.Rd +++ b/man/geom_map.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_path.Rd b/man/geom_path.Rd index 833ee757c6..88913a5a7b 100644 --- a/man/geom_path.Rd +++ b/man/geom_path.Rd @@ -70,7 +70,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_point.Rd b/man/geom_point.Rd index 762d4a1f80..56264c0a36 100644 --- a/man/geom_point.Rd +++ b/man/geom_point.Rd @@ -38,7 +38,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_polygon.Rd b/man/geom_polygon.Rd index 22670cbb8b..241490284a 100644 --- a/man/geom_polygon.Rd +++ b/man/geom_polygon.Rd @@ -39,7 +39,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_ribbon.Rd b/man/geom_ribbon.Rd index 2c7e805fc7..d4f5a707e1 100644 --- a/man/geom_ribbon.Rd +++ b/man/geom_ribbon.Rd @@ -66,7 +66,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_rug.Rd b/man/geom_rug.Rd index 6e84a4d985..1cc10e785a 100644 --- a/man/geom_rug.Rd +++ b/man/geom_rug.Rd @@ -41,7 +41,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_segment.Rd b/man/geom_segment.Rd index fc3adbbd8c..392ba20669 100644 --- a/man/geom_segment.Rd +++ b/man/geom_segment.Rd @@ -60,7 +60,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_spoke.Rd b/man/geom_spoke.Rd index 7fe6a9d9ee..ea28f601c1 100644 --- a/man/geom_spoke.Rd +++ b/man/geom_spoke.Rd @@ -39,7 +39,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/geom_text.Rd b/man/geom_text.Rd index f50563730c..91c241ab4b 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -62,7 +62,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -79,7 +79,7 @@ can be used in various ways, including to prevent overplotting and improving the display. The \code{position} argument accepts the following: \itemize{ \item The result of calling a position function, such as \code{position_jitter()}. -\item A string nameing the position adjustment. To give the position as a +\item A string naming the position adjustment. To give the position as a string, strip the function name of the \code{position_} prefix. For example, to use \code{position_jitter()}, give the position as \code{"jitter"}. \item For more information and other ways to specify the position, see the diff --git a/man/geom_tile.Rd b/man/geom_tile.Rd index 326f36a2f4..34b9bb30bc 100644 --- a/man/geom_tile.Rd +++ b/man/geom_tile.Rd @@ -67,7 +67,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/ggsf.Rd b/man/ggsf.Rd index 3b8ff90bd7..c4ec76bed1 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -197,7 +197,7 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/layer.Rd b/man/layer.Rd index b4070fbe2a..e34ee05245 100644 --- a/man/layer.Rd +++ b/man/layer.Rd @@ -35,7 +35,7 @@ give the geom as \code{"point"}. \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. diff --git a/man/layer_sf.Rd b/man/layer_sf.Rd index cda8db1d2e..a10dfa8805 100644 --- a/man/layer_sf.Rd +++ b/man/layer_sf.Rd @@ -33,7 +33,7 @@ give the geom as \code{"point"}. \item{stat}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. From 6d2ed6de1cd367f79e432b81d7faa8dce411ca0e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 13:14:14 +0200 Subject: [PATCH 102/264] Extra documentation for `ggplot_add()` (#5968) --- R/plot-construction.R | 25 ++++++++++++++++++++++++- man/ggplot_add.Rd | 25 +++++++++++++++++++++++++ 2 files changed, 49 insertions(+), 1 deletion(-) diff --git a/R/plot-construction.R b/R/plot-construction.R index de1306098f..43a3f5b494 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -84,9 +84,32 @@ add_ggplot <- function(p, object, objectname) { #' @param object_name The name of the object to add #' #' @return A modified ggplot object +#' @details +#' Custom methods for `ggplot_add()` are intended to update the `plot` variable +#' using information from a custom `object`. This can become convenient when +#' writing extensions that don't build on the pre-existing grammar like +#' layers, facets, coords and themes. The `ggplot_add()` function is never +#' intended to be used directly, but it is triggered when an object is added +#' to a plot via the `+` operator. Please note that the full `plot` object is +#' exposed at this point, which comes with the responsibility of returning +#' the plot intact. #' #' @keywords internal #' @export +#' @examples +#' # making a new method for the generic +#' # in this example, we apply a text element to the text theme setting +#' ggplot_add.element_text <- function(object, plot, object_name) { +#' plot + theme(text = object) +#' } +#' +#' # we can now use `+` to add our object to a plot +#' ggplot(mpg, aes(displ, cty)) + +#' geom_point() + +#' element_text(colour = "red") +#' +#' # clean-up +#' rm(ggplot_add.element_text) ggplot_add <- function(object, plot, object_name) { UseMethod("ggplot_add") } @@ -152,7 +175,7 @@ ggplot_add.Facet <- function(object, plot, object_name) { #' @export ggplot_add.list <- function(object, plot, object_name) { for (o in object) { - plot <- plot %+% o + plot <- ggplot_add(o, plot, object_name) } plot } diff --git a/man/ggplot_add.Rd b/man/ggplot_add.Rd index 0bd2e2a698..c71d6f863e 100644 --- a/man/ggplot_add.Rd +++ b/man/ggplot_add.Rd @@ -20,4 +20,29 @@ A modified ggplot object This generic allows you to add your own methods for adding custom objects to a ggplot with \link{+.gg}. } +\details{ +Custom methods for \code{ggplot_add()} are intended to update the \code{plot} variable +using information from a custom \code{object}. This can become convenient when +writing extensions that don't build on the pre-existing grammar like +layers, facets, coords and themes. The \code{ggplot_add()} function is never +intended to be used directly, but it is triggered when an object is added +to a plot via the \code{+} operator. Please note that the full \code{plot} object is +exposed at this point, which comes with the responsibility of returning +the plot intact. +} +\examples{ +# making a new method for the generic +# in this example, we apply a text element to the text theme setting +ggplot_add.element_text <- function(object, plot, object_name) { + plot + theme(text = object) +} + +# we can now use `+` to add our object to a plot +ggplot(mpg, aes(displ, cty)) + + geom_point() + + element_text(colour = "red") + +# clean-up +rm(ggplot_add.element_text) +} \keyword{internal} From 5482939bec47e4abe3d449667680aa323ed47b2a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 13:19:44 +0200 Subject: [PATCH 103/264] Layers have names (#5967) * use `%||%` for `na.rm` * simplify special `key_glyph` case * add `name` field to LayerInstance objects * helper for layer names * apply layer names * add tests * add bullet * fallback for direct `layer()` calls --- NEWS.md | 1 + R/layer.R | 21 +++++++-------------- R/plot-construction.R | 19 +++++++++++++++++++ tests/testthat/test-layer.R | 16 ++++++++++++++++ 4 files changed, 43 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4e38488231..fac6706ae8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Layers can have names (@teunbrand, #4066). * (internal) improvements to `pal_qualitative()` (@teunbrand, #5013) * `coord_radial(clip = "on")` clips to the panel area when the graphics device supports clipping paths (@teunbrand, #5952). diff --git a/R/layer.R b/R/layer.R index bcad622d98..59a9dba096 100644 --- a/R/layer.R +++ b/R/layer.R @@ -130,16 +130,7 @@ layer <- function(geom = NULL, stat = NULL, position <- check_subclass(position, "Position", env = parent.frame(), call = call_env) # Special case for na.rm parameter needed by all layers - if (is.null(params$na.rm)) { - params$na.rm <- FALSE - } - - # Special case for key_glyph parameter which is handed in through - # params since all geoms/stats forward ... to params - if (!is.null(params$key_glyph)) { - key_glyph <- params$key_glyph - params$key_glyph <- NULL # remove to avoid warning about unknown parameter - } + params$na.rm <- params$na.rm %||% FALSE # Split up params between aesthetics, geom, and stat params <- rename_aes(params) @@ -147,7 +138,8 @@ layer <- function(geom = NULL, stat = NULL, geom_params <- params[intersect(names(params), geom$parameters(TRUE))] stat_params <- params[intersect(names(params), stat$parameters(TRUE))] - all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics()) + ignore <- c("key_glyph", "name") + all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics(), ignore) # Take care of plain patterns provided as aesthetic pattern <- vapply(aes_params, is_pattern, logical(1)) @@ -181,9 +173,9 @@ layer <- function(geom = NULL, stat = NULL, } # adjust the legend draw key if requested - geom <- set_draw_key(geom, key_glyph) + geom <- set_draw_key(geom, key_glyph %||% params$key_glyph) - fr_call <- layer_class$constructor %||% frame_call(call_env) + fr_call <- layer_class$constructor %||% frame_call(call_env) %||% current_call() ggproto("LayerInstance", layer_class, constructor = fr_call, @@ -196,7 +188,8 @@ layer <- function(geom = NULL, stat = NULL, aes_params = aes_params, position = position, inherit.aes = inherit.aes, - show.legend = show.legend + show.legend = show.legend, + name = params$name ) } diff --git a/R/plot-construction.R b/R/plot-construction.R index 43a3f5b494..14f2badaed 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -186,6 +186,25 @@ ggplot_add.by <- function(object, plot, object_name) { #' @export ggplot_add.Layer <- function(object, plot, object_name) { + layers_names <- new_layer_names(object, names(plot$layers)) plot$layers <- append(plot$layers, object) + names(plot$layers) <- layers_names plot } + +new_layer_names <- function(layer, existing) { + new_name <- layer$name + if (is.null(new_name)) { + # Construct a name from the layer's call + new_name <- call_name(layer$constructor) + + if (new_name %in% existing) { + names <- c(existing, new_name) + names <- vec_as_names(names, repair = "unique", quiet = TRUE) + new_name <- names[length(names)] + } + } + + names <- c(existing, new_name) + vec_as_names(names, repair = "check_unique") +} diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index ea7f9c8c60..8be6c8555f 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -138,6 +138,22 @@ test_that("layer warns for constant aesthetics", { expect_snapshot_warning(ggplot_build(p)) }) +test_that("layer names can be resolved", { + + p <- ggplot() + geom_point() + geom_point() + expect_equal(names(p$layers), c("geom_point", "geom_point...2")) + + p <- ggplot() + geom_point(name = "foo") + geom_point(name = "bar") + expect_equal(names(p$layers), c("foo", "bar")) + + l <- geom_point(name = "foobar") + expect_error( + p + l + l, + "names are duplicated" + ) +}) + + # Data extraction --------------------------------------------------------- test_that("AsIs data passes unmodified", { From 332a8ea743d3d1efae819e1b7938afb6b27ffc18 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 13:44:57 +0200 Subject: [PATCH 104/264] `n.breaks` propagate to `sec.axis` (#5973) * capture `n.breaks` parameter upon initialisation * add test * add news bullet --- NEWS.md | 1 + R/axis-secondary.R | 8 +++++++- tests/testthat/test-sec-axis.R | 19 +++++++++++++++++++ 3 files changed, 27 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index fac6706ae8..cd4ed0771d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483). * Layers can have names (@teunbrand, #4066). * (internal) improvements to `pal_qualitative()` (@teunbrand, #5013) * `coord_radial(clip = "on")` clips to the panel area when the graphics device diff --git a/R/axis-secondary.R b/R/axis-secondary.R index e535b1a95a..2999bd79b5 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -188,7 +188,13 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, if (scale$is_discrete()) { self$breaks <- scale$get_breaks() } else { - self$breaks <- scale$get_transformation()$breaks + breaks <- scale$get_transformation()$breaks + n_breaks <- scale$n.breaks + if (!is.null(n_breaks) && "n" %in% fn_fmls_names(breaks)) { + self$breaks <- function(x) breaks(x, n = n_breaks) + } else { + self$breaks <- breaks + } } } if (is.derived(self$labels)) self$labels <- scale$labels diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index 56a788b469..02846e9f81 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -400,3 +400,22 @@ test_that("discrete scales can have secondary axes", { expect_equal(y$.value, c(1.5, 2.5), ignore_attr = TRUE) expect_equal(y$.label, c("grault", "garply")) }) + +test_that("n.breaks is respected by secondary axes (#4483)", { + + b <- ggplot_build( + ggplot(data.frame(x = c(0, 10)), aes(x, x)) + + scale_y_continuous( + n.breaks = 11, + sec.axis = sec_axis(~.x*100) + ) + ) + + # We get scale breaks via guide data + prim <- get_guide_data(b, "y") + sec <- get_guide_data(b, "y.sec") + + expect_equal(prim$.value, sec$.value) # .value is in primary scale + expect_equal(prim$.label, as.character(seq(0, 10, length.out = 11))) + expect_equal(sec$.label, as.character(seq(0, 1000, length.out = 11))) +}) From 78b3f3ab0fa45b81c9c7f1d27888699dfc55c6a1 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:07:14 +0200 Subject: [PATCH 105/264] move `make_summary_fun()` to `setup_params()` (#5971) * move `make_summary_fun()` to `setup_params()` * add news bullet --- NEWS.md | 2 ++ R/stat-summary-bin.R | 16 ++++++++++------ R/stat-summary.R | 16 ++++++++++------ 3 files changed, 22 insertions(+), 12 deletions(-) diff --git a/NEWS.md b/NEWS.md index cd4ed0771d..3755e43011 100644 --- a/NEWS.md +++ b/NEWS.md @@ -148,6 +148,8 @@ (@teunbrand, #5938, #4327). * Fixed bug where empty discrete scales weren't recognised as such (@teunbrand, #5945). +* (internal) The summary function of `stat_summary()` and `stat_summary_bin()` + is setup once in total instead of once per group (@teunbrand, #5971) # ggplot2 3.5.1 diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index e9cd675e09..3a4fea585e 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -64,24 +64,28 @@ stat_summary_bin <- function(mapping = NULL, data = NULL, StatSummaryBin <- ggproto("StatSummaryBin", Stat, required_aes = c("x", "y"), - extra_params = c("na.rm", "orientation"), + extra_params = c("na.rm", "orientation", "fun.data", "fun.max", "fun.min", "fun.args"), + setup_params = function(data, params) { - params$flipped_aes <- has_flipped_aes(data, params, ambiguous = TRUE) + params$flipped_aes <- has_flipped_aes(data, params) + params$fun <- make_summary_fun( + params$fun.data, params$fun, + params$fun.max, params$fun.min, + params$fun.args %||% list() + ) params }, - compute_group = function(data, scales, fun.data = NULL, fun = NULL, - fun.max = NULL, fun.min = NULL, fun.args = list(), + compute_group = function(data, scales, fun = NULL, bins = 30, binwidth = NULL, breaks = NULL, origin = NULL, right = FALSE, na.rm = FALSE, flipped_aes = FALSE) { data <- flip_data(data, flipped_aes) - fun <- make_summary_fun(fun.data, fun, fun.max, fun.min, fun.args) x <- flipped_names(flipped_aes)$x breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, right = right) data$bin <- cut(data$x, breaks, include.lowest = TRUE, labels = FALSE) - out <- dapply(data, "bin", fun) + out <- dapply(data, "bin", fun %||% function(df) mean_se(df$y)) locs <- bin_loc(breaks, out$bin) out$x <- locs$mid diff --git a/R/stat-summary.R b/R/stat-summary.R index cf2e2ef4c7..6476021fc5 100644 --- a/R/stat-summary.R +++ b/R/stat-summary.R @@ -181,18 +181,22 @@ stat_summary <- function(mapping = NULL, data = NULL, StatSummary <- ggproto("StatSummary", Stat, required_aes = c("x", "y"), - extra_params = c("na.rm", "orientation"), + extra_params = c("na.rm", "orientation", "fun.data", "fun.max", "fun.min", "fun.args"), + setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params) + params$fun <- make_summary_fun( + params$fun.data, params$fun, + params$fun.max, params$fun.min, + params$fun.args %||% list() + ) params }, - compute_panel = function(data, scales, fun.data = NULL, fun = NULL, - fun.max = NULL, fun.min = NULL, fun.args = list(), - na.rm = FALSE, flipped_aes = FALSE) { + compute_panel = function(data, scales, fun = NULL, + na.rm = FALSE, flipped_aes = FALSE) { data <- flip_data(data, flipped_aes) - fun <- make_summary_fun(fun.data, fun, fun.max, fun.min, fun.args) - summarised <- summarise_by_x(data, fun) + summarised <- summarise_by_x(data, fun %||% function(df) mean_se(df$y)) summarised$flipped_aes <- flipped_aes flip_data(summarised, flipped_aes) } From c108758cc8cfa0ee3dafa6b72c88e8b3207312cf Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:07:33 +0200 Subject: [PATCH 106/264] Variable panel size (`space`) for `facet_wrap()` (#5956) * add space argument * add test * document * add news bullet * accept new snapshot --- NEWS.md | 2 ++ R/facet-wrap.R | 37 ++++++++++++++++++++++++--- man/facet_wrap.Rd | 8 ++++++ tests/testthat/_snaps/facet-layout.md | 4 +++ tests/testthat/test-facet-layout.R | 21 +++++++++++++++ 5 files changed, 69 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3755e43011..7fbbc1967b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `facet_wrap()` can have `space = "free_x"` with 1-row layouts and + `space = "free_y"` with 1-column layouts (@teunbrand) * Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483). * Layers can have names (@teunbrand, #4066). * (internal) improvements to `pal_qualitative()` (@teunbrand, #5013) diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 854aacdd80..8564f319b7 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -18,6 +18,12 @@ NULL #' @param scales Should scales be fixed (`"fixed"`, the default), #' free (`"free"`), or free in one dimension (`"free_x"`, #' `"free_y"`)? +#' @param space If `"fixed"` (default), all panels have the same size and +#' the number of rows and columns in the layout can be arbitrary. If +#' `"free_x"`, panels have widths proportional to the length of the x-scale, +#' but the layout is constrained to one row. If `"free_y"`, panels have +#' heights proportional to the length of the y-scale, but the layout is +#' constrained to one column. #' @param strip.position By default, the labels are displayed on the top of #' the plot. Using `strip.position` it is possible to place the labels on #' either of the four sides by setting \code{strip.position = c("top", @@ -109,9 +115,9 @@ NULL #' geom_point() + #' facet_wrap(vars(class), dir = "tr") facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", - shrink = TRUE, labeller = "label_value", as.table = TRUE, - switch = deprecated(), drop = TRUE, dir = "h", - strip.position = 'top', axes = "margins", + space = "fixed", shrink = TRUE, labeller = "label_value", + as.table = TRUE, switch = deprecated(), drop = TRUE, + dir = "h", strip.position = 'top', axes = "margins", axis.labels = "all") { scales <- arg_match0(scales %||% "fixed", c("fixed", "free_x", "free_y", "free")) dir <- arg_match0(dir, c("h", "v", "lt", "tl", "lb", "bl", "rt", "tr", "rb", "br")) @@ -128,6 +134,30 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", y = any(scales %in% c("free_y", "free")) ) + # We cannot have free space in both directions + space <- arg_match0(space, c("free_x", "free_y", "fixed")) + space_free <- list(x = space == "free_x", y = space == "free_y") + if (space_free$x) { + if ((nrow %||% 1) != 1 || !is.null(ncol)) { + cli::cli_warn( + "Cannot use {.code space = \"free_x\"} with custom \\ + {.arg nrow} or {.arg ncol}." + ) + } + ncol <- NULL + nrow <- 1L + } + if (space_free$y) { + if ((ncol %||% 1) != 1 || !is.null(nrow)) { + cli::cli_warn( + "Cannot use {.code space= \"free_y\"} with custom \\ + {.arg nrow} or {.arg ncol}." + ) + } + ncol <- 1L + nrow <- NULL + } + # If scales are free, always draw the axes draw_axes <- arg_match0(axes, c("margins", "all_x", "all_y", "all")) draw_axes <- list( @@ -174,6 +204,7 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", drop = drop, ncol = ncol, nrow = nrow, + space_free = space_free, labeller = labeller, dir = dir, draw_axes = draw_axes, diff --git a/man/facet_wrap.Rd b/man/facet_wrap.Rd index d431f0098a..66716f5c5f 100644 --- a/man/facet_wrap.Rd +++ b/man/facet_wrap.Rd @@ -9,6 +9,7 @@ facet_wrap( nrow = NULL, ncol = NULL, scales = "fixed", + space = "fixed", shrink = TRUE, labeller = "label_value", as.table = TRUE, @@ -35,6 +36,13 @@ or a character vector, \code{c("a", "b")}.} free (\code{"free"}), or free in one dimension (\code{"free_x"}, \code{"free_y"})?} +\item{space}{If \code{"fixed"} (default), all panels have the same size and +the number of rows and columns in the layout can be arbitrary. If +\code{"free_x"}, panels have widths proportional to the length of the x-scale, +but the layout is constrained to one row. If \code{"free_y"}, panels have +heights proportional to the length of the y-scale, but the layout is +constrained to one column.} + \item{shrink}{If \code{TRUE}, will shrink scales to fit output of statistics, not raw data. If \code{FALSE}, will be range of raw data before statistical summary.} diff --git a/tests/testthat/_snaps/facet-layout.md b/tests/testthat/_snaps/facet-layout.md index 142bde22fe..1ab4474443 100644 --- a/tests/testthat/_snaps/facet-layout.md +++ b/tests/testthat/_snaps/facet-layout.md @@ -22,6 +22,10 @@ `nrow` must be a whole number or `NULL`, not the number 1.5. +--- + + Cannot use `space = "free_x"` with custom `nrow` or `ncol`. + --- Need 3 panels, but together `nrow` and `ncol` only provide 1. diff --git a/tests/testthat/test-facet-layout.R b/tests/testthat/test-facet-layout.R index 70a4ed30e8..767abe5c8c 100644 --- a/tests/testthat/test-facet-layout.R +++ b/tests/testthat/test-facet-layout.R @@ -172,6 +172,25 @@ test_that("grid: drop = FALSE preserves unused levels", { expect_equal(as.character(grid_ab$b), as.character(rep(4:1, 4))) }) +test_that("wrap: space = 'free_x/y' sets panel sizes", { + + df <- data.frame(x = 1:3) + p <- ggplot(df, aes(x, x)) + + geom_point() + + scale_x_continuous(limits = c(0, NA), expand = c(0, 0)) + + scale_y_continuous(limits = c(0, NA), expand = c(0, 0)) + + # Test free_x + gt <- ggplotGrob(p + facet_wrap(~x, scales = "free_x", space = "free_x")) + test <- gt$widths[panel_cols(gt)$l] + expect_equal(as.numeric(test), 1:3) + + # Test free_y + gt <- ggplotGrob(p + facet_wrap(~x, scales = "free_y", space = "free_y")) + test <- gt$heights[panel_rows(gt)$t] + expect_equal(as.numeric(test), 1:3) +}) + # Missing behaviour ---------------------------------------------------------- a3 <- data_frame( @@ -207,6 +226,8 @@ test_that("facet_wrap throws errors at bad layout specs", { expect_snapshot_error(facet_wrap(~test, nrow = -1)) expect_snapshot_error(facet_wrap(~test, nrow = 1.5)) + expect_snapshot_warning(facet_wrap(~test, nrow = 2, space = "free_x")) + p <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + facet_wrap(~gear, ncol = 1, nrow = 1) From c38606ffeacfecf54ac32c37c8430d7d9f074fec Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:44:06 +0200 Subject: [PATCH 107/264] Function to reset all aesthetics defaults (#5976) * reset functions * document * add test * add news bullet * fix typo --- NAMESPACE | 2 ++ NEWS.md | 2 ++ R/geom-defaults.R | 36 ++++++++++++++++++++++++++++++++++-- man/update_defaults.Rd | 17 ++++++++++++++--- tests/testthat/test-geom-.R | 7 +++++++ 5 files changed, 59 insertions(+), 5 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 6a57c5132d..ea62e9b076 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -513,6 +513,8 @@ export(remove_missing) export(render_axes) export(render_strips) export(replace_theme) +export(reset_geom_defaults) +export(reset_stat_defaults) export(reset_theme_settings) export(resolution) export(scale_alpha) diff --git a/NEWS.md b/NEWS.md index 7fbbc1967b..39fab0861b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or + stat default aesthetics at once (@teunbrand, #5975). * `facet_wrap()` can have `space = "free_x"` with 1-row layouts and `space = "free_y"` with 1-column layouts (@teunbrand) * Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483). diff --git a/R/geom-defaults.R b/R/geom-defaults.R index 8b81eeef94..e4e09ce71c 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -1,5 +1,7 @@ #' Modify geom/stat aesthetic defaults for future plots #' +#' Functions to update or reset the default aesthetics of geoms and stats. +#' #' @param stat,geom Name of geom/stat to modify (like `"point"` or #' `"bin"`), or a Geom/Stat object (like `GeomPoint` or #' `StatBin`). @@ -17,9 +19,11 @@ #' GeomPoint$default_aes #' ggplot(mtcars, aes(mpg, wt)) + geom_point() #' -#' # reset default +#' # reset single default #' update_geom_defaults("point", NULL) #' +#' # reset all defaults +#' reset_geom_defaults() #' #' # updating a stat's default aesthetic settings #' # example: change stat_bin()'s default y-axis to the density scale @@ -30,9 +34,12 @@ #' geom_histogram() + #' geom_function(fun = dnorm, color = "red") #' -#' # reset default +#' # reset single default #' update_stat_defaults("bin", NULL) #' +#' # reset all defaults +#' reset_stat_defaults() +#' #' @rdname update_defaults update_geom_defaults <- function(geom, new) { update_defaults(geom, "Geom", new, env = parent.frame()) @@ -44,6 +51,14 @@ update_stat_defaults <- function(stat, new) { update_defaults(stat, "Stat", new, env = parent.frame()) } +#' @rdname update_defaults +#' @export +reset_geom_defaults <- function() reset_defaults("geom") + +#' @rdname update_defaults +#' @export +reset_stat_defaults <- function() reset_defaults("stat") + cache_defaults <- new_environment() update_defaults <- function(name, subclass, new, env = parent.frame()) { @@ -73,3 +88,20 @@ update_defaults <- function(name, subclass, new, env = parent.frame()) { } } + +reset_defaults <- function(type) { + # Lookup matching names in cache + prefix <- paste0("^", type, "_") + full_names <- grep(prefix, ls(cache_defaults), value = TRUE) + # Early exit if there is nothing to reset + if (length(full_names) < 1) { + return(invisible()) + } + # Format names without prefix + short_names <- gsub(prefix, "", full_names) + names(short_names) <- full_names + + # Run updates + update <- switch(type, geom = update_geom_defaults, update_stat_defaults) + invisible(lapply(short_names, update, new = NULL)) +} diff --git a/man/update_defaults.Rd b/man/update_defaults.Rd index 8006bf8246..334dffed8e 100644 --- a/man/update_defaults.Rd +++ b/man/update_defaults.Rd @@ -3,11 +3,17 @@ \name{update_geom_defaults} \alias{update_geom_defaults} \alias{update_stat_defaults} +\alias{reset_geom_defaults} +\alias{reset_stat_defaults} \title{Modify geom/stat aesthetic defaults for future plots} \usage{ update_geom_defaults(geom, new) update_stat_defaults(stat, new) + +reset_geom_defaults() + +reset_stat_defaults() } \arguments{ \item{new}{One of the following: @@ -21,7 +27,7 @@ update_stat_defaults(stat, new) \code{StatBin}).} } \description{ -Modify geom/stat aesthetic defaults for future plots +Functions to update or reset the default aesthetics of geoms and stats. } \examples{ @@ -32,9 +38,11 @@ update_geom_defaults("point", aes(color = "red")) GeomPoint$default_aes ggplot(mtcars, aes(mpg, wt)) + geom_point() -# reset default +# reset single default update_geom_defaults("point", NULL) +# reset all defaults +reset_geom_defaults() # updating a stat's default aesthetic settings # example: change stat_bin()'s default y-axis to the density scale @@ -45,8 +53,11 @@ ggplot(data.frame(x = rnorm(1e3)), aes(x)) + geom_histogram() + geom_function(fun = dnorm, color = "red") -# reset default +# reset single default update_stat_defaults("bin", NULL) +# reset all defaults +reset_stat_defaults() + } \keyword{internal} diff --git a/tests/testthat/test-geom-.R b/tests/testthat/test-geom-.R index 61063d5d95..e0a0ca060a 100644 --- a/tests/testthat/test-geom-.R +++ b/tests/testthat/test-geom-.R @@ -20,6 +20,13 @@ test_that("geom defaults can be set and reset", { test <- l$geom$use_defaults(data_frame0()) expect_equal(test$colour, "black") expect_equal(inv$colour, "red") + + inv <- update_geom_defaults("line", list(colour = "blue")) + reset <- reset_geom_defaults() + + expect_equal(reset$geom_line$colour, "blue") + expect_equal(reset$geom_point$colour, GeomPoint$default_aes$colour) + expect_equal(GeomLine$default_aes$colour, inv$colour) }) test_that("updating geom aesthetic defaults preserves class and order", { From 3a7ae74a4c9ba7e93dcfa01bb19091302567eaa2 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:44:40 +0200 Subject: [PATCH 108/264] `facet_grid(space = "free")` can work with `coord_fixed()` (#5977) * allow coord aspect ratio when space is free * add test * add news bullet --- NEWS.md | 2 ++ R/facet-.R | 20 ++++++++++++-------- tests/testthat/test-facet-layout.R | 17 +++++++++++++++++ 3 files changed, 31 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index 39fab0861b..f6e8221ac0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -154,6 +154,8 @@ (@teunbrand, #5945). * (internal) The summary function of `stat_summary()` and `stat_summary_bin()` is setup once in total instead of once per group (@teunbrand, #5971) +* `facet_grid(space = "free")` can now be combined with `coord_fixed()` + (@teunbrand, #4584). # ggplot2 3.5.1 diff --git a/R/facet-.R b/R/facet-.R index 780c8bd184..a5e6f35101 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -139,18 +139,22 @@ Facet <- ggproto("Facet", NULL, free <- params$free %||% list(x = FALSE, y = FALSE) space <- params$space_free %||% list(x = FALSE, y = FALSE) - if ((free$x || free$y) && !coord$is_free()) { - cli::cli_abort( - "{.fn {snake_class(self)}} can't use free scales with \\ - {.fn {snake_class(coord)}}." - ) - } - aspect_ratio <- theme$aspect.ratio if (!is.null(aspect_ratio) && (space$x || space$y)) { cli::cli_abort("Free scales cannot be mixed with a fixed aspect ratio.") } + if (!coord$is_free()) { + if (space$x && space$y) { + aspect_ratio <- aspect_ratio %||% coord$ratio + } else if (free$x || free$y) { + cli::cli_abort( + "{.fn {snake_class(self)}} can't use free scales with \\ + {.fn {snake_class(coord)}}." + ) + } + } + table <- self$init_gtable( panels, layout, theme, ranges, params, aspect_ratio = aspect_ratio %||% coord$aspect(ranges[[1]]) @@ -219,7 +223,7 @@ Facet <- ggproto("Facet", NULL, if (space$y) { idx <- layout$PANEL[layout$COL == 1] heights <- vapply(idx, function(i) diff(ranges[[i]]$y.range), numeric(1)) - heights <- unit(heights, "null") + heights <- unit(heights * abs(aspect_ratio %||% 1), "null") } # Build gtable diff --git a/tests/testthat/test-facet-layout.R b/tests/testthat/test-facet-layout.R index 767abe5c8c..a008a0c80d 100644 --- a/tests/testthat/test-facet-layout.R +++ b/tests/testthat/test-facet-layout.R @@ -253,6 +253,23 @@ test_that("facet_grid throws errors at bad layout specs", { expect_snapshot_error(ggplotGrob(p)) }) +test_that("facet_grid can respect coord aspect with free scales/space", { + df <- expand.grid(x = letters[1:6], y = LETTERS[1:3]) + p <- ggplot(df, aes(x, y)) + + geom_tile() + + facet_grid( + rows = vars(y == "C"), + cols = vars(x %in% c("e", "f")), + scales = "free", space = "free" + ) + + coord_fixed(3, expand = FALSE) + gt <- ggplotGrob(p) + width <- gt$widths[panel_cols(gt)$l] + height <- gt$heights[panel_rows(gt)$t] + expect_equal(as.numeric(width), c(4, 2)) + expect_equal(as.numeric(height), c(6, 3)) +}) + test_that("facet_wrap and facet_grid throws errors when using reserved words", { mtcars2 <- mtcars mtcars2$PANEL <- mtcars2$cyl From 8ca3bbccc99e44d13e731c90629ba844e20a9d3f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 15:18:36 +0200 Subject: [PATCH 109/264] Update `theme_classic()` (#5981) * update `theme_classic()` * accept snapshots * add news bullet --- NEWS.md | 2 + R/theme-defaults.R | 6 ++- .../_snaps/theme/theme-classic-large.svg | 44 +++++++++---------- tests/testthat/_snaps/theme/theme-classic.svg | 44 +++++++++---------- 4 files changed, 50 insertions(+), 46 deletions(-) diff --git a/NEWS.md b/NEWS.md index f6e8221ac0..ffdd113269 100644 --- a/NEWS.md +++ b/NEWS.md @@ -156,6 +156,8 @@ is setup once in total instead of once per group (@teunbrand, #5971) * `facet_grid(space = "free")` can now be combined with `coord_fixed()` (@teunbrand, #4584). +* `theme_classic()` now has black ticks and text instead of dark gray. In + addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978). # ggplot2 3.5.1 diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 9c94e9dce5..522c978c68 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -460,10 +460,12 @@ theme_classic <- function(base_size = 11, base_family = "", panel.grid.minor = element_blank(), # show axes - axis.line = element_line(colour = "black", linewidth = rel(1)), + axis.text = element_text(size = rel(0.8)), + axis.line = element_line(lineend = "square"), + axis.ticks = element_line(), # simple, black and white strips - strip.background = element_rect(fill = "white", colour = "black", linewidth = rel(2)), + strip.background = element_rect(linewidth = rel(2)), # NB: size is 1 but clipped, it looks like the 0.5 of the axes complete = TRUE diff --git a/tests/testthat/_snaps/theme/theme-classic-large.svg b/tests/testthat/_snaps/theme/theme-classic-large.svg index 96767cc14f..8a4643dba1 100644 --- a/tests/testthat/_snaps/theme/theme-classic-large.svg +++ b/tests/testthat/_snaps/theme/theme-classic-large.svg @@ -43,28 +43,28 @@ 1 - - - - - - -1.0 -1.5 -2.0 -2.5 -3.0 - -1.0 -1.5 -2.0 -2.5 -3.0 - - - - - + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 + +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + x y diff --git a/tests/testthat/_snaps/theme/theme-classic.svg b/tests/testthat/_snaps/theme/theme-classic.svg index 8588be9819..45ef7ef076 100644 --- a/tests/testthat/_snaps/theme/theme-classic.svg +++ b/tests/testthat/_snaps/theme/theme-classic.svg @@ -43,28 +43,28 @@ 1 - - - - - - -1.0 -1.5 -2.0 -2.5 -3.0 - -1.0 -1.5 -2.0 -2.5 -3.0 - - - - - + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 + +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + x y From bcb87fc120becf836f130fc6c84edca577b11cfd Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 15:18:51 +0200 Subject: [PATCH 110/264] Move {mgcv} to suggests (#5987) * move all method setup to `setup_params()` * fallback to `method = "lm"` in absence of {mgcv} * adjust tests * move {mgcv} from Imports to Suggests * add news bullet * Revert "fallback to `method = "lm"` in absence of {mgcv}" This reverts commit 5824b1df9e300d246e8adeae37a2d462770f199f. * homebrew an install prompt * change fallback * fix `gam_method()` in absence of mgcv * tweak message --- DESCRIPTION | 2 +- NEWS.md | 1 + R/stat-smooth.R | 66 +++++++++++++++++++------------ R/utilities.R | 29 ++++++++++++++ tests/testthat/test-geom-smooth.R | 14 +++++++ 5 files changed, 86 insertions(+), 26 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d97ce7e689..6a14039f20 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,7 +39,6 @@ Imports: isoband, lifecycle (> 1.0.1), MASS, - mgcv, rlang (>= 1.1.0), scales (>= 1.3.0), stats, @@ -55,6 +54,7 @@ Suggests: knitr, mapproj, maps, + mgcv, multcomp, munsell, nlme, diff --git a/NEWS.md b/NEWS.md index ffdd113269..6a66ca97d4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Moved {mgcv} from Imports to Suggests (@teunbrand, #5986) * New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or stat default aesthetics at once (@teunbrand, #5975). * `facet_wrap()` can have `space = "free_x"` with 1-row layouts and diff --git a/R/stat-smooth.R b/R/stat-smooth.R index 9c72d3570c..147bd06e41 100644 --- a/R/stat-smooth.R +++ b/R/stat-smooth.R @@ -95,36 +95,63 @@ StatSmooth <- ggproto("StatSmooth", Stat, setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params, ambiguous = TRUE) msg <- character() - if (is.null(params$method) || identical(params$method, "auto")) { + method <- params$method + if (is.null(method) || identical(method, "auto")) { # Use loess for small datasets, gam with a cubic regression basis for # larger. Based on size of the _largest_ group to avoid bad memory # behaviour of loess max_group <- max(table(interaction(data$group, data$PANEL, drop = TRUE))) if (max_group < 1000) { - params$method <- "loess" + method <- "loess" } else { - params$method <- "gam" + method <- "gam" } - msg <- c(msg, paste0("method = '", params$method, "'")) + msg <- c(msg, paste0("method = '", method, "'")) + } + + if (identical(method, "gam") && + !prompt_install("mgcv", "for using {.code method = \"gam\"}")) { + cli::cli_inform(c( + "The {.arg method} was set to {.val gam}, but {.pkg mgcv} is not installed.", + "!" = "Falling back to {.code method = \"lm\"}.", + i = "Install {.pkg mgcv} or change the {.arg method} argument to \\ + resolve this issue." + )) + method <- "lm" } if (is.null(params$formula)) { - if (identical(params$method, "gam")) { + if (identical(method, "gam")) { params$formula <- y ~ s(x, bs = "cs") } else { params$formula <- y ~ x } msg <- c(msg, paste0("formula = '", deparse(params$formula), "'")) } - if (identical(params$method, "gam")) { - params$method <- gam_method() + + # Special case span because it's the most commonly used model argument + if (identical(method, "loess")) { + params$method.args$span <- params$span %||% 0.75 + } + + if (is.character(method)) { + if (identical(method, "gam")) { + method <- gam_method() + } else { + method <- match.fun(method) + } + } + # If gam and gam's method is not specified by the user then use REML + if (identical(method, gam_method())) { + params$method.args$method <- params$method.args$method %||% "REML" } if (length(msg) > 0) { cli::cli_inform("{.fn geom_smooth} using {msg}") } + params$method <- method params }, @@ -159,23 +186,6 @@ StatSmooth <- ggproto("StatSmooth", Stat, } } - # Special case span because it's the most commonly used model argument - if (identical(method, "loess")) { - method.args$span <- span - } - - if (is.character(method)) { - if (identical(method, "gam")) { - method <- gam_method() - } else { - method <- match.fun(method) - } - } - # If gam and gam's method is not specified by the user then use REML - if (identical(method, gam_method()) && is.null(method.args$method)) { - method.args$method <- "REML" - } - prediction <- try_fetch( { model <- inject(method( @@ -205,4 +215,10 @@ StatSmooth <- ggproto("StatSmooth", Stat, ) # This function exists to silence an undeclared import warning -gam_method <- function() mgcv::gam +gam_method <- function() { + if (is_installed("mgcv")) { + mgcv::gam + } else { + NA + } +} diff --git a/R/utilities.R b/R/utilities.R index a3357e6119..0bddb4b4c6 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -846,3 +846,32 @@ as_unordered_factor <- function(x) { class(x) <- setdiff(class(x), "ordered") x } + +# TODO: Replace me if rlang/#1730 gets implemented +# Similar to `rlang::check_installed()` but returns boolean and misses +# features such as versions, comparisons and using {pak}. +prompt_install <- function(pkg, reason = NULL) { + if (length(pkg) < 1 || is_installed(pkg)) { + return(TRUE) + } + if (!interactive()) { + return(FALSE) + } + + pkg <- pkg[!vapply(pkg, is_installed, logical(1))] + + message <- "The {.pkg {pkg}} package{?s} {?is/are} required" + if (is.null(reason)) { + message <- paste0(message, ".") + } else { + message <- paste0(message, " ", reason) + } + question <- "Would you like to install {cli::qty(pkg)}{?it/them}?" + + cli::cli_bullets(c("!" = message, "i" = question)) + if (utils::menu(c("Yes", "No")) != 1) { + return(FALSE) + } + utils::install.packages(pkg) + is_installed(pkg) +} diff --git a/tests/testthat/test-geom-smooth.R b/tests/testthat/test-geom-smooth.R index 5f8282c176..42c82108c7 100644 --- a/tests/testthat/test-geom-smooth.R +++ b/tests/testthat/test-geom-smooth.R @@ -57,6 +57,8 @@ test_that("default smoothing methods for small and large data sets work", { y = x^2 + 0.5 * rnorm(1001) ) + skip_if_not_installed("mgcv") + m <- mgcv::gam(y ~ s(x, bs = "cs"), data = df, method = "REML") range <- range(df$x, na.rm = TRUE) xseq <- seq(range[1], range[2], length.out = 80) @@ -96,6 +98,18 @@ test_that("geom_smooth() works when one group fails", { expect_gte(nrow(ld), 2) }) +test_that("a fallback message is thrown when `method = 'gam'` and {mgcv} is absent", { + p <- ggplot(mpg, aes(displ, hwy)) + + geom_smooth(method = "gam", formula = y ~ x) + + with_mocked_bindings( + expect_message( + ggplot_build(p), regexp = "Falling back to `method = \"lm\"`" + ), + is_installed = function(...) FALSE + ) +}) + # Visual tests ------------------------------------------------------------ test_that("geom_smooth() works with alternative stats", { From 8bb9641ab6e6aa9b1e12bea311599967cde6afe2 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 16:07:03 +0200 Subject: [PATCH 111/264] Move {tibble} to suggests (#5990) * don't use `tibble()` in code * remove `tibble()` from examples/tests * redocument * add news bullet --- DESCRIPTION | 2 +- NAMESPACE | 1 - NEWS.md | 1 + R/facet-.R | 2 +- R/position-stack.R | 12 ++++----- R/summarise-plot.R | 4 +-- R/utilities.R | 4 --- man/position_stack.Rd | 12 ++++----- tests/testthat/test-geom-quantile.R | 2 +- tests/testthat/test-geom-tile.R | 9 +++---- tests/testthat/test-scale-discrete.R | 7 +++-- tests/testthat/test-sec-axis.R | 2 +- tests/testthat/test-stat-align.R | 39 +++++++++------------------- 13 files changed, 36 insertions(+), 61 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6a14039f20..b4cd9ec950 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -42,7 +42,6 @@ Imports: rlang (>= 1.1.0), scales (>= 1.3.0), stats, - tibble, vctrs (>= 0.6.0), withr (>= 2.5.0) Suggests: @@ -67,6 +66,7 @@ Suggests: sf (>= 0.7-3), svglite (>= 2.1.2), testthat (>= 3.1.5), + tibble, vdiffr (>= 1.0.6), xml2 Enhances: diff --git a/NAMESPACE b/NAMESPACE index ea62e9b076..197845db89 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -735,7 +735,6 @@ importFrom(grid,unit) importFrom(lifecycle,deprecated) importFrom(scales,alpha) importFrom(stats,setNames) -importFrom(tibble,tibble) importFrom(utils,.DollarNames) importFrom(utils,head) importFrom(utils,tail) diff --git a/NEWS.md b/NEWS.md index 6a66ca97d4..b4636c5166 100644 --- a/NEWS.md +++ b/NEWS.md @@ -159,6 +159,7 @@ (@teunbrand, #4584). * `theme_classic()` now has black ticks and text instead of dark gray. In addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978). +* {tibble} is now suggested instead of imported (@teunbrand, #5986) # ggplot2 3.5.1 diff --git a/R/facet-.R b/R/facet-.R index a5e6f35101..2e349f6f97 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -564,7 +564,7 @@ is_facets <- function(x) { # but that seems like a reasonable tradeoff. eval_facets <- function(facets, data, possible_columns = NULL) { vars <- compact(lapply(facets, eval_facet, data, possible_columns = possible_columns)) - data_frame0(tibble::as_tibble(vars)) + data_frame0(!!!vars) } eval_facet <- function(facet, data, possible_columns = NULL) { # Treat the case when `facet` is a quosure of a symbol specifically diff --git a/R/position-stack.R b/R/position-stack.R index 2da5c91ef6..6d77269a1f 100644 --- a/R/position-stack.R +++ b/R/position-stack.R @@ -116,14 +116,12 @@ #' #' # Negative values ----------------------------------------------------------- #' -#' df <- tibble::tribble( -#' ~x, ~y, ~grp, -#' "a", 1, "x", -#' "a", 2, "y", -#' "b", 1, "x", -#' "b", 3, "y", -#' "b", -1, "y" +#' df <- data.frame( +#' x = rep(c("a", "b"), 2:3), +#' y = c(1, 2, 1, 3, -1), +#' grp = c("x", "y", "x", "y", "y") #' ) +#' #' ggplot(data = df, aes(x, y, group = grp)) + #' geom_col(aes(fill = grp), position = position_stack(reverse = TRUE)) + #' geom_hline(yintercept = 0) diff --git a/R/summarise-plot.R b/R/summarise-plot.R index bdb7cc7af4..9ab046cb8c 100644 --- a/R/summarise-plot.R +++ b/R/summarise-plot.R @@ -66,7 +66,7 @@ summarise_layout <- function(p) { l <- p$layout layout <- l$layout - layout <- tibble( + layout <- data_frame0( panel = l$layout$PANEL, row = l$layout$ROW, col = l$layout$COL @@ -134,7 +134,7 @@ summarise_layers <- function(p) { # This currently only returns the mappings, but in the future, other # information could be added. - tibble( + data_frame0( mapping = layer_mappings ) } diff --git a/R/utilities.R b/R/utilities.R index 0bddb4b4c6..6a7ca5921d 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -371,10 +371,6 @@ seq_asc <- function(to, from) { } } -# Needed to trigger package loading -#' @importFrom tibble tibble -NULL - # Wrapping vctrs data_frame constructor with no name repair data_frame0 <- function(...) data_frame(..., .name_repair = "minimal") diff --git a/man/position_stack.Rd b/man/position_stack.Rd index 024bfd80a4..646ab3c515 100644 --- a/man/position_stack.Rd +++ b/man/position_stack.Rd @@ -126,14 +126,12 @@ ggplot(series, aes(time, value, group = type)) + # Negative values ----------------------------------------------------------- -df <- tibble::tribble( - ~x, ~y, ~grp, - "a", 1, "x", - "a", 2, "y", - "b", 1, "x", - "b", 3, "y", - "b", -1, "y" +df <- data.frame( + x = rep(c("a", "b"), 2:3), + y = c(1, 2, 1, 3, -1), + grp = c("x", "y", "x", "y", "y") ) + ggplot(data = df, aes(x, y, group = grp)) + geom_col(aes(fill = grp), position = position_stack(reverse = TRUE)) + geom_hline(yintercept = 0) diff --git a/tests/testthat/test-geom-quantile.R b/tests/testthat/test-geom-quantile.R index 742e2850ed..7b6feecb9b 100644 --- a/tests/testthat/test-geom-quantile.R +++ b/tests/testthat/test-geom-quantile.R @@ -8,7 +8,7 @@ test_that("geom_quantile matches quantile regression", { set.seed(6531) x <- rnorm(10) - df <- tibble::tibble( + df <- data_frame0( x = x, y = x^2 + 0.5 * rnorm(10) ) diff --git a/tests/testthat/test-geom-tile.R b/tests/testthat/test-geom-tile.R index 581963a4b2..9034e3c9f7 100644 --- a/tests/testthat/test-geom-tile.R +++ b/tests/testthat/test-geom-tile.R @@ -17,11 +17,10 @@ test_that("accepts width and height aesthetics", { geom_tile(fill = NA, colour = "black", linewidth = 1) out <- get_layer_data(p) - boundary <- as.data.frame(tibble::tribble( - ~xmin, ~xmax, ~ymin, ~ymax, - -1, 1, -1, 1, - -2, 2, -2, 2 - )) + boundary <- data_frame0( + xmin = c(-1, -2), xmax = c(1, 2), + ymin = c(-1, -2), ymax = c(1, 2) + ) expect_equal(out[c("xmin", "xmax", "ymin", "ymax")], boundary) }) diff --git a/tests/testthat/test-scale-discrete.R b/tests/testthat/test-scale-discrete.R index 084511571f..9e8eeaf717 100644 --- a/tests/testthat/test-scale-discrete.R +++ b/tests/testthat/test-scale-discrete.R @@ -1,10 +1,9 @@ # Missing values ---------------------------------------------------------- -df <- tibble::tibble( +df <- data_frame0( x1 = c("a", "b", NA), - x2 = factor(x1), - x3 = addNA(x2), - + x2 = factor(c("a", "b", NA)), + x3 = factor(c("a", "b", NA), levels = c("a", "b", NA), exclude = NULL), y = 1:3 ) diff --git a/tests/testthat/test-sec-axis.R b/tests/testthat/test-sec-axis.R index 02846e9f81..7530c4a70c 100644 --- a/tests/testthat/test-sec-axis.R +++ b/tests/testthat/test-sec-axis.R @@ -171,7 +171,7 @@ test_that("sec axis works with tidy eval", { g } - t <- tibble(x = letters, y = seq(10, 260, 10), z = 1:26) + t <- data_frame0(x = letters, y = seq(10, 260, 10), z = 1:26) p <- f(t, x, y, z) diff --git a/tests/testthat/test-stat-align.R b/tests/testthat/test-stat-align.R index 4c418037b3..457992e747 100644 --- a/tests/testthat/test-stat-align.R +++ b/tests/testthat/test-stat-align.R @@ -1,44 +1,29 @@ test_that("standard alignment works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 2, - "a", 3, 5, - "a", 5, 1, - "b", 2, 3, - "b", 4, 6, - "b", 6, 7 + df <- data_frame0( + g = rep(c("a", "b"), each = 3L), + x = c(1, 3, 5, 2, 4, 6), + y = c(2, 5, 1, 3, 6, 7) ) p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas", p) }) test_that("alignment with cliffs works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 2, - "a", 3, 5, - "a", 5, 1, - "b", 2, 3, - "b", 4, 3, - "b", 4, 6, - "b", 6, 7 + df <- data_frame0( + g = rep(c("a", "b"), 3:4), + x = c(1, 3, 5, 2, 4, 4, 6), + y = c(2, 5, 1, 3, 3, 6, 7) ) - p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas with cliff", p) }) test_that("alignment with negative and positive values works", { - df <- tibble::tribble( - ~g, ~x, ~y, - "a", 1, 1, - "a", 2, 4, - "a", 3, -4, - "a", 8, 0, - "b", 2, 4, - "b", 6, -4 + df <- data_frame0( + g = rep(c("a", "b"), c(4L, 2L)), + x = c(1, 2, 3, 8, 2, 6), + y = c(1, 4, -4, 0, 4, -4) ) - p <- ggplot(df, aes(x, y, fill = g)) + geom_area(color = "black") expect_doppelganger("align two areas with pos/neg y", p) }) From e69687a407addd2c29510153de52a128bde4701e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 16:10:19 +0200 Subject: [PATCH 112/264] Ignore empty non-mapped aesthetics (#6011) * drop empty aesthetics with warning * add test * add news bullet --- NEWS.md | 2 ++ R/layer.R | 9 +++++++++ tests/testthat/test-layer.R | 7 +++++++ 3 files changed, 18 insertions(+) diff --git a/NEWS.md b/NEWS.md index b4636c5166..4cab4f4c79 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Passing empty unmapped aesthetics to layers raises a warning instead of + throwing an error (@teunbrand, #6009). * Moved {mgcv} from Imports to Suggests (@teunbrand, #5986) * New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or stat default aesthetics at once (@teunbrand, #5975). diff --git a/R/layer.R b/R/layer.R index 59a9dba096..eba8666de4 100644 --- a/R/layer.R +++ b/R/layer.R @@ -146,6 +146,15 @@ layer <- function(geom = NULL, stat = NULL, if (any(pattern)) { aes_params[pattern] <- lapply(aes_params[pattern], list) } + # Drop empty aesthetics + empty_aes <- names(aes_params)[lengths(aes_params) == 0] + if (length(empty_aes) > 0) { + cli::cli_warn( + "Ignoring empty aesthetic{?s}: {.arg {empty_aes}}.", + call = call_env + ) + aes_params <- aes_params[setdiff(names(aes_params), empty_aes)] + } # Warn about extra params and aesthetics extra_param <- setdiff(names(params), all) diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 8be6c8555f..51f0cd9eee 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -25,6 +25,13 @@ test_that("unknown aesthetics create warning", { expect_warning(geom_point(aes(blah = "red")), "unknown aesthetics") }) +test_that("empty aesthetics create warning", { + expect_warning( + geom_point(fill = NULL, shape = character()), + "Ignoring empty aesthetics" + ) +}) + test_that("invalid aesthetics throws errors", { # We want to test error and ignore the scale search message suppressMessages({ From 5971ff46bc5dfeb1114a5c1e2229bd0a3b897041 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 26 Aug 2024 16:11:47 +0200 Subject: [PATCH 113/264] chore: merge isoband/isolines functions (#6021) * merge isoband/isolines functions * Update R/stat-contour.R Co-authored-by: Thomas Lin Pedersen --------- Co-authored-by: Thomas Lin Pedersen --- R/stat-contour.R | 53 +++++++++++------------------------------------- 1 file changed, 12 insertions(+), 41 deletions(-) diff --git a/R/stat-contour.R b/R/stat-contour.R index 882879430d..e0590f2ec9 100644 --- a/R/stat-contour.R +++ b/R/stat-contour.R @@ -108,7 +108,7 @@ StatContour <- ggproto("StatContour", Stat, breaks <- contour_breaks(z.range, bins, binwidth, breaks) isolines <- withr::with_options(list(OutDec = "."), xyz_to_isolines(data, breaks)) - path_df <- iso_to_path(isolines, data$group[1]) + path_df <- iso_to_geom(isolines, data$group[1], geom = "path") path_df$level <- as.numeric(path_df$level) path_df$nlevel <- rescale_max(path_df$level) @@ -142,7 +142,7 @@ StatContourFilled <- ggproto("StatContourFilled", Stat, isobands <- withr::with_options(list(OutDec = "."), xyz_to_isobands(data, breaks)) names(isobands) <- pretty_isoband_levels(names(isobands)) - path_df <- iso_to_polygon(isobands, data$group[1]) + path_df <- iso_to_geom(isobands, data$group[1], geom = "polygon") path_df$level <- ordered(path_df$level, levels = names(isobands)) path_df$level_low <- breaks[as.numeric(path_df$level)] @@ -259,51 +259,17 @@ isoband_z_matrix <- function(data) { raster } -#' Convert the output of isolines functions -#' -#' @param iso the output of [isoband::isolines()] -#' @param group the name of the group -#' -#' @return A data frame that can be passed to [geom_path()]. -#' @noRd -#' -iso_to_path <- function(iso, group = 1) { - lengths <- vapply(iso, function(x) length(x$x), integer(1)) - - if (all(lengths == 0)) { - cli::cli_warn("{.fn stat_contour}: Zero contours were generated") - return(data_frame0()) - } - - levels <- names(iso) - xs <- unlist(lapply(iso, "[[", "x"), use.names = FALSE) - ys <- unlist(lapply(iso, "[[", "y"), use.names = FALSE) - ids <- unlist(lapply(iso, "[[", "id"), use.names = FALSE) - item_id <- rep(seq_along(iso), lengths) - - # Add leading zeros so that groups can be properly sorted - groups <- paste(group, sprintf("%03d", item_id), sprintf("%03d", ids), sep = "-") - groups <- factor(groups) - - data_frame0( - level = rep(levels, lengths), - x = xs, - y = ys, - piece = as.integer(groups), - group = groups, - .size = length(xs) - ) -} - #' Convert the output of isoband functions #' -#' @param iso the output of [isoband::isobands()] +#' @param iso the output of [isoband::isobands()] or [isoband::isolines()] #' @param group the name of the group +#' @param geom The type of geometry to return. Either `"path"` or `"polygon"` +#' for isolines and isobands respectively. #' -#' @return A data frame that can be passed to [geom_polygon()]. +#' @return A data frame that can be passed to [geom_polygon()] or [geom_path()]. #' @noRd #' -iso_to_polygon <- function(iso, group = 1) { +iso_to_geom <- function(iso, group = 1, geom = "path") { lengths <- vapply(iso, function(x) length(x$x), integer(1)) if (all(lengths == 0)) { @@ -319,6 +285,11 @@ iso_to_polygon <- function(iso, group = 1) { # Add leading zeros so that groups can be properly sorted groups <- paste(group, sprintf("%03d", item_id), sep = "-") + if (geom == "path") { + groups <- paste(groups, sprintf("%03d", ids), sep = "-") + ids <- NULL + } + groups <- factor(groups) data_frame0( From 2e08bba0910c11a46b6de9e375fade78b75d10dc Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 27 Aug 2024 14:43:07 +0200 Subject: [PATCH 114/264] Geom aesthetics based on theme (#5833) * draft new `geom` element in themes * plumbing for providing theme to Geom$use_defaults() * make `from_theme()` as eval helper * Evaluate default aesthetics from theme * allow user-specified `from_theme()` * plumbing for guides to observe theme * Add text settings * accept minor fontsize difference (11.04pt -> 11.00pt) * temporarily disable `sf_grob()` default lookups * temporary shim for colour mixing * Get all `colour`/`fill`/`linewidth` from theme * test theme has `geom` element * adapt tests * `geom_sf()` has themed defaults * we don't expect complete themes anymore * shim auto-replaces itself when exported from scales * theme defaults for point size/shape * boxplot point shape/size default from `GeomBoxplot$default_aes` * accept larger points in large theme snapshots * Point to theme setting in `update_geom_defaults()` * document `from_theme()` * add news bullet * Update R/geom-pointrange.R Co-authored-by: Thomas Lin Pedersen * Run revdepcheck * implement @yutannihilation's suggestion * run revdepcheck * revdepcheck once again * protect against missing `theme` * skip empty sf layers * getter for geom defaults * add `linetype` to `element_geom()` * `geom_path()` treats integer `1L` as solid (in addition to numeric `1`) * get linetype from theme * swap thin/thick for linewidth/borderwidth and distinguish linetype and bordertype * point stroke counts as border * deduplicate argument documentation --------- Co-authored-by: Thomas Lin Pedersen --- NAMESPACE | 3 + NEWS.md | 6 + R/aes-evaluation.R | 20 + R/annotation-logticks.R | 7 +- R/geom-.R | 24 +- R/geom-abline.R | 8 +- R/geom-boxplot.R | 16 +- R/geom-contour.R | 6 +- R/geom-crossbar.R | 9 +- R/geom-curve.R | 9 +- R/geom-defaults.R | 54 + R/geom-density.R | 2 +- R/geom-density2d.R | 7 +- R/geom-dotplot.R | 10 +- R/geom-errorbar.R | 10 +- R/geom-errorbarh.R | 10 +- R/geom-hex.R | 6 +- R/geom-hline.R | 7 +- R/geom-label.R | 7 +- R/geom-linerange.R | 8 +- R/geom-path.R | 9 +- R/geom-point.R | 5 +- R/geom-pointrange.R | 8 +- R/geom-polygon.R | 9 +- R/geom-quantile.R | 2 +- R/geom-raster.R | 2 +- R/geom-rect.R | 7 +- R/geom-ribbon.R | 16 +- R/geom-rug.R | 7 +- R/geom-segment.R | 9 +- R/geom-sf.R | 25 +- R/geom-smooth.R | 9 +- R/geom-text.R | 7 +- R/geom-tile.R | 11 +- R/geom-violin.R | 10 +- R/geom-vline.R | 8 +- R/guide-.R | 6 +- R/guide-axis-stack.R | 2 +- R/guide-colorbar.R | 2 +- R/guide-legend.R | 8 +- R/guide-old.R | 2 +- R/guides-.R | 8 +- R/layer-sf.R | 1 + R/layer.R | 9 +- R/plot-build.R | 12 +- R/theme-defaults.R | 16 + R/theme-elements.R | 66 +- R/theme.R | 2 + R/utilities.R | 18 + man/aes_eval.Rd | 11 + man/element.Rd | 46 +- man/geom_boxplot.Rd | 4 +- man/get_geom_defaults.Rd | 43 + man/theme.Rd | 3 + man/update_defaults.Rd | 4 + revdep/README.md | 394 +- revdep/cran.md | 917 +- revdep/failures.md | 7476 +++++++---------- revdep/problems.md | 3721 +++----- ...clip-on-by-default-only-inside-visible.svg | 16 +- ...ed-off-both-inside-and-outside-visible.svg | 16 +- .../bottom-half-circle-with-rotated-text.svg | 24 +- .../geom-sf/labels-for-north-carolina.svg | 4 +- .../geom-sf/texts-for-north-carolina.svg | 2 +- .../testthat/_snaps/theme/theme-bw-large.svg | 10 +- .../_snaps/theme/theme-classic-large.svg | 10 +- .../_snaps/theme/theme-dark-large.svg | 10 +- .../_snaps/theme/theme-gray-large.svg | 10 +- .../_snaps/theme/theme-light-large.svg | 10 +- .../_snaps/theme/theme-linedraw-large.svg | 10 +- .../_snaps/theme/theme-minimal-large.svg | 10 +- tests/testthat/_snaps/utilities-break.md | 2 +- tests/testthat/test-geom-.R | 24 +- tests/testthat/test-stats.R | 2 +- tests/testthat/test-theme.R | 2 - 75 files changed, 6029 insertions(+), 7277 deletions(-) create mode 100644 man/get_geom_defaults.Rd diff --git a/NAMESPACE b/NAMESPACE index 197845db89..f0ccf3bec1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -344,6 +344,7 @@ export(draw_key_vpath) export(dup_axis) export(el_def) export(element_blank) +export(element_geom) export(element_grob) export(element_line) export(element_rect) @@ -367,6 +368,7 @@ export(find_panel) export(flip_data) export(flipped_names) export(fortify) +export(from_theme) export(geom_abline) export(geom_area) export(geom_bar) @@ -422,6 +424,7 @@ export(geom_violin) export(geom_vline) export(get_alt_text) export(get_element_tree) +export(get_geom_defaults) export(get_guide_data) export(get_last_plot) export(get_layer_data) diff --git a/NEWS.md b/NEWS.md index 4cab4f4c79..8c5ca3c555 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,11 @@ # ggplot2 (development version) +* (Breaking) The defaults for all geoms can be set at one in the theme. + (@teunbrand based on pioneering work by @dpseidel, #2239) + * A new `theme(geom)` argument is used to track these defaults. + * The `element_geom()` function can be used to populate that argument. + * The `from_theme()` function allows access to the theme default fields from + inside the `aes()` function. * Passing empty unmapped aesthetics to layers raises a warning instead of throwing an error (@teunbrand, #6009). * Moved {mgcv} from Imports to Suggests (@teunbrand, #5986) diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index 4c682e3f63..5554b54772 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -109,6 +109,13 @@ #' fun.data = ~ round(data.frame(mean = mean(.x), sd = sd(.x)), 2) #' ) #' ``` +#' +#' ## Theme access +#' The `from_theme()` function can be used to acces the [`element_geom()`] +#' fields of the `theme(geom)` argument. Using `aes(colour = from_theme(ink))` +#' and `aes(colour = from_theme(accent))` allows swapping between foreground and +#' accent colours. +#' #' @rdname aes_eval #' @name aes_eval #' @@ -192,6 +199,13 @@ stat <- function(x) { after_scale <- function(x) { x } + +#' @rdname aes_eval +#' @export +from_theme <- function(x) { + x +} + #' @rdname aes_eval #' @export stage <- function(start = NULL, after_stat = NULL, after_scale = NULL) { @@ -221,6 +235,9 @@ is_scaled_aes <- function(aesthetics) { is_staged_aes <- function(aesthetics) { vapply(aesthetics, is_staged, logical(1), USE.NAMES = FALSE) } +is_themed_aes <- function(aesthetics) { + vapply(aesthetics, is_themed, logical(1), USE.NAMES = FALSE) +} is_calculated <- function(x, warn = FALSE) { if (is_call(get_expr(x), "after_stat")) { return(TRUE) @@ -263,6 +280,9 @@ is_scaled <- function(x) { is_staged <- function(x) { is_call(get_expr(x), "stage") } +is_themed <- function(x) { + is_call(get_expr(x), "from_theme") +} # Strip dots from expressions strip_dots <- function(expr, env, strip_pronoun = FALSE) { diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R index 13c8f609f5..aa03d472cf 100644 --- a/R/annotation-logticks.R +++ b/R/annotation-logticks.R @@ -228,7 +228,12 @@ GeomLogticks <- ggproto("GeomLogticks", Geom, gTree(children = inject(gList(!!!ticks))) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = 1) + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = 1 + ) ) diff --git a/R/geom-.R b/R/geom-.R index c3da9be244..5b6a2af09d 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -114,7 +114,8 @@ Geom <- ggproto("Geom", setup_data = function(data, params) data, # Combine data with defaults and set aesthetics from parameters - use_defaults = function(self, data, params = list(), modifiers = aes(), default_aes = NULL, ...) { + use_defaults = function(self, data, params = list(), modifiers = aes(), + default_aes = NULL, theme = NULL, ...) { default_aes <- default_aes %||% self$default_aes # Inherit size as linewidth if no linewidth aesthetic and param exist @@ -131,8 +132,11 @@ Geom <- ggproto("Geom", # Fill in missing aesthetics with their defaults missing_aes <- setdiff(names(default_aes), names(data)) + default_aes <- default_aes[missing_aes] + themed_defaults <- eval_from_theme(default_aes, theme) + default_aes[names(themed_defaults)] <- themed_defaults - missing_eval <- lapply(default_aes[missing_aes], eval_tidy) + missing_eval <- lapply(default_aes, eval_tidy) # Needed for geoms with defaults set to NULL (e.g. GeomSf) missing_eval <- compact(missing_eval) @@ -142,6 +146,13 @@ Geom <- ggproto("Geom", data[names(missing_eval)] <- missing_eval } + themed <- is_themed_aes(modifiers) + if (any(themed)) { + themed <- eval_from_theme(modifiers[themed], theme) + modifiers <- modifiers[setdiff(names(modifiers), names(themed))] + data[names(themed)] <- themed + } + # If any after_scale mappings are detected they will be resolved here # This order means that they will have access to all default aesthetics if (length(modifiers) != 0) { @@ -226,6 +237,15 @@ Geom <- ggproto("Geom", ) +eval_from_theme <- function(aesthetics, theme) { + themed <- is_themed_aes(aesthetics) + if (!any(themed)) { + return(aesthetics) + } + settings <- calc_element("geom", theme) %||% .default_geom_element + lapply(aesthetics[themed], eval_tidy, data = settings) +} + #' Graphical units #' #' Multiply size in mm by these constants in order to convert to the units diff --git a/R/geom-abline.R b/R/geom-abline.R index da65483635..e9775e33fb 100644 --- a/R/geom-abline.R +++ b/R/geom-abline.R @@ -142,7 +142,13 @@ GeomAbline <- ggproto("GeomAbline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + required_aes = c("slope", "intercept"), draw_key = draw_key_abline, diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index 399f92d7a8..1ac23ba80f 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -117,8 +117,8 @@ geom_boxplot <- function(mapping = NULL, data = NULL, outlier.colour = NULL, outlier.color = NULL, outlier.fill = NULL, - outlier.shape = 19, - outlier.size = 1.5, + outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, @@ -223,8 +223,8 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, draw_group = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre", fatten = 2, outlier.colour = NULL, - outlier.fill = NULL, outlier.shape = 19, - outlier.size = 1.5, outlier.stroke = 0.5, + outlier.fill = NULL, outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, flipped_aes = FALSE) { data <- check_linewidth(data, snake_class(self)) @@ -327,8 +327,12 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, draw_key = draw_key_boxplot, - default_aes = aes(weight = 1, colour = "grey20", fill = "white", size = NULL, - alpha = NA, shape = 19, linetype = "solid", linewidth = 0.5), + default_aes = aes( + weight = 1, colour = from_theme(col_mix(ink, paper, 0.2)), + fill = from_theme(paper), size = from_theme(pointsize), + alpha = NA, shape = from_theme(pointshape), linetype = from_theme(bordertype), + linewidth = from_theme(borderwidth) + ), required_aes = c("x|y", "lower|xlower", "upper|xupper", "middle|xmiddle", "ymin|xmin", "ymax|xmax"), diff --git a/R/geom-contour.R b/R/geom-contour.R index 7dfe9fb228..a73bc3a135 100644 --- a/R/geom-contour.R +++ b/R/geom-contour.R @@ -126,9 +126,9 @@ geom_contour_filled <- function(mapping = NULL, data = NULL, GeomContour <- ggproto("GeomContour", GeomPath, default_aes = aes( weight = 1, - colour = "#3366FF", - linewidth = 0.5, - linetype = 1, + colour = from_theme(accent), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), alpha = NA ) ) diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index 36c3d4b9ff..1f7c66f832 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -40,8 +40,13 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, GeomErrorbar$setup_data(data, params) }, - default_aes = aes(colour = "black", fill = NA, linewidth = 0.5, linetype = 1, - alpha = NA), + default_aes = aes( + colour = from_theme(ink), + fill = NA, + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y", "ymin|xmin", "ymax|xmax"), diff --git a/R/geom-curve.R b/R/geom-curve.R index 4c5b60e2c5..e1c38d1cd4 100644 --- a/R/geom-curve.R +++ b/R/geom-curve.R @@ -40,7 +40,14 @@ geom_curve <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomCurve <- ggproto("GeomCurve", GeomSegment, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + draw_panel = function(data, panel_params, coord, curvature = 0.5, angle = 90, ncp = 5, arrow = NULL, arrow.fill = NULL, lineend = "butt", na.rm = FALSE) { diff --git a/R/geom-defaults.R b/R/geom-defaults.R index e4e09ce71c..65974f841a 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -9,6 +9,9 @@ #' * A named list of aesthetics to serve as new defaults. #' * `NULL` to reset the defaults. #' @keywords internal +#' @note +#' Please note that geom defaults can be set *en masse* via the `theme(geom)` +#' argument. #' @export #' @examples #' @@ -51,6 +54,57 @@ update_stat_defaults <- function(stat, new) { update_defaults(stat, "Stat", new, env = parent.frame()) } +#' Resolve and get geom defaults +#' +#' @param geom Some definition of a geom: +#' * A `function` that creates a layer, e.g. `geom_path()`. +#' * A layer created by such function +#' * A string naming a geom class in snake case without the `geom_`-prefix, +#' e.g. `"contour_filled"`. +#' * A geom class object. +#' @param theme A [`theme`] object. Defaults to the current global theme. +#' +#' @return A list of aesthetics +#' @export +#' @keywords internal +#' +#' @examples +#' # Using a function +#' get_geom_defaults(geom_raster) +#' +#' # Using a layer includes static aesthetics as default +#' get_geom_defaults(geom_tile(fill = "white")) +#' +#' # Using a class name +#' get_geom_defaults("density_2d") +#' +#' # Using a class +#' get_geom_defaults(GeomPoint) +#' +#' # Changed theme +#' get_geom_defaults("point", theme(geom = element_geom(ink = "purple"))) +get_geom_defaults <- function(geom, theme = theme_get()) { + theme <- theme %||% list(geom = .default_geom_element) + + if (is.function(geom)) { + geom <- geom() + } + if (is.layer(geom)) { + data <- data_frame0(.id = 1L) + data <- geom$compute_geom_2(data = data, theme = theme) + data$.id <- NULL + return(data) + } + if (is.character(geom)) { + geom <- check_subclass(geom, "Geom") + } + if (inherits(geom, "Geom")) { + out <- geom$use_defaults(data = NULL, theme = theme) + return(out) + } + stop_input_type(geom, as_cli("a layer function, string or {.cls Geom} object")) +} + #' @rdname update_defaults #' @export reset_geom_defaults <- function() reset_defaults("geom") diff --git a/R/geom-density.R b/R/geom-density.R index c71a9f98eb..a4a7754f2e 100644 --- a/R/geom-density.R +++ b/R/geom-density.R @@ -93,7 +93,7 @@ geom_density <- function(mapping = NULL, data = NULL, #' @include geom-ribbon.R GeomDensity <- ggproto("GeomDensity", GeomArea, default_aes = defaults( - aes(fill = NA, weight = 1, colour = "black", alpha = NA), + aes(fill = NA, weight = 1, colour = from_theme(ink), alpha = NA), GeomArea$default_aes ) ) diff --git a/R/geom-density2d.R b/R/geom-density2d.R index e95a8b2c31..832546b563 100644 --- a/R/geom-density2d.R +++ b/R/geom-density2d.R @@ -106,7 +106,12 @@ geom_density2d <- geom_density_2d #' @usage NULL #' @export GeomDensity2d <- ggproto("GeomDensity2d", GeomPath, - default_aes = aes(colour = "#3366FF", linewidth = 0.5, linetype = 1, alpha = NA) + default_aes = aes( + colour = from_theme(accent), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ) ) #' @export diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index 7a0f9a5e08..54b7ce1f57 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -188,8 +188,14 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, required_aes = c("x", "y"), non_missing_aes = c("size", "shape"), - default_aes = aes(colour = "black", fill = "black", alpha = NA, - stroke = 1, linetype = "solid", weight = 1), + default_aes = aes( + colour = from_theme(ink), + fill = from_theme(ink), + alpha = NA, + stroke = from_theme(borderwidth * 2), + linetype = from_theme(linetype), + weight = 1 + ), setup_data = function(data, params) { data$width <- data$width %||% diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R index c02ab16ed9..3e40b20318 100644 --- a/R/geom-errorbar.R +++ b/R/geom-errorbar.R @@ -28,8 +28,14 @@ geom_errorbar <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomErrorbar <- ggproto("GeomErrorbar", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, width = 0.5, - alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + width = 0.5, + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-errorbarh.R b/R/geom-errorbarh.R index b23d125da4..c38b9b7cd6 100644 --- a/R/geom-errorbarh.R +++ b/R/geom-errorbarh.R @@ -51,8 +51,14 @@ geom_errorbarh <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomErrorbarh <- ggproto("GeomErrorbarh", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, height = 0.5, - alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + height = 0.5, + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-hex.R b/R/geom-hex.R index 8573d6d8ba..0eb777b808 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -107,9 +107,9 @@ GeomHex <- ggproto("GeomHex", Geom, default_aes = aes( colour = NA, - fill = "grey50", - linewidth = 0.5, - linetype = 1, + fill = from_theme(col_mix(ink, paper)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), alpha = NA ), diff --git a/R/geom-hline.R b/R/geom-hline.R index 6b80d0bb08..2650066183 100644 --- a/R/geom-hline.R +++ b/R/geom-hline.R @@ -56,7 +56,12 @@ GeomHline <- ggproto("GeomHline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), required_aes = "yintercept", draw_key = draw_key_path, diff --git a/R/geom-label.R b/R/geom-label.R index a265850f91..4168c98d94 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -56,8 +56,11 @@ GeomLabel <- ggproto("GeomLabel", Geom, required_aes = c("x", "y", "label"), default_aes = aes( - colour = "black", fill = "white", size = 3.88, angle = 0, - hjust = 0.5, vjust = 0.5, alpha = NA, family = "", fontface = 1, + colour = from_theme(ink), fill = from_theme(paper), + family = from_theme(family), + size = from_theme(fontsize), + angle = 0, + hjust = 0.5, vjust = 0.5, alpha = NA, fontface = 1, lineheight = 1.2 ), diff --git a/R/geom-linerange.R b/R/geom-linerange.R index 7144d0084a..83360800e2 100644 --- a/R/geom-linerange.R +++ b/R/geom-linerange.R @@ -91,7 +91,13 @@ geom_linerange <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomLinerange <- ggproto("GeomLinerange", Geom, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), draw_key = draw_key_linerange, diff --git a/R/geom-path.R b/R/geom-path.R index b63a1a1877..72c4f7154e 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -135,7 +135,12 @@ geom_path <- function(mapping = NULL, data = NULL, GeomPath <- ggproto("GeomPath", Geom, required_aes = c("x", "y"), - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), non_missing_aes = c("linewidth", "colour", "linetype"), @@ -181,7 +186,7 @@ GeomPath <- ggproto("GeomPath", Geom, attr <- dapply(munched, "group", function(df) { linetype <- unique0(df$linetype) data_frame0( - solid = identical(linetype, 1) || identical(linetype, "solid"), + solid = length(linetype) == 1 && (identical(linetype, "solid") || linetype == 1), constant = nrow(unique0(df[, names(df) %in% c("alpha", "colour", "linewidth", "linetype")])) == 1, .size = 1 ) diff --git a/R/geom-point.R b/R/geom-point.R index 26e6705398..3efa394c31 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -135,8 +135,9 @@ GeomPoint <- ggproto("GeomPoint", Geom, required_aes = c("x", "y"), non_missing_aes = c("size", "shape", "colour"), default_aes = aes( - shape = 19, colour = "black", size = 1.5, fill = NA, - alpha = NA, stroke = 0.5 + shape = from_theme(pointshape), + colour = from_theme(ink), size = from_theme(pointsize), fill = NA, + alpha = NA, stroke = from_theme(borderwidth) ), draw_panel = function(self, data, panel_params, coord, na.rm = FALSE) { diff --git a/R/geom-pointrange.R b/R/geom-pointrange.R index ccecfc0d95..d0e5194311 100644 --- a/R/geom-pointrange.R +++ b/R/geom-pointrange.R @@ -30,8 +30,12 @@ geom_pointrange <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomPointrange <- ggproto("GeomPointrange", Geom, - default_aes = aes(colour = "black", size = 0.5, linewidth = 0.5, linetype = 1, - shape = 19, fill = NA, alpha = NA, stroke = 1), + default_aes = aes( + colour = from_theme(ink), size = from_theme(pointsize / 3), + linewidth = from_theme(linewidth), linetype = from_theme(linetype), + shape = from_theme(pointshape), fill = NA, alpha = NA, + stroke = from_theme(borderwidth * 2) + ), draw_key = draw_key_pointrange, diff --git a/R/geom-polygon.R b/R/geom-polygon.R index 8e812e2737..a271ef5011 100644 --- a/R/geom-polygon.R +++ b/R/geom-polygon.R @@ -175,8 +175,13 @@ GeomPolygon <- ggproto("GeomPolygon", Geom, } }, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, - alpha = NA, subgroup = NULL), + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.2)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA, subgroup = NULL + ), handle_na = function(data, params) { data diff --git a/R/geom-quantile.R b/R/geom-quantile.R index bb3ff581ab..732ab62f8a 100644 --- a/R/geom-quantile.R +++ b/R/geom-quantile.R @@ -66,7 +66,7 @@ geom_quantile <- function(mapping = NULL, data = NULL, #' @include geom-path.R GeomQuantile <- ggproto("GeomQuantile", GeomPath, default_aes = defaults( - aes(weight = 1, colour = "#3366FF", linewidth = 0.5), + aes(weight = 1, colour = from_theme(accent)), GeomPath$default_aes ) ) diff --git a/R/geom-raster.R b/R/geom-raster.R index 2d4ecd85d2..94b1775373 100644 --- a/R/geom-raster.R +++ b/R/geom-raster.R @@ -44,7 +44,7 @@ geom_raster <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRaster <- ggproto("GeomRaster", Geom, - default_aes = aes(fill = "grey20", alpha = NA), + default_aes = aes(fill = from_theme(col_mix(ink, paper, 0.2)), alpha = NA), non_missing_aes = c("fill", "xmin", "xmax", "ymin", "ymax"), required_aes = c("x", "y"), diff --git a/R/geom-rect.R b/R/geom-rect.R index 0a9d4bdeed..8473474525 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -28,8 +28,11 @@ geom_rect <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRect <- ggproto("GeomRect", Geom, - default_aes = aes(colour = NA, fill = "grey35", linewidth = 0.5, linetype = 1, - alpha = NA), + default_aes = aes( + colour = NA, fill = from_theme(col_mix(ink, paper, 0.35)), + linewidth = from_theme(borderwidth), linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x|width|xmin|xmax", "y|height|ymin|ymax"), diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 549320deb9..470c013eee 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -96,7 +96,11 @@ geom_ribbon <- function(mapping = NULL, data = NULL, #' @usage NULL #' @export GeomRibbon <- ggproto("GeomRibbon", Geom, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.799)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), alpha = NA), required_aes = c("x|y", "ymin|xmin", "ymax|xmax"), @@ -292,8 +296,14 @@ geom_area <- function(mapping = NULL, data = NULL, stat = "align", #' @usage NULL #' @export GeomArea <- ggproto("GeomArea", GeomRibbon, - default_aes = aes(colour = NA, fill = "grey20", linewidth = 0.5, linetype = 1, - alpha = NA), + + default_aes = aes( + colour = NA, + fill = from_theme(col_mix(ink, paper, 0.2)), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-rug.R b/R/geom-rug.R index eca79951d8..d675474f43 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -153,7 +153,12 @@ GeomRug <- ggproto("GeomRug", Geom, gTree(children = inject(gList(!!!rugs))) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), draw_key = draw_key_path, diff --git a/R/geom-segment.R b/R/geom-segment.R index 303a040337..00d9eff87a 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -104,7 +104,14 @@ geom_segment <- function(mapping = NULL, data = NULL, GeomSegment <- ggproto("GeomSegment", Geom, required_aes = c("x", "y", "xend|yend"), non_missing_aes = c("linetype", "linewidth"), - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + draw_panel = function(self, data, panel_params, coord, arrow = NULL, arrow.fill = NULL, lineend = "butt", linejoin = "round", na.rm = FALSE) { data$xend <- data$xend %||% data$x diff --git a/R/geom-sf.R b/R/geom-sf.R index 457b8c272d..2e9aee78b8 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -126,14 +126,17 @@ GeomSf <- ggproto("GeomSf", Geom, fill = NULL, size = NULL, linewidth = NULL, - linetype = 1, + linetype = from_theme(linetype), alpha = NA, stroke = 0.5 ), use_defaults = function(self, data, params = list(), modifiers = aes(), - default_aes = NULL, ...) { - data <- ggproto_parent(Geom, self)$use_defaults(data, params, modifiers, default_aes) + default_aes = NULL, theme = NULL, ...) { + data <- ggproto_parent(Geom, self)$use_defaults( + data, params, modifiers, default_aes, theme = theme, ... + ) + # Early exit for e.g. legend data that don't have geometry columns if (!"geometry" %in% names(data)) { return(data) } @@ -156,24 +159,29 @@ GeomSf <- ggproto("GeomSf", Geom, if (length(index$point) > 0) { points <- GeomPoint$use_defaults( vec_slice(data, index$point), - params, modifiers + params, modifiers, theme = theme ) } if (length(index$line) > 0) { lines <- GeomLine$use_defaults( vec_slice(data, index$line), - params, modifiers + params, modifiers, theme = theme ) } other_default <- modify_list( GeomPolygon$default_aes, - list(fill = "grey90", colour = "grey35", linewidth = 0.2) + aes( + fill = from_theme(col_mix(ink, paper, 0.9)), + colour = from_theme(col_mix(ink, paper, 0.35)), + linewidth = from_theme(0.4 * borderwidth) + ) ) if (length(index$other) > 0) { others <- GeomPolygon$use_defaults( vec_slice(data, index$other), params, modifiers, - default_aes = other_default + default_aes = other_default, + theme = theme ) } if (length(index$collection) > 0) { @@ -185,7 +193,8 @@ GeomSf <- ggproto("GeomSf", Geom, collections <- Geom$use_defaults( vec_slice(data, index$collection), params, modifiers, - default_aes = modified + default_aes = modified, + theme = theme ) } diff --git a/R/geom-smooth.R b/R/geom-smooth.R index 8874ef491c..08e1099df0 100644 --- a/R/geom-smooth.R +++ b/R/geom-smooth.R @@ -168,8 +168,13 @@ GeomSmooth <- ggproto("GeomSmooth", Geom, required_aes = c("x", "y"), optional_aes = c("ymin", "ymax"), - default_aes = aes(colour = "#3366FF", fill = "grey60", linewidth = 1, - linetype = 1, weight = 1, alpha = 0.4), + default_aes = aes( + colour = from_theme(accent), + fill = from_theme(col_mix(ink, paper, 0.6)), + linewidth = from_theme(2 * linewidth), + linetype = from_theme(linetype), + weight = 1, alpha = 0.4 + ), rename_size = TRUE ) diff --git a/R/geom-text.R b/R/geom-text.R index a913227e4b..b7f0d3f320 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -216,8 +216,11 @@ GeomText <- ggproto("GeomText", Geom, non_missing_aes = "angle", default_aes = aes( - colour = "black", size = 3.88, angle = 0, hjust = 0.5, - vjust = 0.5, alpha = NA, family = "", fontface = 1, lineheight = 1.2 + colour = from_theme(ink), + family = from_theme(family), + size = from_theme(fontsize), + angle = 0, hjust = 0.5, + vjust = 0.5, alpha = NA, fontface = 1, lineheight = 1.2 ), draw_panel = function(data, panel_params, coord, parse = FALSE, diff --git a/R/geom-tile.R b/R/geom-tile.R index a5e3232080..e7bb6bc9e3 100644 --- a/R/geom-tile.R +++ b/R/geom-tile.R @@ -110,7 +110,7 @@ GeomTile <- ggproto("GeomTile", GeomRect, extra_params = c("na.rm"), setup_data = function(data, params) { - + data$width <- data$width %||% params$width %||% stats::ave(data$x, data$PANEL, FUN = function(x) resolution(x, FALSE, TRUE)) data$height <- data$height %||% params$height %||% @@ -122,8 +122,13 @@ GeomTile <- ggproto("GeomTile", GeomRect, ) }, - default_aes = aes(fill = "grey20", colour = NA, linewidth = 0.1, linetype = 1, - alpha = NA, width = NA, height = NA), + default_aes = aes( + fill = from_theme(col_mix(ink, paper, 0.2)), + colour = NA, + linewidth = from_theme(0.4 * borderwidth), + linetype = from_theme(bordertype), + alpha = NA, width = NA, height = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-violin.R b/R/geom-violin.R index 0ac6cd29df..17a2d40e94 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -197,8 +197,14 @@ GeomViolin <- ggproto("GeomViolin", Geom, draw_key = draw_key_polygon, - default_aes = aes(weight = 1, colour = "grey20", fill = "white", linewidth = 0.5, - alpha = NA, linetype = "solid"), + default_aes = aes( + weight = 1, + colour = from_theme(col_mix(ink, paper, 0.2)), + fill = from_theme(paper), + linewidth = from_theme(borderwidth), + linetype = from_theme(bordertype), + alpha = NA + ), required_aes = c("x", "y"), diff --git a/R/geom-vline.R b/R/geom-vline.R index 85cacf3e63..a9a50e6ff3 100644 --- a/R/geom-vline.R +++ b/R/geom-vline.R @@ -56,7 +56,13 @@ GeomVline <- ggproto("GeomVline", Geom, GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, - default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA), + default_aes = aes( + colour = from_theme(ink), + linewidth = from_theme(linewidth), + linetype = from_theme(linetype), + alpha = NA + ), + required_aes = "xintercept", draw_key = draw_key_vline, diff --git a/R/guide-.R b/R/guide-.R index 1856394ee3..4cb77ee7bb 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -265,11 +265,11 @@ Guide <- ggproto( # Function for extracting information from the layers. # Mostly applies to `guide_legend()` and `guide_binned()` - process_layers = function(self, params, layers, data = NULL) { - self$get_layer_key(params, layers, data) + process_layers = function(self, params, layers, data = NULL, theme = NULL) { + self$get_layer_key(params, layers, data, theme) }, - get_layer_key = function(params, layers, data = NULL) { + get_layer_key = function(params, layers, data = NULL, theme = NULL) { return(params) }, diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R index b11a969b8f..74fe2b2b3a 100644 --- a/R/guide-axis-stack.R +++ b/R/guide-axis-stack.R @@ -134,7 +134,7 @@ GuideAxisStack <- ggproto( }, # Just loops through guides - get_layer_key = function(params, layers) { + get_layer_key = function(params, layers, ...) { for (i in seq_along(params$guides)) { params$guide_params[[i]] <- params$guides[[i]]$get_layer_key( params = params$guide_params[[i]], diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index 5154c67c07..d03484edae 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -269,7 +269,7 @@ GuideColourbar <- ggproto( return(list(guide = self, params = params)) }, - get_layer_key = function(params, layers, data = NULL) { + get_layer_key = function(params, layers, data = NULL, theme = NULL) { params }, diff --git a/R/guide-legend.R b/R/guide-legend.R index 6e3524b5bd..6f0b98ac33 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -209,7 +209,7 @@ GuideLegend <- ggproto( }, # Arrange common data for vertical and horizontal legends - process_layers = function(self, params, layers, data = NULL) { + process_layers = function(self, params, layers, data = NULL, theme = NULL) { include <- vapply(layers, function(layer) { aes <- matched_aes(layer, params) @@ -220,10 +220,10 @@ GuideLegend <- ggproto( return(NULL) } - self$get_layer_key(params, layers[include], data[include]) + self$get_layer_key(params, layers[include], data[include], theme) }, - get_layer_key = function(params, layers, data) { + get_layer_key = function(params, layers, data, theme = NULL) { # Return empty guides as-is if (nrow(params$key) < 1) { @@ -242,7 +242,7 @@ GuideLegend <- ggproto( single_params <- layer$aes_params[single_params] # Use layer to populate defaults - key <- layer$compute_geom_2(key, single_params) + key <- layer$compute_geom_2(key, single_params, theme) # Filter non-existing levels if (length(matched_aes) > 0) { diff --git a/R/guide-old.R b/R/guide-old.R index b2a137fffd..de870965fd 100644 --- a/R/guide-old.R +++ b/R/guide-old.R @@ -103,7 +103,7 @@ GuideOld <- ggproto( guide_transform(params, coord, panel_params) }, - process_layers = function(self, params, layers, data = NULL) { + process_layers = function(self, params, layers, data = NULL, theme = NULL) { guide_geom(params, layers, default_mapping = NULL) }, diff --git a/R/guides-.R b/R/guides-.R index d45f55e892..fcd65bb94a 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -285,7 +285,7 @@ Guides <- ggproto( # # The resulting guide is then drawn in ggplot_gtable - build = function(self, scales, layers, labels, layer_data) { + build = function(self, scales, layers, labels, layer_data, theme) { # Empty guides list custom <- self$get_custom() @@ -312,7 +312,7 @@ Guides <- ggproto( # Merge and process layers guides$merge() - guides$process_layers(layers, layer_data) + guides$process_layers(layers, layer_data, theme) if (length(guides$guides) == 0) { return(no_guides) } @@ -460,9 +460,9 @@ Guides <- ggproto( }, # Loop over guides to let them extract information from layers - process_layers = function(self, layers, data = NULL) { + process_layers = function(self, layers, data = NULL, theme = NULL) { self$params <- Map( - function(guide, param) guide$process_layers(param, layers, data), + function(guide, param) guide$process_layers(param, layers, data, theme), guide = self$guides, param = self$params ) diff --git a/R/layer-sf.R b/R/layer-sf.R index 437ecef3df..3a282e734f 100644 --- a/R/layer-sf.R +++ b/R/layer-sf.R @@ -72,6 +72,7 @@ LayerSf <- ggproto("LayerSf", Layer, }, compute_geom_2 = function(self, data, params = self$aes_params, ...) { + if (empty(data)) return(data) data$geometry <- data$geometry %||% self$computed_geom_params$legend ggproto_parent(Layer, self)$compute_geom_2(data, params, ...) } diff --git a/R/layer.R b/R/layer.R index eba8666de4..8acb438c9e 100644 --- a/R/layer.R +++ b/R/layer.R @@ -293,8 +293,9 @@ Layer <- ggproto("Layer", NULL, set <- names(aesthetics) %in% names(self$aes_params) calculated <- is_calculated_aes(aesthetics, warn = TRUE) modifiers <- is_scaled_aes(aesthetics) + themed <- is_themed_aes(aesthetics) - aesthetics <- aesthetics[!set & !calculated & !modifiers] + aesthetics <- aesthetics[!set & !calculated & !modifiers & !themed] # Override grouping if set in layer if (!is.null(self$geom_params$group)) { @@ -442,14 +443,14 @@ Layer <- ggproto("Layer", NULL, self$position$compute_layer(data, params, layout) }, - compute_geom_2 = function(self, data, params = self$aes_params, ...) { + compute_geom_2 = function(self, data, params = self$aes_params, theme = NULL, ...) { # Combine aesthetics, defaults, & params if (empty(data)) return(data) aesthetics <- self$computed_mapping - modifiers <- aesthetics[is_scaled_aes(aesthetics) | is_staged_aes(aesthetics)] + modifiers <- aesthetics[is_scaled_aes(aesthetics) | is_staged_aes(aesthetics) | is_themed_aes(aesthetics)] - self$geom$use_defaults(data, params, modifiers, ...) + self$geom$use_defaults(data, params, modifiers, theme = theme, ...) }, finish_statistics = function(self, data) { diff --git a/R/plot-build.R b/R/plot-build.R index 23d2a11b0f..36f33616fd 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -100,11 +100,14 @@ ggplot_build.ggplot <- function(plot) { # Hand off position guides to layout layout$setup_panel_guides(plot$guides, plot$layers) + # Complete the plot's theme + plot$theme <- plot_theme(plot) + # Train and map non-position scales and guides npscales <- scales$non_position_scales() if (npscales$n() > 0) { lapply(data, npscales$train_df) - plot$guides <- plot$guides$build(npscales, plot$layers, plot$labels, data) + plot$guides <- plot$guides$build(npscales, plot$layers, plot$labels, data, plot$theme) data <- lapply(data, npscales$map_df) } else { # Only keep custom guides if there are no non-position scales @@ -113,7 +116,10 @@ ggplot_build.ggplot <- function(plot) { data <- .expose_data(data) # Fill in defaults etc. - data <- by_layer(function(l, d) l$compute_geom_2(d), layers, data, "setting up geom aesthetics") + data <- by_layer( + function(l, d) l$compute_geom_2(d, theme = plot$theme), + layers, data, "setting up geom aesthetics" + ) # Let layer stat have a final say before rendering data <- by_layer(function(l, d) l$finish_statistics(d), layers, data, "finishing layer stat") @@ -199,7 +205,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot <- data$plot layout <- data$layout data <- data$data - theme <- plot_theme(plot) + theme <- plot$theme geom_grobs <- by_layer(function(l, d) l$draw_geom(d, layout), plot$layers, data, "converting geom to grob") diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 522c978c68..77b36e243e 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -143,6 +143,14 @@ theme_grey <- function(base_size = 11, base_family = "", spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), + geom = element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = base_line_size, borderwidth = base_line_size, + linetype = 1L, bordertype = 1L, + family = base_family, fontsize = base_size, + pointsize = (base_size / 11) * 1.5, pointshape = 19 + ), + axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, @@ -576,6 +584,14 @@ theme_test <- function(base_size = 11, base_family = "", title = element_text(family = header_family), spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), + geom = element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = base_line_size, borderwidth = base_line_size, + family = base_family, fontsize = base_size, + linetype = 1L, + pointsize = (base_size / 11) * 1.5, pointshape = 19 + ), + axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, diff --git a/R/theme-elements.R b/R/theme-elements.R index 4a0bfce774..747bb0cf78 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -8,14 +8,15 @@ #' - `element_rect()`: borders and backgrounds. #' - `element_line()`: lines. #' - `element_text()`: text. +#' - `element_geom()`: defaults for drawing layers. #' #' `rel()` is used to specify sizes relative to the parent, #' `margin()` is used to specify the margins of elements. #' #' @param fill Fill colour. #' @param colour,color Line/border colour. Color is an alias for colour. -#' @param linewidth Line/border size in mm. -#' @param size text size in pts. +#' @param linewidth,borderwidth Line/border size in mm. +#' @param size,fontsize text size in pts. #' @param arrow.fill Fill colour for arrows. #' @param inherit.blank Should this element inherit the existence of an #' `element_blank` among its parents? If `TRUE` the existence of @@ -48,6 +49,14 @@ #' linewidth = 1 #' ) #' ) +#' +#' ggplot(mpg, aes(displ, hwy)) + +#' geom_point() + +#' geom_smooth(formula = y ~ x, method = "lm") + +#' theme(geom = element_geom( +#' ink = "red", accent = "black", +#' pointsize = 1, linewidth = 2 +#' )) #' @name element #' @aliases NULL NULL @@ -81,10 +90,10 @@ element_rect <- function(fill = NULL, colour = NULL, linewidth = NULL, #' @export #' @rdname element -#' @param linetype Line type. An integer (0:8), a name (blank, solid, -#' dashed, dotted, dotdash, longdash, twodash), or a string with -#' an even number (up to eight) of hexadecimal digits which give the -#' lengths in consecutive positions in the string. +#' @param linetype,bordertype Line type for lines and borders respectively. An +#' integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, +#' twodash), or a string with an even number (up to eight) of hexadecimal +#' digits which give the lengths in consecutive positions in the string. #' @param lineend Line end Line end style (round, butt, square) #' @param arrow Arrow specification, as created by [grid::arrow()] element_line <- function(colour = NULL, linewidth = NULL, linetype = NULL, @@ -148,6 +157,50 @@ element_text <- function(family = NULL, face = NULL, colour = NULL, ) } +#' @param ink Foreground colour. +#' @param paper Background colour. +#' @param accent Accent colour. +#' @param pointsize Size for points in mm. +#' @param pointshape Shape for points (1-25). +#' @export +#' @rdname element +element_geom <- function( + # colours + ink = NULL, paper = NULL, accent = NULL, + # linewidth + linewidth = NULL, borderwidth = NULL, + # linetype + linetype = NULL, bordertype = NULL, + # text + family = NULL, fontsize = NULL, + # points + pointsize = NULL, pointshape = NULL) { + + if (!is.null(fontsize)) { + fontsize <- fontsize / .pt + } + + structure( + list( + ink = ink, + paper = paper, + accent = accent, + linewidth = linewidth, borderwidth = borderwidth, + linetype = linetype, bordertype = bordertype, + family = family, fontsize = fontsize, + pointsize = pointsize, pointshape = pointshape + ), + class = c("element_geom", "element") + ) +} + +.default_geom_element <- element_geom( + ink = "black", paper = "white", accent = "#3366FF", + linewidth = 0.5, borderwidth = 0.5, + linetype = 1L, bordertype = 1L, + family = "", fontsize = 11, + pointsize = 1.5, pointshape = 19 +) #' @export print.element <- function(x, ...) utils::str(x) @@ -429,6 +482,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { line = el_def("element_line"), rect = el_def("element_rect"), text = el_def("element_text"), + geom = el_def("element_geom"), title = el_def("element_text", "text"), spacing = el_def("unit"), margins = el_def(c("margin", "unit")), diff --git a/R/theme.R b/R/theme.R index 7e8a794a11..43c379f9b6 100644 --- a/R/theme.R +++ b/R/theme.R @@ -25,6 +25,7 @@ #' @param text all text elements ([element_text()]) #' @param title all title elements: plot, axes, legends ([element_text()]; #' inherits from `text`) +#' @param geom defaults for geoms ([element_geom()]) #' @param spacing all spacings ([`unit()`][grid::unit]) #' @param margins all margins ([margin()]) #' @param aspect.ratio aspect ratio of the panel @@ -315,6 +316,7 @@ theme <- function(..., rect, text, title, + geom, spacing, margins, aspect.ratio, diff --git a/R/utilities.R b/R/utilities.R index 6a7ca5921d..2585de5acc 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -843,6 +843,24 @@ as_unordered_factor <- function(x) { x } +# Shim for scales/#424 +col_mix <- function(a, b, amount = 0.5) { + input <- vec_recycle_common(a = a, b = b, amount = amount) + a <- grDevices::col2rgb(input$a, TRUE) + b <- grDevices::col2rgb(input$b, TRUE) + new <- (a * (1 - input$amount) + b * input$amount) + grDevices::rgb( + new["red", ], new["green", ], new["blue", ], + alpha = new["alpha", ], maxColorValue = 255 + ) +} + +on_load({ + if ("col_mix" %in% getNamespaceExports("scales")) { + col_mix <- scales::col_mix + } +}) + # TODO: Replace me if rlang/#1730 gets implemented # Similar to `rlang::check_installed()` but returns boolean and misses # features such as versions, comparisons and using {pak}. diff --git a/man/aes_eval.Rd b/man/aes_eval.Rd index 827bc6a876..11b8d2f1bd 100644 --- a/man/aes_eval.Rd +++ b/man/aes_eval.Rd @@ -5,6 +5,7 @@ \alias{after_stat} \alias{stat} \alias{after_scale} +\alias{from_theme} \alias{stage} \title{Control aesthetic evaluation} \usage{ @@ -16,6 +17,8 @@ after_stat(x) after_scale(x) +from_theme(x) + stage(start = NULL, after_stat = NULL, after_scale = NULL) } \arguments{ @@ -127,6 +130,14 @@ ggplot(mpg, aes(class, displ)) + ) }\if{html}{\out{}} } + +\subsection{Theme access}{ + +The \code{from_theme()} function can be used to acces the \code{\link[=element_geom]{element_geom()}} +fields of the \code{theme(geom)} argument. Using \code{aes(colour = from_theme(ink))} +and \code{aes(colour = from_theme(accent))} allows swapping between foreground and +accent colours. +} } \examples{ diff --git a/man/element.Rd b/man/element.Rd index 2a4f68e2eb..adb1b7eb22 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -5,6 +5,7 @@ \alias{element_rect} \alias{element_line} \alias{element_text} +\alias{element_geom} \alias{rel} \alias{margin} \title{Theme elements} @@ -48,6 +49,20 @@ element_text( inherit.blank = FALSE ) +element_geom( + ink = NULL, + paper = NULL, + accent = NULL, + linewidth = NULL, + borderwidth = NULL, + linetype = NULL, + bordertype = NULL, + family = NULL, + fontsize = NULL, + pointsize = NULL, + pointshape = NULL +) + rel(x) margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") @@ -57,12 +72,12 @@ margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") \item{colour, color}{Line/border colour. Color is an alias for colour.} -\item{linewidth}{Line/border size in mm.} +\item{linewidth, borderwidth}{Line/border size in mm.} -\item{linetype}{Line type. An integer (0:8), a name (blank, solid, -dashed, dotted, dotdash, longdash, twodash), or a string with -an even number (up to eight) of hexadecimal digits which give the -lengths in consecutive positions in the string.} +\item{linetype, bordertype}{Line type for lines and borders respectively. An +integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, +twodash), or a string with an even number (up to eight) of hexadecimal +digits which give the lengths in consecutive positions in the string.} \item{inherit.blank}{Should this element inherit the existence of an \code{element_blank} among its parents? If \code{TRUE} the existence of @@ -70,7 +85,7 @@ a blank element among its parents will cause this element to be blank as well. If \code{FALSE} any blank parent element will be ignored when calculating final element state.} -\item{size}{text size in pts.} +\item{size, fontsize}{text size in pts.} \item{lineend}{Line end Line end style (round, butt, square)} @@ -98,6 +113,16 @@ side of the text facing towards the center of the plot.} rectangle behind the complete text area, and a point where each label is anchored.} +\item{ink}{Foreground colour.} + +\item{paper}{Background colour.} + +\item{accent}{Accent colour.} + +\item{pointsize}{Size for points in mm.} + +\item{pointshape}{Shape for points (1-25).} + \item{x}{A single number specifying size relative to parent element.} \item{t, r, b, l}{Dimensions of each margin. (To remember order, think trouble).} @@ -116,6 +141,7 @@ specify the display of how non-data components of the plot are drawn. \item \code{element_rect()}: borders and backgrounds. \item \code{element_line()}: lines. \item \code{element_text()}: text. +\item \code{element_geom()}: defaults for drawing layers. } \code{rel()} is used to specify sizes relative to the parent, @@ -146,4 +172,12 @@ plot + theme( linewidth = 1 ) ) + +ggplot(mpg, aes(displ, hwy)) + + geom_point() + + geom_smooth(formula = y ~ x, method = "lm") + + theme(geom = element_geom( + ink = "red", accent = "black", + pointsize = 1, linewidth = 2 + )) } diff --git a/man/geom_boxplot.Rd b/man/geom_boxplot.Rd index 918b082d4b..3fc39d212b 100644 --- a/man/geom_boxplot.Rd +++ b/man/geom_boxplot.Rd @@ -15,8 +15,8 @@ geom_boxplot( outlier.colour = NULL, outlier.color = NULL, outlier.fill = NULL, - outlier.shape = 19, - outlier.size = 1.5, + outlier.shape = NULL, + outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, diff --git a/man/get_geom_defaults.Rd b/man/get_geom_defaults.Rd new file mode 100644 index 0000000000..a39f80d720 --- /dev/null +++ b/man/get_geom_defaults.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/geom-defaults.R +\name{get_geom_defaults} +\alias{get_geom_defaults} +\title{Resolve and get geom defaults} +\usage{ +get_geom_defaults(geom, theme = theme_get()) +} +\arguments{ +\item{geom}{Some definition of a geom: +\itemize{ +\item A \code{function} that creates a layer, e.g. \code{geom_path()}. +\item A layer created by such function +\item A string naming a geom class in snake case without the \code{geom_}-prefix, +e.g. \code{"contour_filled"}. +\item A geom class object. +}} + +\item{theme}{A \code{\link{theme}} object. Defaults to the current global theme.} +} +\value{ +A list of aesthetics +} +\description{ +Resolve and get geom defaults +} +\examples{ +# Using a function +get_geom_defaults(geom_raster) + +# Using a layer includes static aesthetics as default +get_geom_defaults(geom_tile(fill = "white")) + +# Using a class name +get_geom_defaults("density_2d") + +# Using a class +get_geom_defaults(GeomPoint) + +# Changed theme +get_geom_defaults("point", theme(geom = element_geom(ink = "purple"))) +} +\keyword{internal} diff --git a/man/theme.Rd b/man/theme.Rd index 1f12df3ba9..829254ecdf 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -10,6 +10,7 @@ theme( rect, text, title, + geom, spacing, margins, aspect.ratio, @@ -161,6 +162,8 @@ these should also be defined in the \verb{element tree} argument. \link[rlang:sp \item{title}{all title elements: plot, axes, legends (\code{\link[=element_text]{element_text()}}; inherits from \code{text})} +\item{geom}{defaults for geoms (\code{\link[=element_geom]{element_geom()}})} + \item{spacing}{all spacings (\code{\link[grid:unit]{unit()}})} \item{margins}{all margins (\code{\link[=margin]{margin()}})} diff --git a/man/update_defaults.Rd b/man/update_defaults.Rd index 334dffed8e..777182e24f 100644 --- a/man/update_defaults.Rd +++ b/man/update_defaults.Rd @@ -29,6 +29,10 @@ reset_stat_defaults() \description{ Functions to update or reset the default aesthetics of geoms and stats. } +\note{ +Please note that geom defaults can be set \emph{en masse} via the \code{theme(geom)} +argument. +} \examples{ # updating a geom's default aesthetic settings diff --git a/revdep/README.md b/revdep/README.md index d6c6b43f5e..8976e81c90 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,68 +1,57 @@ # Revdeps -## Failed to check (146) +## Failed to check (132) |package |version |error |warning |note | |:----------------------|:----------|:------|:-------|:----| |abctools |1.1.7 |1 | | | -|AnanseSeurat |? | | | | |animalEKF |1.2 |1 | | | |ANOM |0.5 |1 | | | -|APackOfTheClones |? | | | | |atRisk |0.1.0 |1 | | | |AutoScore |1.0.0 |1 | | | |bayesdfa |1.3.3 |1 | | | |bayesDP |1.3.6 |1 | | | |BayesianFactorZoo |0.0.0.2 |1 | | | -|BCClong |1.0.2 |1 | |1 | +|BayesSurvive |0.0.2 |1 | | | +|BCClong |1.0.3 |1 | | | +|BGGM |2.1.3 |1 | | | |binsreg |1.0 |1 | | | |bmstdr |0.7.9 |1 | | | |bspcov |1.0.0 |1 | | | -|CalibrationCurves |2.0.1 |1 | | | -|Canek |? | | | | +|BuyseTest |3.0.4 |1 | | | +|CalibrationCurves |2.0.3 |1 | | | |CARBayesST |4.0 |1 | | | |CaseBasedReasoning |0.3 |1 | | | -|cellpypes |? | | | | |CGPfunctions |0.6.3 |1 | | | -|CIARA |? | | | | -|ClustAssess |? | | | | -|clustree |? | | | | |cmprskcoxmsm |0.2.1 |1 | | | -|combiroc |? | | | | -|conos |? | | | | |contrast |0.24.2 |1 | | | -|countland |? | | | | |coxed |0.3.3 |1 | | | -|CRMetrics |? | | | | +|CRMetrics |0.3.0 |1 | | | |csmpv |1.0.3 |1 | | | |ctsem |3.10.0 |1 | | | -|CytoSimplex |? | | | | |DepthProc |2.1.5 |1 | | | -|DIscBIO |? | | | | -|DR.SC |? | | | | -|dyngen |? | | | | -|EcoEnsemble |1.0.5 |1 | | | +|DR.SC |3.4 |1 | | | +|DynNom |5.1 |1 | | | +|easybgm |0.1.2 |1 | | | |ecolottery |1.0.0 |1 | | | |EpiEstim |2.2-4 |1 | | | |evolqg |0.3-4 |1 | | | |ForecastComb |1.3.1 |1 | | | |gapfill |0.9.6-1 |1 | |1 | |GeomComb |1.0 |1 | | | -|[geostan](failures.md#geostan)|0.6.1 |__+1__ | |-3 | -|ggrcs |0.3.8 |1 | | | +|ggrcs |0.4.0 |1 | | | |ggrisk |1.3 |1 | | | -|ggsector |? | | | | |gJLS2 |0.2.0 |1 | | | -|grandR |? | | | | |Greg |2.0.2 |1 | | | |greport |0.7-4 |1 | | | -|harmony |? | | | | |hettx |0.1.3 |1 | | | |hIRT |0.3.0 |1 | | | |Hmsc |3.0-13 |1 | | | +|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | |iNZightPlots |2.15.3 |1 | | | |iNZightRegression |1.3.4 |1 | | | |IRexamples |0.0.4 |1 | | | +|jmBIG |0.1.2 |1 | | | |joineRML |0.4.6 |1 | | | |JWileymisc |1.4.1 |1 | | | |kmc |0.4-2 |1 | | | @@ -74,11 +63,10 @@ |MendelianRandomization |0.10.0 |1 | | | |MetabolicSurv |1.1.2 |1 | | | |miWQS |0.4.4 |1 | | | -|mlmts |1.1.1 |1 | | | |MRZero |0.2.0 |1 | | | |Multiaovbay |0.1.0 |1 | | | |multilevelTools |0.1.1 |1 | | | -|multinma |0.7.0 |1 | | | +|multinma |0.7.1 |1 | | | |NCA |4.0.1 |1 | | | |netcmc |1.0.2 |1 | | | |NetworkChange |0.8 |1 | | | @@ -92,11 +80,12 @@ |pould |1.0.1 |1 | | | |powerly |1.8.6 |1 | | | |pre |1.0.7 |1 | | | -|PRECAST |? | | | | |ProFAST |? | | | | +|psbcSpeedUp |2.0.7 |1 | | | |pscore |0.4.0 |1 | | | |psfmi |1.4.0 |1 | | | -|qreport |1.0-0 |1 | | | +|qPCRtools |1.0.1 |1 | | | +|qreport |1.0-1 |1 | | | |qris |1.1.1 |1 | | | |qte |1.3.1 |1 | | | |quid |0.0.1 |1 | | | @@ -104,35 +93,33 @@ |RcmdrPlugin.RiskDemo |3.2 |1 | | | |rddtools |1.6.0 |1 | | | |riskRegression |2023.12.21 |1 | | | -|rliger |? | | | | -|rms |6.8-0 |1 | |1 | -|rmsb |1.1-0 |1 | | | +|rms |6.8-1 |1 | |1 | +|rmsb |1.1-1 |1 | | | |robmed |1.0.2 |1 | | | |robmedExtra |0.1.0 |1 | | | |RPPanalyzer |1.4.9 |1 | | | -|rstanarm |2.32.1 |1 | | | -|scCustomize |? | | | | -|SCdeconR |? | | | | -|scDiffCom |? | | | | -|scGate |? | | | | -|scMappR |? | | | | -|SCORPIUS |? | | | | -|scpoisson |? | | | | -|SCpubr |? | | | | -|scRNAstat |? | | | | +|RQdeltaCT |1.3.0 |1 | | | +|scCustomize |2.1.2 |1 | |1 | +|SCdeconR |1.0.0 |1 | | | +|scGate |1.6.2 |1 | | | +|SCIntRuler |0.99.6 |1 | | | +|scMappR |1.0.11 |1 | | | +|scpi |2.2.5 |1 | | | +|scRNAstat |0.1.1 |1 | | | |sectorgap |0.1.0 |1 | | | |SEERaBomb |2019.2 |1 | | | |semicmprskcoxmsm |0.2.0 |1 | | | |SensMap |0.7 |1 | | | -|Signac |? | | | | +|Seurat |5.1.0 |1 | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|Signac |1.13.0 |1 | | | |SimplyAgree |0.2.0 |1 | | | |sMSROC |0.1.2 |1 | | | |SNPassoc |2.1-0 |1 | | | |snplinkage |? | | | | -|SoupX |? | | | | -|SpaDES.core |2.0.5 |1 | | | +|SoupX |1.6.2 |1 | | | |sparsereg |1.2 |1 | | | -|SPECK |? | | | | |spikeSlabGAM |1.1-19 |1 | | | |statsr |0.3.0 |1 | | | |streamDAG |? | | | | @@ -141,82 +128,259 @@ |tempted |0.1.1 |1 | | | |[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | |tidyEdSurvey |0.1.3 |1 | | | -|tidyseurat |? | | | | +|tidyseurat |0.8.0 |1 | | | |tidyvpc |1.5.1 |1 | | | -|treefit |? | | | | |TriDimRegression |1.0.2 |1 | | | |TSrepr |1.1.0 |1 | | | |twang |2.6 |1 | | | -|valse |0.1-0 |1 | | | |vdg |1.2.3 |1 | | | +|visa |0.1.0 |1 | | | |WRTDStidal |1.1.4 |1 | | | -## New problems (64) +## New problems (242) -|package |version |error |warning |note | -|:---------------|:--------|:--------|:--------|:--------| -|[asmbPLS](problems.md#asmbpls)|1.0.0 | |__+1__ |1 | -|[bdl](problems.md#bdl)|1.0.5 | |__+1__ | | -|[bdscale](problems.md#bdscale)|2.0.0 |__+1__ | |__+1__ | -|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | -|[brolgar](problems.md#brolgar)|1.0.1 |__+2__ | |__+1__ | -|[bSi](problems.md#bsi)|1.0.0 | |__+1__ | | -|[CausalImpact](problems.md#causalimpact)|1.3.0 |__+2__ | |__+1__ | -|[ClusROC](problems.md#clusroc)|1.0.2 | |__+1__ | | -|[clustEff](problems.md#clusteff)|0.3.1 | |__+1__ | | -|[CLVTools](problems.md#clvtools)|0.10.0 |__+1__ | |1 __+1__ | -|[coda4microbiome](problems.md#coda4microbiome)|0.2.3 | |__+1__ | | -|[CompAREdesign](problems.md#comparedesign)|2.3.1 | |__+1__ | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[Coxmos](problems.md#coxmos)|1.0.2 |1 |__+1__ |1 | -|[csa](problems.md#csa)|0.7.1 | |__+1__ | | -|[deeptime](problems.md#deeptime)|1.1.1 |__+2__ | | | -|[DEGRE](problems.md#degre)|0.2.0 | |__+1__ | | -|[did](problems.md#did)|2.1.2 | |1 __+1__ | | -|[EpiCurve](problems.md#epicurve)|2.4-2 |__+1__ | |1 __+1__ | -|[epiR](problems.md#epir)|2.0.74 |__+1__ | |__+1__ | -|[FuncNN](problems.md#funcnn)|1.0 | |__+1__ |1 | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | -|[ggfortify](problems.md#ggfortify)|0.4.17 | | |__+1__ | -|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | -|[ggheatmap](problems.md#ggheatmap)|2.2 | |__+1__ | | -|[ggScatRidges](problems.md#ggscatridges)|0.1.1 | |__+1__ | | -|[GimmeMyPlot](problems.md#gimmemyplot)|0.1.0 | |__+1__ | | -|[hilldiv](problems.md#hilldiv)|1.5.1 | |__+1__ | | -|[hJAM](problems.md#hjam)|1.0.0 | |__+1__ | | -|[iglu](problems.md#iglu)|4.0.0 |__+2__ | |__+1__ | -|[ImFoR](problems.md#imfor)|0.1.0 | |__+1__ | | -|[iNEXT.4steps](problems.md#inext4steps)|1.0.0 | |__+1__ | | -|[insane](problems.md#insane)|1.0.3 | |__+1__ | | -|[MarketMatching](problems.md#marketmatching)|1.2.1 |__+1__ | | | -|[mc2d](problems.md#mc2d)|0.2.0 | |__+1__ |1 | -|[MetaIntegrator](problems.md#metaintegrator)|2.1.3 | |__+1__ |2 | -|[MF.beta4](problems.md#mfbeta4)|1.0.3 | |1 __+1__ | | -|[MIMSunit](problems.md#mimsunit)|0.11.2 |__+1__ | | | -|[missingHE](problems.md#missinghe)|1.5.0 | |__+1__ |1 | -|[MSPRT](problems.md#msprt)|3.0 | |__+1__ |1 | -|[nzelect](problems.md#nzelect)|0.4.0 |__+1__ | |2 | -|[OenoKPM](problems.md#oenokpm)|2.4.1 | |__+1__ | | -|[posologyr](problems.md#posologyr)|1.2.4 |__+1__ | | | -|[qicharts](problems.md#qicharts)|0.5.8 |__+1__ | | | -|[qicharts2](problems.md#qicharts2)|0.7.5 |__+1__ | |__+1__ | -|[QuadratiK](problems.md#quadratik)|1.1.0 | |__+1__ |1 | -|[RCTrep](problems.md#rctrep)|1.2.0 | |__+1__ | | -|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | -|[SCOUTer](problems.md#scouter)|1.0.0 | |__+1__ | | -|[sievePH](problems.md#sieveph)|1.0.4 | |__+1__ | | -|[SouthParkRshiny](problems.md#southparkrshiny)|1.0.0 | |__+1__ |2 | -|[SqueakR](problems.md#squeakr)|1.3.0 |1 |__+1__ |1 | -|[survminer](problems.md#survminer)|0.4.9 | |__+1__ |1 | -|[symptomcheckR](problems.md#symptomcheckr)|0.1.3 | |__+1__ | | -|[tcgaViz](problems.md#tcgaviz)|1.0.2 | |__+1__ | | -|[TestGardener](problems.md#testgardener)|3.3.3 | |__+1__ | | -|[tis](problems.md#tis)|1.39 |__+1__ | |1 | -|[UniprotR](problems.md#uniprotr)|2.4.0 | |__+1__ | | -|[VALERIE](problems.md#valerie)|1.1.0 | |__+1__ |1 | -|[vannstats](problems.md#vannstats)|1.3.4.14 | |__+1__ | | -|[vici](problems.md#vici)|0.7.3 | |__+1__ | | -|[Wats](problems.md#wats)|1.0.1 |__+2__ | |__+1__ | -|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|package |version |error |warning |note | +|:------------------|:-------|:--------|:-------|:--------| +|[activAnalyzer](problems.md#activanalyzer)|2.1.1 |__+1__ | |1 __+1__ | +|[actxps](problems.md#actxps)|1.5.0 |__+1__ | |__+1__ | +|[AeRobiology](problems.md#aerobiology)|2.0.1 |1 | |__+1__ | +|[agricolaeplotr](problems.md#agricolaeplotr)|0.5.0 |__+1__ | | | +|[AnalysisLin](problems.md#analysislin)|0.1.2 |__+1__ | | | +|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | | +|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 | +|[aplot](problems.md#aplot)|0.2.3 |__+1__ | | | +|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | +|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+1__ | |1 | +|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | +|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | |__+1__ | +|[bartMan](problems.md#bartman)|0.1.0 |__+1__ | | | +|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | +|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | +|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+2__ | |__+1__ | +|[BayesMallows](problems.md#bayesmallows)|2.2.1 |__+1__ | |1 | +|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+1__ | |1 | +|[bayestestR](problems.md#bayestestr)|0.13.2 |1 __+1__ | | | +|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | +|[besthr](problems.md#besthr)|0.3.2 |__+2__ | |__+1__ | +|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | +|[biodosetools](problems.md#biodosetools)|3.6.1 |__+1__ | | | +|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | | +|[braidReports](problems.md#braidreports)|0.5.4 |__+1__ | | | +|[breathtestcore](problems.md#breathtestcore)|0.8.7 |__+1__ | | | +|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | +|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | +|[cartographr](problems.md#cartographr)|0.2.2 |__+1__ | |1 | +|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | +|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | +|[chillR](problems.md#chillr)|0.75 |__+1__ | | | +|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | +|[circhelp](problems.md#circhelp)|1.1 |__+2__ | |__+1__ | +|[clifro](problems.md#clifro)|3.2-5 |__+1__ | | | +|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | +|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | +|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | +|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | | +|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 | +|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | +|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | +|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | +|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | +|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | +|[cubble](problems.md#cubble)|0.3.1 |__+1__ | |1 __+1__ | +|[deeptime](problems.md#deeptime)|1.1.1 |__+1__ | | | +|[distributional](problems.md#distributional)|0.4.0 |__+1__ | | | +|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | +|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | +|[entropart](problems.md#entropart)|1.6-13 |__+2__ | |__+1__ | +|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 | +|[esci](problems.md#esci)|1.0.3 |__+2__ | | | +|[evalITR](problems.md#evalitr)|1.0.0 |1 | |1 __+1__ | +|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | | +|[EvoPhylo](problems.md#evophylo)|0.3.2 |1 __+1__ | |1 __+1__ | +|[expirest](problems.md#expirest)|0.1.6 |__+1__ | | | +|[explainer](problems.md#explainer)|1.0.1 |__+1__ | |1 | +|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | | +|[ezplot](problems.md#ezplot)|0.7.13 |__+2__ | |__+1__ | +|[fable.prophet](problems.md#fableprophet)|0.1.0 |__+1__ | |1 __+1__ | +|[fabletools](problems.md#fabletools)|0.4.2 |__+2__ | | | +|[factoextra](problems.md#factoextra)|1.0.7 |__+1__ | | | +|[fairmodels](problems.md#fairmodels)|1.2.1 |__+1__ | | | +|[fddm](problems.md#fddm)|1.0-2 |__+1__ | |1 | +|[feasts](problems.md#feasts)|0.3.2 |__+1__ | | | +|[ffp](problems.md#ffp)|0.2.2 |__+1__ | | | +|[fido](problems.md#fido)|1.1.1 |1 __+2__ | |2 | +|[flipr](problems.md#flipr)|0.3.3 |1 | |1 __+1__ | +|[foqat](problems.md#foqat)|2.0.8.2 |__+1__ | |__+1__ | +|[forestly](problems.md#forestly)|0.1.1 |__+1__ | |__+1__ | +|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | +|[funcharts](problems.md#funcharts)|1.4.1 |__+1__ | | | +|[geomtextpath](problems.md#geomtextpath)|0.1.4 |__+2__ | | | +|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | +|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | +|[ggbrain](problems.md#ggbrain)|0.8.1 |__+1__ | |1 __+1__ | +|[ggbreak](problems.md#ggbreak)|0.1.2 |__+2__ | |__+1__ | +|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | +|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | +|[ggDoubleHeat](problems.md#ggdoubleheat)|0.1.2 |__+1__ | | | +|[ggeasy](problems.md#ggeasy)|0.1.4 |__+3__ | |__+1__ | +|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | +|[ggESDA](problems.md#ggesda)|0.2.0 |__+1__ | | | +|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | +|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 | +|[ggformula](problems.md#ggformula)|0.12.0 | |__+1__ |1 | +|[ggfortify](problems.md#ggfortify)|0.4.17 |__+1__ | | | +|[gggenomes](problems.md#gggenomes)|1.0.0 |__+2__ | |__+1__ | +|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | +|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ | |__+1__ | +|[ggHoriPlot](problems.md#gghoriplot)|1.0.1 |__+1__ | |__+1__ | +|[ggiraph](problems.md#ggiraph)|0.8.10 |__+2__ | |1 | +|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+2__ | |__+1__ | +|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | |__+1__ | +|[ggmulti](problems.md#ggmulti)|1.0.7 |__+3__ | |__+1__ | +|[ggnewscale](problems.md#ggnewscale)|0.4.10 |__+2__ | | | +|[ggparallel](problems.md#ggparallel)|0.4.0 |__+1__ | | | +|[ggpicrust2](problems.md#ggpicrust2)|1.7.3 |__+1__ | |1 | +|[ggpie](problems.md#ggpie)|0.2.5 |__+2__ | |__+1__ | +|[ggplotlyExtra](problems.md#ggplotlyextra)|0.0.1 |__+1__ | |1 | +|[ggpol](problems.md#ggpol)|0.0.7 |__+1__ | |2 | +|[ggpubr](problems.md#ggpubr)|0.6.0 |__+1__ | | | +|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | |1 __+1__ | +|[ggredist](problems.md#ggredist)|0.0.2 |__+1__ | | | +|[ggRtsy](problems.md#ggrtsy)|0.1.0 |__+2__ | |1 __+1__ | +|[ggseqplot](problems.md#ggseqplot)|0.8.4 |__+3__ | |__+1__ | +|[ggside](problems.md#ggside)|0.3.1 |__+1__ |__+1__ | | +|[ggspatial](problems.md#ggspatial)|1.1.9 |__+2__ | | | +|[ggtern](problems.md#ggtern)|3.5.0 |__+1__ | |2 | +|[ggupset](problems.md#ggupset)|0.4.0 |__+1__ | | | +|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 __+1__ | +|[greatR](problems.md#greatr)|2.0.0 |__+1__ | |__+1__ | +|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | | +|[gtExtras](problems.md#gtextras)|0.5.0 |__+1__ | | | +|[HaploCatcher](problems.md#haplocatcher)|1.0.4 |__+1__ | |__+1__ | +|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 __+1__ | +|[healthyR.ts](problems.md#healthyrts)|0.3.0 |__+2__ | |1 __+1__ | +|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |1 __+1__ | +|[hermiter](problems.md#hermiter)|2.3.1 |__+1__ | |2 __+1__ | +|[hesim](problems.md#hesim)|0.5.4 |__+1__ | |2 | +|[hidecan](problems.md#hidecan)|1.1.0 |1 __+1__ | |__+1__ | +|[HVT](problems.md#hvt)|24.5.2 |__+1__ | | | +|[hypsoLoop](problems.md#hypsoloop)|0.2.0 | |__+1__ | | +|[ICvectorfields](problems.md#icvectorfields)|0.1.2 |__+1__ | |__+1__ | +|[idopNetwork](problems.md#idopnetwork)|0.1.2 |__+1__ | |__+1__ | +|[inferCSN](problems.md#infercsn)|1.0.5 |__+1__ | |1 | +|[insurancerating](problems.md#insurancerating)|0.7.4 |__+1__ | | | +|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.3 |__+2__ | |1 __+1__ | +|[karel](problems.md#karel)|0.1.1 |__+2__ | |1 | +|[kDGLM](problems.md#kdglm)|1.2.0 |1 __+1__ | | | +|[latentcor](problems.md#latentcor)|2.0.1 |__+1__ | | | +|[lcars](problems.md#lcars)|0.3.8 |__+2__ | | | +|[lemon](problems.md#lemon)|0.4.9 |__+3__ | |__+1__ | +|[lfproQC](problems.md#lfproqc)|0.1.0 |__+2__ | |1 __+1__ | +|[LMoFit](problems.md#lmofit)|0.1.7 |__+1__ | |1 __+1__ | +|[manydata](problems.md#manydata)|0.9.3 |__+1__ | |1 | +|[MARVEL](problems.md#marvel)|1.4.0 |__+2__ | |__+1__ | +|[MBNMAdose](problems.md#mbnmadose)|0.4.3 |__+1__ | |1 __+1__ | +|[MBNMAtime](problems.md#mbnmatime)|0.2.4 |1 | |__+1__ | +|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | +|[metR](problems.md#metr)|0.15.0 |__+2__ | |1 __+1__ | +|[migraph](problems.md#migraph)|1.3.4 |__+1__ | | | +|[MiMIR](problems.md#mimir)|1.5 |__+1__ | | | +|[miRetrieve](problems.md#miretrieve)|1.3.4 |__+1__ | | | +|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | | +|[mizer](problems.md#mizer)|2.5.1 |__+1__ | |1 | +|[mlr3spatiotempcv](problems.md#mlr3spatiotempcv)|2.3.1 |1 __+1__ | |1 | +|[mlr3viz](problems.md#mlr3viz)|0.9.0 |__+1__ | | | +|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 | +|[move](problems.md#move)|4.2.4 |1 | |__+1__ | +|[mtb](problems.md#mtb)|0.1.8 |__+1__ | | | +|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | +|[NetFACS](problems.md#netfacs)|0.5.0 |__+2__ | | | +|[NeuralSens](problems.md#neuralsens)|1.1.3 |__+1__ | | | +|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 | +|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 __+1__ | +|[OBIC](problems.md#obic)|3.0.2 |__+1__ | |1 __+1__ | +|[OmicNavigator](problems.md#omicnavigator)|1.13.13 |__+1__ | |1 | +|[oncomsm](problems.md#oncomsm)|0.1.4 |__+2__ | |2 __+1__ | +|[pafr](problems.md#pafr)|0.0.2 |__+1__ | |1 | +|[patchwork](problems.md#patchwork)|1.2.0 |__+1__ | | | +|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | | +|[pcutils](problems.md#pcutils)|0.2.6 |__+1__ | | | +|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 __+1__ | +|[personalized](problems.md#personalized)|0.2.7 |__+1__ | | | +|[phylepic](problems.md#phylepic)|0.2.0 |__+1__ | |__+1__ | +|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | | +|[platetools](problems.md#platetools)|0.1.7 |__+1__ | | | +|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 | +|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 | +|[pmartR](problems.md#pmartr)|2.4.5 |__+1__ | |1 | +|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |1 | +|[posterior](problems.md#posterior)|1.6.0 |1 | |__+1__ | +|[PPQplan](problems.md#ppqplan)|1.1.0 |1 | |2 __+1__ | +|[ppseq](problems.md#ppseq)|0.2.4 |__+1__ | |1 __+1__ | +|[precrec](problems.md#precrec)|0.14.4 |__+1__ | |1 __+1__ | +|[priorsense](problems.md#priorsense)|1.0.1 |__+2__ | |__+1__ | +|[ProAE](problems.md#proae)|1.0.1 |__+1__ | |__+1__ | +|[probably](problems.md#probably)|1.0.3 |__+1__ | | | +|[processmapR](problems.md#processmapr)|0.5.4 |__+1__ | | | +|[psborrow](problems.md#psborrow)|0.2.1 |__+1__ | | | +|[r2dii.plot](problems.md#r2diiplot)|0.4.0 |__+1__ | | | +|[Radviz](problems.md#radviz)|0.9.3 |__+2__ | |__+1__ | +|[rassta](problems.md#rassta)|1.0.5 |__+3__ | | | +|[REddyProc](problems.md#reddyproc)|1.3.3 | | |__+1__ | +|[redist](problems.md#redist)|4.2.0 |__+1__ | |1 __+1__ | +|[reReg](problems.md#rereg)|1.4.6 |__+1__ | | | +|[reservr](problems.md#reservr)|0.0.3 |1 __+1__ | |2 __+1__ | +|[rKOMICS](problems.md#rkomics)|1.3 |__+1__ | |2 | +|[RKorAPClient](problems.md#rkorapclient)|0.8.1 |__+1__ | | | +|[RNAseqQC](problems.md#rnaseqqc)|0.2.1 |__+1__ | |1 __+1__ | +|[roahd](problems.md#roahd)|1.4.3 |__+1__ | |1 | +|[romic](problems.md#romic)|1.1.3 |__+1__ | | | +|[roptions](problems.md#roptions)|1.0.3 |__+1__ | |1 | +|[santaR](problems.md#santar)|1.2.4 |1 __+1__ | | | +|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | +|[scoringutils](problems.md#scoringutils)|1.2.2 |1 __+1__ | |__+1__ | +|[scUtils](problems.md#scutils)|0.1.0 |__+1__ | |1 | +|[SCVA](problems.md#scva)|1.3.1 |__+1__ | | | +|[SDMtune](problems.md#sdmtune)|1.3.1 |1 __+1__ | |1 | +|[SeaVal](problems.md#seaval)|1.2.0 |__+1__ | |1 | +|[sglg](problems.md#sglg)|0.2.2 |__+1__ | | | +|[sgsR](problems.md#sgsr)|1.4.5 |__+1__ | | | +|[SHAPforxgboost](problems.md#shapforxgboost)|0.1.3 |__+1__ | | | +|[SHELF](problems.md#shelf)|1.10.0 | | |__+1__ | +|[shinipsum](problems.md#shinipsum)|0.1.1 |__+1__ | | | +|[SimNPH](problems.md#simnph)|0.5.5 |__+1__ | | | +|[smallsets](problems.md#smallsets)|2.0.0 |__+2__ | |1 __+1__ | +|[spbal](problems.md#spbal)|1.0.0 |__+1__ | |__+1__ | +|[spinifex](problems.md#spinifex)|0.3.7.0 |__+1__ | | | +|[sport](problems.md#sport)|0.2.1 |__+1__ | |1 | +|[SqueakR](problems.md#squeakr)|1.3.0 |1 | |1 __+1__ | +|[statgenGWAS](problems.md#statgengwas)|1.0.9 |__+1__ | |2 | +|[surveyexplorer](problems.md#surveyexplorer)|0.2.0 |__+1__ | | | +|[Sysrecon](problems.md#sysrecon)|0.1.3 |__+1__ | |1 | +|[tabledown](problems.md#tabledown)|1.0.0 |__+1__ | |1 | +|[TCIU](problems.md#tciu)|1.2.6 |__+2__ | |1 __+1__ | +|[tensorEVD](problems.md#tensorevd)|0.1.3 |__+1__ | |__+1__ | +|[thematic](problems.md#thematic)|0.1.5 |__+2__ | | | +|[tidybayes](problems.md#tidybayes)|3.0.6 |2 __+1__ | | | +|[tidycat](problems.md#tidycat)|0.1.2 |__+2__ | |1 __+1__ | +|[tidyCDISC](problems.md#tidycdisc)|0.2.1 |__+1__ | |1 | +|[tidysdm](problems.md#tidysdm)|0.9.5 |__+1__ | |1 __+1__ | +|[tidytreatment](problems.md#tidytreatment)|0.2.2 |__+1__ | |1 __+1__ | +|[timetk](problems.md#timetk)|2.9.0 |__+1__ | |1 | +|[tinyarray](problems.md#tinyarray)|2.4.2 |__+1__ | | | +|[tornado](problems.md#tornado)|0.1.3 |__+3__ | |__+1__ | +|[TOSTER](problems.md#toster)|0.8.3 |__+3__ | |__+1__ | +|[TreatmentPatterns](problems.md#treatmentpatterns)|2.6.7 |__+1__ | | | +|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 |__+1__ | | | +|[tricolore](problems.md#tricolore)|1.2.4 |__+2__ | |1 __+1__ | +|[triptych](problems.md#triptych)|0.1.3 |__+1__ | | | +|[tsnet](problems.md#tsnet)|0.1.0 |__+1__ | |2 | +|[umiAnalyzer](problems.md#umianalyzer)|1.0.0 |__+1__ | | | +|[valr](problems.md#valr)|0.8.1 |__+1__ | |1 | +|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 __+1__ | +|[vivid](problems.md#vivid)|0.2.8 |__+1__ | | | +|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | | +|[wilson](problems.md#wilson)|2.4.2 |__+1__ | | | +|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|[yamlet](problems.md#yamlet)|1.0.3 |__+2__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index f1da4a685a..4a9f813633 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,96 +1,332 @@ ## revdepcheck results -We checked 5034 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 5166 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 64 new problems - * We failed to check 146 packages + * We saw 242 new problems + * We failed to check 132 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* asmbPLS - checking whether package ‘asmbPLS’ can be installed ... WARNING +* activAnalyzer + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* actxps + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AeRobiology + checking re-building of vignette outputs ... NOTE + +* agricolaeplotr + checking tests ... ERROR + +* AnalysisLin + checking examples ... ERROR + +* animbook + checking examples ... ERROR + +* ANN2 + checking tests ... ERROR + +* aplot + checking examples ... ERROR + +* applicable + checking tests ... ERROR + +* ASRgenomics + checking examples ... ERROR + +* autoplotly + checking examples ... ERROR + checking tests ... ERROR + +* autoReg + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* bartMan + checking examples ... ERROR + +* bayesAB + checking tests ... ERROR -* bdl - checking whether package ‘bdl’ can be installed ... WARNING +* BayesGrowth + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BayesianReasoning + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BayesMallows + checking tests ... ERROR + +* bayesplot + checking tests ... ERROR + +* bayestestR + checking examples ... ERROR + +* beastt + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* bdscale +* besthr + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * biclustermd checking tests ... ERROR +* biodosetools + checking tests ... ERROR + +* boxly + checking tests ... ERROR + +* braidReports + checking examples ... ERROR + +* breathtestcore + checking tests ... ERROR + * brolgar checking examples ... ERROR + +* cartograflow + checking examples ... ERROR + +* cartographr + checking tests ... ERROR + +* cats + checking examples ... ERROR + +* cheem + checking tests ... ERROR + +* chillR + checking examples ... ERROR + +* chronicle + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* circhelp + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* bSi - checking whether package ‘bSi’ can be installed ... WARNING +* clifro + checking tests ... ERROR -* CausalImpact +* clinDataReview + checking examples ... ERROR checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* clinUtils + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* CohortPlat + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ClusROC - checking whether package ‘ClusROC’ can be installed ... WARNING +* CoreMicrobiomeR + checking examples ... ERROR -* clustEff - checking whether package ‘clustEff’ can be installed ... WARNING +* correlationfunnel + checking tests ... ERROR -* CLVTools +* corrViz + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* coda4microbiome - checking whether package ‘coda4microbiome’ can be installed ... WARNING - -* CompAREdesign - checking whether package ‘CompAREdesign’ can be installed ... WARNING +* countfitteR + checking tests ... ERROR * covidcast checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* Coxmos - checking Rd files ... WARNING +* crosshap + checking examples ... ERROR + +* ctrialsgov + checking tests ... ERROR -* csa - checking whether package ‘csa’ can be installed ... WARNING +* cubble + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * deeptime checking examples ... ERROR + +* distributional + checking examples ... ERROR + +* dittoViz + checking examples ... ERROR + checking tests ... ERROR + +* EGM + checking tests ... ERROR + +* entropart + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* epiCleanr + checking examples ... ERROR + +* esci + checking examples ... ERROR + checking tests ... ERROR + +* evalITR + checking re-building of vignette outputs ... NOTE + +* eventstudyr + checking tests ... ERROR + +* EvoPhylo + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* expirest + checking tests ... ERROR + +* explainer + checking examples ... ERROR + +* ezEDA + checking tests ... ERROR + +* ezplot + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fable.prophet + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fabletools + checking examples ... ERROR + checking tests ... ERROR + +* factoextra + checking examples ... ERROR + +* fairmodels + checking tests ... ERROR + +* fddm + checking running R code from vignettes ... ERROR + +* feasts + checking tests ... ERROR + +* ffp + checking examples ... ERROR + +* fido + checking examples ... ERROR + checking tests ... ERROR + +* flipr + checking re-building of vignette outputs ... NOTE + +* foqat + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* forestly + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* frailtyEM + checking examples ... ERROR + +* funcharts + checking examples ... ERROR + +* geomtextpath + checking examples ... ERROR checking tests ... ERROR -* DEGRE - checking whether package ‘DEGRE’ can be installed ... WARNING +* GGally + checking tests ... ERROR -* did - checking whether package ‘did’ can be installed ... WARNING +* gganimate + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* EpiCurve +* ggbrain checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* epiR +* ggbreak + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* FuncNN - checking whether package ‘FuncNN’ can be installed ... WARNING +* ggdark + checking examples ... ERROR + checking tests ... ERROR + +* ggdist + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggDoubleHeat + checking examples ... ERROR + +* ggeasy + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggedit checking examples ... ERROR +* ggESDA + checking examples ... ERROR + * ggfixest checking tests ... ERROR +* ggforce + checking examples ... ERROR + +* ggformula + checking for code/documentation mismatches ... WARNING + * ggfortify + checking tests ... ERROR + +* gggenomes + checking examples ... ERROR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * ggh4x @@ -98,189 +334,607 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... NOTE -* ggheatmap - checking whether package ‘ggheatmap’ can be installed ... WARNING +* gghighlight + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* ggScatRidges - checking whether package ‘ggScatRidges’ can be installed ... WARNING +* ggHoriPlot + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* GimmeMyPlot - checking whether package ‘GimmeMyPlot’ can be installed ... WARNING +* ggiraph + checking examples ... ERROR + checking tests ... ERROR -* hilldiv - checking whether package ‘hilldiv’ can be installed ... WARNING +* ggiraphExtra + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* hJAM - checking whether package ‘hJAM’ can be installed ... WARNING +* ggmice + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* iglu +* ggmulti checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ImFoR - checking whether package ‘ImFoR’ can be installed ... WARNING +* ggnewscale + checking examples ... ERROR + checking tests ... ERROR -* iNEXT.4steps - checking whether package ‘iNEXT.4steps’ can be installed ... WARNING +* ggparallel + checking tests ... ERROR -* insane - checking whether package ‘insane’ can be installed ... WARNING +* ggpicrust2 + checking examples ... ERROR -* MarketMatching - checking re-building of vignette outputs ... ERROR +* ggpie + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* mc2d - checking whether package ‘mc2d’ can be installed ... WARNING +* ggplotlyExtra + checking examples ... ERROR -* MetaIntegrator - checking whether package ‘MetaIntegrator’ can be installed ... WARNING +* ggpol + checking examples ... ERROR -* MF.beta4 - checking whether package ‘MF.beta4’ can be installed ... WARNING +* ggpubr + checking tests ... ERROR -* MIMSunit +* ggraph checking examples ... ERROR + checking re-building of vignette outputs ... NOTE -* missingHE - checking whether package ‘missingHE’ can be installed ... WARNING +* ggredist + checking examples ... ERROR -* MSPRT - checking whether package ‘MSPRT’ can be installed ... WARNING +* ggRtsy + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* nzelect +* ggseqplot checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* OenoKPM - checking whether package ‘OenoKPM’ can be installed ... WARNING +* ggside + checking tests ... ERROR + checking for code/documentation mismatches ... WARNING -* posologyr - checking running R code from vignettes ... ERROR +* ggspatial + checking examples ... ERROR + checking tests ... ERROR -* qicharts +* ggtern checking examples ... ERROR -* qicharts2 +* ggupset + checking examples ... ERROR + +* ggVennDiagram checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* QuadratiK - checking whether package ‘QuadratiK’ can be installed ... WARNING +* greatR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* RCTrep - checking whether package ‘RCTrep’ can be installed ... WARNING +* Greymodels + checking examples ... ERROR -* scdtb +* gtExtras checking tests ... ERROR -* SCOUTer - checking whether package ‘SCOUTer’ can be installed ... WARNING - -* sievePH - checking whether package ‘sievePH’ can be installed ... WARNING +* HaploCatcher + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* SouthParkRshiny - checking whether package ‘SouthParkRshiny’ can be installed ... WARNING +* healthyR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* SqueakR - checking whether package ‘SqueakR’ can be installed ... WARNING +* healthyR.ts + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* survminer - checking whether package ‘survminer’ can be installed ... WARNING +* heatmaply + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* symptomcheckR - checking whether package ‘symptomcheckR’ can be installed ... WARNING +* hermiter + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* tcgaViz - checking whether package ‘tcgaViz’ can be installed ... WARNING +* hesim + checking tests ... ERROR -* TestGardener - checking whether package ‘TestGardener’ can be installed ... WARNING +* hidecan + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE -* tis +* HVT checking examples ... ERROR -* UniprotR - checking whether package ‘UniprotR’ can be installed ... WARNING +* hypsoLoop + checking whether package ‘hypsoLoop’ can be installed ... WARNING -* VALERIE - checking whether package ‘VALERIE’ can be installed ... WARNING +* ICvectorfields + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* vannstats - checking whether package ‘vannstats’ can be installed ... WARNING +* idopNetwork + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* vici - checking whether package ‘vici’ can be installed ... WARNING +* inferCSN + checking examples ... ERROR -* Wats +* insurancerating checking examples ... ERROR + +* inTextSummaryTable + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* xaringanthemer +* karel + checking examples ... ERROR + checking tests ... ERROR + +* kDGLM + checking examples ... ERROR + +* latentcor + checking examples ... ERROR + +* lcars + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* lemon + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* lfproQC + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* LMoFit + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* manydata + checking tests ... ERROR + +* MARVEL + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MBNMAdose + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MBNMAtime + checking re-building of vignette outputs ... NOTE + +* MetaNet + checking examples ... ERROR + +* metR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* migraph + checking tests ... ERROR + +* MiMIR + checking examples ... ERROR + +* miRetrieve + checking tests ... ERROR + +* misspi + checking examples ... ERROR + +* mizer + checking tests ... ERROR + +* mlr3spatiotempcv + checking examples ... ERROR + +* mlr3viz + checking examples ... ERROR + +* modeltime.resample + checking tests ... ERROR + +* move + checking installed package size ... NOTE + +* mtb + checking tests ... ERROR + +* neatmaps + checking examples ... ERROR + +* NetFACS + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* NeuralSens + checking examples ... ERROR + +* NHSRplotthedots + checking tests ... ERROR + +* NIMAA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* OBIC + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* OmicNavigator + checking tests ... ERROR + +* oncomsm + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* pafr + checking tests ... ERROR + +* patchwork + checking examples ... ERROR + +* pathviewr + checking tests ... ERROR + +* pcutils + checking examples ... ERROR + +* pdxTrees + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* personalized + checking tests ... ERROR + +* phylepic + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* Plasmidprofiler + checking examples ... ERROR + +* platetools + checking tests ... ERROR + +* plotDK + checking tests ... ERROR + +* plotly + checking examples ... ERROR + checking tests ... ERROR + +* pmartR + checking tests ... ERROR + +* pmxTools + checking tests ... ERROR + +* posterior + checking re-building of vignette outputs ... NOTE + +* PPQplan + checking re-building of vignette outputs ... NOTE + +* ppseq + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* precrec + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* priorsense + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ProAE + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* probably + checking tests ... ERROR + +* processmapR + checking tests ... ERROR + +* psborrow + checking tests ... ERROR + +* r2dii.plot + checking tests ... ERROR + +* Radviz + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rassta + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + +* REddyProc + checking installed package size ... NOTE + +* redist + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reReg + checking examples ... ERROR + +* reservr + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* rKOMICS + checking examples ... ERROR + +* RKorAPClient + checking tests ... ERROR + +* RNAseqQC + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* roahd + checking examples ... ERROR + +* romic + checking tests ... ERROR + +* roptions + checking examples ... ERROR + +* santaR + checking tests ... ERROR + +* scdtb + checking tests ... ERROR + +* scoringutils + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* scUtils + checking tests ... ERROR + +* SCVA + checking examples ... ERROR + +* SDMtune + checking tests ... ERROR + +* SeaVal + checking examples ... ERROR + +* sglg + checking examples ... ERROR + +* sgsR + checking tests ... ERROR + +* SHAPforxgboost + checking examples ... ERROR + +* SHELF + checking re-building of vignette outputs ... NOTE + +* shinipsum + checking tests ... ERROR + +* SimNPH + checking tests ... ERROR + +* smallsets + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* spbal + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* spinifex + checking tests ... ERROR + +* sport + checking tests ... ERROR + +* SqueakR + checking re-building of vignette outputs ... NOTE + +* statgenGWAS + checking tests ... ERROR + +* surveyexplorer + checking examples ... ERROR + +* Sysrecon + checking examples ... ERROR + +* tabledown + checking examples ... ERROR + +* TCIU + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tensorEVD + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* thematic + checking examples ... ERROR + checking tests ... ERROR + +* tidybayes + checking examples ... ERROR + +* tidycat + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tidyCDISC + checking tests ... ERROR + +* tidysdm + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tidytreatment + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* timetk + checking tests ... ERROR + +* tinyarray + checking examples ... ERROR + +* tornado + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* TOSTER + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* TreatmentPatterns + checking tests ... ERROR + +* trelliscopejs + checking tests ... ERROR + +* tricolore + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* triptych + checking examples ... ERROR + +* tsnet + checking tests ... ERROR + +* umiAnalyzer + checking examples ... ERROR + +* valr + checking tests ... ERROR + +* vivaldi + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vivid + checking examples ... ERROR + +* vvshiny + checking tests ... ERROR + +* wilson + checking tests ... ERROR + +* xaringanthemer + checking tests ... ERROR + +* yamlet + checking examples ... ERROR checking tests ... ERROR ### Failed to check * abctools (NA) -* AnanseSeurat (NA) * animalEKF (NA) * ANOM (NA) -* APackOfTheClones (NA) * atRisk (NA) * AutoScore (NA) * bayesdfa (NA) * bayesDP (NA) * BayesianFactorZoo (NA) +* BayesSurvive (NA) * BCClong (NA) +* BGGM (NA) * binsreg (NA) * bmstdr (NA) * bspcov (NA) +* BuyseTest (NA) * CalibrationCurves (NA) -* Canek (NA) * CARBayesST (NA) * CaseBasedReasoning (NA) -* cellpypes (NA) * CGPfunctions (NA) -* CIARA (NA) -* ClustAssess (NA) -* clustree (NA) * cmprskcoxmsm (NA) -* combiroc (NA) -* conos (NA) * contrast (NA) -* countland (NA) * coxed (NA) * CRMetrics (NA) * csmpv (NA) * ctsem (NA) -* CytoSimplex (NA) * DepthProc (NA) -* DIscBIO (NA) * DR.SC (NA) -* dyngen (NA) -* EcoEnsemble (NA) +* DynNom (NA) +* easybgm (NA) * ecolottery (NA) * EpiEstim (NA) * evolqg (NA) * ForecastComb (NA) * gapfill (NA) * GeomComb (NA) -* geostan (NA) * ggrcs (NA) * ggrisk (NA) -* ggsector (NA) * gJLS2 (NA) -* grandR (NA) * Greg (NA) * greport (NA) -* harmony (NA) * hettx (NA) * hIRT (NA) * Hmsc (NA) +* inventorize (NA) * iNZightPlots (NA) * iNZightRegression (NA) * IRexamples (NA) +* jmBIG (NA) * joineRML (NA) * JWileymisc (NA) * kmc (NA) @@ -292,7 +946,6 @@ Issues with CRAN packages are summarised below. * MendelianRandomization (NA) * MetabolicSurv (NA) * miWQS (NA) -* mlmts (NA) * MRZero (NA) * Multiaovbay (NA) * multilevelTools (NA) @@ -310,10 +963,11 @@ Issues with CRAN packages are summarised below. * pould (NA) * powerly (NA) * pre (NA) -* PRECAST (NA) * ProFAST (NA) +* psbcSpeedUp (NA) * pscore (NA) * psfmi (NA) +* qPCRtools (NA) * qreport (NA) * qris (NA) * qte (NA) @@ -322,35 +976,33 @@ Issues with CRAN packages are summarised below. * RcmdrPlugin.RiskDemo (NA) * rddtools (NA) * riskRegression (NA) -* rliger (NA) * rms (NA) * rmsb (NA) * robmed (NA) * robmedExtra (NA) * RPPanalyzer (NA) -* rstanarm (NA) +* RQdeltaCT (NA) * scCustomize (NA) * SCdeconR (NA) -* scDiffCom (NA) * scGate (NA) +* SCIntRuler (NA) * scMappR (NA) -* SCORPIUS (NA) -* scpoisson (NA) -* SCpubr (NA) +* scpi (NA) * scRNAstat (NA) * sectorgap (NA) * SEERaBomb (NA) * semicmprskcoxmsm (NA) * SensMap (NA) +* Seurat (NA) +* shinyTempSignal (NA) +* sievePH (NA) * Signac (NA) * SimplyAgree (NA) * sMSROC (NA) * SNPassoc (NA) * snplinkage (NA) * SoupX (NA) -* SpaDES.core (NA) * sparsereg (NA) -* SPECK (NA) * spikeSlabGAM (NA) * statsr (NA) * streamDAG (NA) @@ -361,10 +1013,9 @@ Issues with CRAN packages are summarised below. * tidyEdSurvey (NA) * tidyseurat (NA) * tidyvpc (NA) -* treefit (NA) * TriDimRegression (NA) * TSrepr (NA) * twang (NA) -* valse (NA) * vdg (NA) +* visa (NA) * WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 5eb2ead6c6..84ae909aa5 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -69,82 +69,6 @@ ERROR: lazy loading failed for package ‘abctools’ * removing ‘/tmp/workdir/abctools/old/abctools.Rcheck/abctools’ -``` -# AnanseSeurat - -
- -* Version: 1.2.0 -* GitHub: https://github.com/JGASmits/AnanseSeurat -* Source code: https://github.com/cran/AnanseSeurat -* Date/Publication: 2023-11-11 21:43:17 UTC -* Number of recursive dependencies: 201 - -Run `revdepcheck::cloud_details(, "AnanseSeurat")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/AnanseSeurat/new/AnanseSeurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -Package suggested but not available for checking: ‘Signac’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/AnanseSeurat/old/AnanseSeurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘AnanseSeurat/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -Package suggested but not available for checking: ‘Signac’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # animalEKF @@ -216,7 +140,7 @@ ERROR: lazy loading failed for package ‘animalEKF’ * GitHub: https://github.com/PhilipPallmann/ANOM * Source code: https://github.com/cran/ANOM * Date/Publication: 2017-04-12 13:32:33 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 60 Run `revdepcheck::cloud_details(, "ANOM")` for more info @@ -271,82 +195,6 @@ ERROR: lazy loading failed for package ‘ANOM’ * removing ‘/tmp/workdir/ANOM/old/ANOM.Rcheck/ANOM’ -``` -# APackOfTheClones - -
- -* Version: 1.2.0 -* GitHub: https://github.com/Qile0317/APackOfTheClones -* Source code: https://github.com/cran/APackOfTheClones -* Date/Publication: 2024-04-16 09:50:02 UTC -* Number of recursive dependencies: 176 - -Run `revdepcheck::cloud_details(, "APackOfTheClones")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/APackOfTheClones/new/APackOfTheClones.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK -... -* this is package ‘APackOfTheClones’ version ‘1.2.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/APackOfTheClones/old/APackOfTheClones.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘APackOfTheClones/DESCRIPTION’ ... OK -... -* this is package ‘APackOfTheClones’ version ‘1.2.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # atRisk @@ -418,7 +266,7 @@ ERROR: lazy loading failed for package ‘atRisk’ * GitHub: https://github.com/nliulab/AutoScore * Source code: https://github.com/cran/AutoScore * Date/Publication: 2022-10-15 22:15:26 UTC -* Number of recursive dependencies: 180 +* Number of recursive dependencies: 170 Run `revdepcheck::cloud_details(, "AutoScore")` for more info @@ -689,16 +537,94 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’ * removing ‘/tmp/workdir/BayesianFactorZoo/old/BayesianFactorZoo.Rcheck/BayesianFactorZoo’ +``` +# BayesSurvive + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/ocbe-uio/BayesSurvive +* Source code: https://github.com/cran/BayesSurvive +* Date/Publication: 2024-06-04 13:20:12 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info + +
+ +## In both + +* checking whether package ‘BayesSurvive’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BayesSurvive’ ... +** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesSurvive’ +* removing ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/BayesSurvive’ + + +``` +### CRAN + +``` +* installing *source* package ‘BayesSurvive’ ... +** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BayesSurvive’ +* removing ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck/BayesSurvive’ + + ``` # BCClong
-* Version: 1.0.2 +* Version: 1.0.3 * GitHub: NA * Source code: https://github.com/cran/BCClong -* Date/Publication: 2024-02-05 11:50:06 UTC -* Number of recursive dependencies: 142 +* Date/Publication: 2024-06-24 00:00:02 UTC +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "BCClong")` for more info @@ -712,11 +638,6 @@ Run `revdepcheck::cloud_details(, "BCClong")` for more info See ‘/tmp/workdir/BCClong/new/BCClong.Rcheck/00install.out’ for details. ``` -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘joineRML’ - ``` - ## Installation ### Devel @@ -733,8 +654,8 @@ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... -installing to /tmp/workdir/BCClong/new/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -760,8 +681,8 @@ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... -installing to /tmp/workdir/BCClong/old/BCClong.Rcheck/00LOCK-BCClong/00new/BCClong/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -772,6 +693,84 @@ ERROR: lazy loading failed for package ‘BCClong’ * removing ‘/tmp/workdir/BCClong/old/BCClong.Rcheck/BCClong’ +``` +# BGGM + +
+ +* Version: 2.1.3 +* GitHub: https://github.com/donaldRwilliams/BGGM +* Source code: https://github.com/cran/BGGM +* Date/Publication: 2024-07-05 20:30:02 UTC +* Number of recursive dependencies: 208 + +Run `revdepcheck::cloud_details(, "BGGM")` for more info + +
+ +## In both + +* checking whether package ‘BGGM’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BGGM/new/BGGM.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BGGM’ ... +** package ‘BGGM’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C++ compiler... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BGGM’ +* removing ‘/tmp/workdir/BGGM/new/BGGM.Rcheck/BGGM’ + + +``` +### CRAN + +``` +* installing *source* package ‘BGGM’ ... +** package ‘BGGM’ successfully unpacked and MD5 sums checked +** using staged installation +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C++ compiler... yes +checking whether g++ -std=gnu++17 accepts -g... yes +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘BGGM’ +* removing ‘/tmp/workdir/BGGM/old/BGGM.Rcheck/BGGM’ + + ``` # binsreg @@ -839,7 +838,7 @@ ERROR: lazy loading failed for package ‘binsreg’ * GitHub: https://github.com/sujit-sahu/bmstdr * Source code: https://github.com/cran/bmstdr * Date/Publication: 2023-12-18 15:00:02 UTC -* Number of recursive dependencies: 212 +* Number of recursive dependencies: 215 Run `revdepcheck::cloud_details(, "bmstdr")` for more info @@ -917,7 +916,7 @@ ERROR: lazy loading failed for package ‘bmstdr’ * GitHub: https://github.com/statjs/bspcov * Source code: https://github.com/cran/bspcov * Date/Publication: 2024-02-06 16:50:08 UTC -* Number of recursive dependencies: 122 +* Number of recursive dependencies: 121 Run `revdepcheck::cloud_details(, "bspcov")` for more info @@ -971,26 +970,26 @@ ERROR: lazy loading failed for package ‘bspcov’ ``` -# CalibrationCurves +# BuyseTest
-* Version: 2.0.1 -* GitHub: NA -* Source code: https://github.com/cran/CalibrationCurves -* Date/Publication: 2024-03-01 10:12:35 UTC -* Number of recursive dependencies: 78 +* Version: 3.0.4 +* GitHub: https://github.com/bozenne/BuyseTest +* Source code: https://github.com/cran/BuyseTest +* Date/Publication: 2024-07-01 09:20:02 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info +Run `revdepcheck::cloud_details(, "BuyseTest")` for more info
## In both -* checking whether package ‘CalibrationCurves’ can be installed ... ERROR +* checking whether package ‘BuyseTest’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00install.out’ for details. ``` ## Installation @@ -998,114 +997,116 @@ Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info ### Devel ``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BuyseTest’ ... +** package ‘BuyseTest’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘BuyseTest’ Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ +ERROR: lazy loading failed for package ‘BuyseTest’ +* removing ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/BuyseTest’ ``` ### CRAN ``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BuyseTest’ ... +** package ‘BuyseTest’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +... +installing to /tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs +** R ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘BuyseTest’ Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ +ERROR: lazy loading failed for package ‘BuyseTest’ +* removing ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/BuyseTest’ ``` -# Canek +# CalibrationCurves
-* Version: 0.2.5 -* GitHub: https://github.com/MartinLoza/Canek -* Source code: https://github.com/cran/Canek -* Date/Publication: 2023-12-08 05:30:02 UTC -* Number of recursive dependencies: 220 +* Version: 2.0.3 +* GitHub: NA +* Source code: https://github.com/cran/CalibrationCurves +* Date/Publication: 2024-07-02 08:50:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "Canek")` for more info +Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/Canek/new/Canek.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Canek/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘toy_example.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE +* checking whether package ‘CalibrationCurves’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Canek/old/Canek.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Canek/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘toy_example.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - +* installing *source* package ‘CalibrationCurves’ ... +** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘CalibrationCurves’ +* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ ``` @@ -1117,7 +1118,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: https://github.com/duncanplee/CARBayesST * Source code: https://github.com/cran/CARBayesST * Date/Publication: 2023-10-30 16:40:02 UTC -* Number of recursive dependencies: 118 +* Number of recursive dependencies: 117 Run `revdepcheck::cloud_details(, "CARBayesST")` for more info @@ -1258,82 +1259,6 @@ ERROR: lazy loading failed for package ‘CaseBasedReasoning’ * removing ‘/tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ -``` -# cellpypes - -
- -* Version: 0.3.0 -* GitHub: https://github.com/FelixTheStudent/cellpypes -* Source code: https://github.com/cran/cellpypes -* Date/Publication: 2024-01-27 07:30:07 UTC -* Number of recursive dependencies: 183 - -Run `revdepcheck::cloud_details(, "cellpypes")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/cellpypes/new/cellpypes.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘cellpypes/DESCRIPTION’ ... OK -... -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/cellpypes/old/cellpypes.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘cellpypes/DESCRIPTION’ ... OK -... -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 NOTE - - - - - ``` # CGPfunctions @@ -1399,254 +1324,214 @@ ERROR: lazy loading failed for package ‘CGPfunctions’ ``` -# CIARA +# cmprskcoxmsm
-* Version: 0.1.0 +* Version: 0.2.1 * GitHub: NA -* Source code: https://github.com/cran/CIARA -* Date/Publication: 2022-02-22 20:00:02 UTC -* Number of recursive dependencies: 181 +* Source code: https://github.com/cran/cmprskcoxmsm +* Date/Publication: 2021-09-04 05:50:02 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "CIARA")` for more info +Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/CIARA/new/CIARA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CIARA/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CIARA.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... NOTE -Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' -* DONE -Status: 3 NOTEs +* checking whether package ‘cmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CIARA/old/CIARA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CIARA/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CIARA.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... NOTE -Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat' -* DONE -Status: 3 NOTEs - - - +* installing *source* package ‘cmprskcoxmsm’ ... +** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘cmprskcoxmsm’ +* removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ ``` -# ClustAssess +# contrast
-* Version: 0.3.0 -* GitHub: https://github.com/Core-Bioinformatics/ClustAssess -* Source code: https://github.com/cran/ClustAssess -* Date/Publication: 2022-01-26 16:52:46 UTC -* Number of recursive dependencies: 164 +* Version: 0.24.2 +* GitHub: https://github.com/Alanocallaghan/contrast +* Source code: https://github.com/cran/contrast +* Date/Publication: 2022-10-05 17:20:09 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "ClustAssess")` for more info +Run `revdepcheck::cloud_details(, "contrast")` for more info
-## Error before installation +## In both -### Devel +* checking whether package ‘contrast’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. + ``` -``` -* using log directory ‘/tmp/workdir/ClustAssess/new/ClustAssess.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ClustAssess/DESCRIPTION’ ... OK -... ---- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ +## Installation -SUMMARY: processing the following file failed: - ‘ClustAssess.Rmd’ +### Devel -Error: Vignette re-building failed. +``` +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - -* DONE -Status: 1 ERROR, 1 WARNING, 2 NOTEs - - - +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ClustAssess/old/ClustAssess.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ClustAssess/DESCRIPTION’ ... OK -... ---- finished re-building ‘comparing-soft-and-hierarchical.Rmd’ - -SUMMARY: processing the following file failed: - ‘ClustAssess.Rmd’ - -Error: Vignette re-building failed. +* installing *source* package ‘contrast’ ... +** package ‘contrast’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - -* DONE -Status: 1 ERROR, 1 WARNING, 2 NOTEs - - - +ERROR: lazy loading failed for package ‘contrast’ +* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ ``` -# clustree +# coxed
-* Version: 0.5.1 -* GitHub: https://github.com/lazappi/clustree -* Source code: https://github.com/cran/clustree -* Date/Publication: 2023-11-05 19:10:02 UTC -* Number of recursive dependencies: 192 +* Version: 0.3.3 +* GitHub: https://github.com/jkropko/coxed +* Source code: https://github.com/cran/coxed +* Date/Publication: 2020-08-02 01:20:07 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "clustree")` for more info +Run `revdepcheck::cloud_details(, "coxed")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/clustree/new/clustree.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE +* checking whether package ‘coxed’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/clustree/old/clustree.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘coxed’ ... +** package ‘coxed’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘coxed’ +* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ ``` -# cmprskcoxmsm +# CRMetrics
-* Version: 0.2.1 -* GitHub: NA -* Source code: https://github.com/cran/cmprskcoxmsm -* Date/Publication: 2021-09-04 05:50:02 UTC -* Number of recursive dependencies: 71 +* Version: 0.3.0 +* GitHub: https://github.com/khodosevichlab/CRMetrics +* Source code: https://github.com/cran/CRMetrics +* Date/Publication: 2023-09-01 09:00:06 UTC +* Number of recursive dependencies: 239 -Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info +Run `revdepcheck::cloud_details(, "CRMetrics")` for more info
## In both -* checking whether package ‘cmprskcoxmsm’ can be installed ... ERROR +* checking whether package ‘CRMetrics’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. ``` ## Installation @@ -1654,213 +1539,59 @@ Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info ### Devel ``` -* installing *source* package ‘cmprskcoxmsm’ ... -** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘cmprskcoxmsm’ -* removing ‘/tmp/workdir/cmprskcoxmsm/new/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/CRMetrics’ ``` ### CRAN ``` -* installing *source* package ‘cmprskcoxmsm’ ... -** package ‘cmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘cmprskcoxmsm’ -* removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ - - -``` -# combiroc - -
- -* Version: 0.3.4 -* GitHub: https://github.com/ingmbioinfo/combiroc -* Source code: https://github.com/cran/combiroc -* Date/Publication: 2023-07-06 12:53:12 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "combiroc")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/combiroc/new/combiroc.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘combiroc/DESCRIPTION’ ... OK -... - - When sourcing ‘combiroc_vignette_2.R’: -Error: Cannot find the file(s): "/tmp/RtmpA38BUi/file1c6675fecb04/vignettes/vignettes/atlas_dimplot.png" -Execution halted - - ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK - ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/combiroc/old/combiroc.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘combiroc/DESCRIPTION’ ... OK -... - - When sourcing ‘combiroc_vignette_2.R’: -Error: Cannot find the file(s): "/tmp/RtmpD5SHHa/file14446c22f1bc/vignettes/vignettes/atlas_dimplot.png" -Execution halted - - ‘combiroc_vignette_1.Rmd’ using ‘UTF-8’... OK - ‘combiroc_vignette_2.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -# conos - -
- -* Version: 1.5.2 -* GitHub: https://github.com/kharchenkolab/conos -* Source code: https://github.com/cran/conos -* Date/Publication: 2024-02-26 19:30:05 UTC -* Number of recursive dependencies: 239 - -Run `revdepcheck::cloud_details(, "conos")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 2 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK -... -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 2 NOTEs - - - +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/CRMetrics’ ``` -# contrast +# csmpv
-* Version: 0.24.2 -* GitHub: https://github.com/Alanocallaghan/contrast -* Source code: https://github.com/cran/contrast -* Date/Publication: 2022-10-05 17:20:09 UTC -* Number of recursive dependencies: 112 +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/csmpv +* Date/Publication: 2024-03-01 18:12:44 UTC +* Number of recursive dependencies: 178 -Run `revdepcheck::cloud_details(, "contrast")` for more info +Run `revdepcheck::cloud_details(, "csmpv")` for more info
## In both -* checking whether package ‘contrast’ can be installed ... ERROR +* checking whether package ‘csmpv’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. ``` ## Installation @@ -1868,8 +1599,8 @@ Run `revdepcheck::cloud_details(, "contrast")` for more info ### Devel ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -1880,16 +1611,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ ``` ### CRAN ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘csmpv’ ... +** package ‘csmpv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -1900,107 +1631,109 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ +ERROR: lazy loading failed for package ‘csmpv’ +* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ ``` -# countland +# ctsem
-* Version: 0.1.2 -* GitHub: https://github.com/shchurch/countland -* Source code: https://github.com/cran/countland -* Date/Publication: 2024-02-01 18:00:02 UTC -* Number of recursive dependencies: 199 +* Version: 3.10.0 +* GitHub: https://github.com/cdriveraus/ctsem +* Source code: https://github.com/cran/ctsem +* Date/Publication: 2024-05-09 14:40:03 UTC +* Number of recursive dependencies: 158 -Run `revdepcheck::cloud_details(, "countland")` for more info +Run `revdepcheck::cloud_details(, "ctsem")` for more info
-## Error before installation +## In both + +* checking whether package ‘ctsem’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/countland/new/countland.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘countland/DESCRIPTION’ ... OK -... - 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 - 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) - 3. └─base (local) withOneRestart(expr, restarts[[1L]]) - 4. └─base (local) doWithOneRestart(return(expr), restart) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted -* DONE -Status: 2 ERRORs, 1 NOTE - +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/countland/old/countland.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘countland/DESCRIPTION’ ... OK -... - 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1 - 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) - 3. └─base (local) withOneRestart(expr, restarts[[1L]]) - 4. └─base (local) doWithOneRestart(return(expr), restart) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted -* DONE -Status: 2 ERRORs, 1 NOTE - +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ ``` -# coxed +# DepthProc
-* Version: 0.3.3 -* GitHub: https://github.com/jkropko/coxed -* Source code: https://github.com/cran/coxed -* Date/Publication: 2020-08-02 01:20:07 UTC -* Number of recursive dependencies: 109 +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 134 -Run `revdepcheck::cloud_details(, "coxed")` for more info +Run `revdepcheck::cloud_details(, "DepthProc")` for more info
## In both -* checking whether package ‘coxed’ can be installed ... ERROR +* checking whether package ‘DepthProc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. ``` ## Installation @@ -2008,137 +1741,155 @@ Run `revdepcheck::cloud_details(, "coxed")` for more info ### Devel ``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ ``` ### CRAN ``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ ``` -# CRMetrics +# DR.SC
-* Version: 0.3.0 -* GitHub: https://github.com/khodosevichlab/CRMetrics -* Source code: https://github.com/cran/CRMetrics -* Date/Publication: 2023-09-01 09:00:06 UTC -* Number of recursive dependencies: 235 +* Version: 3.4 +* GitHub: https://github.com/feiyoung/DR.SC +* Source code: https://github.com/cran/DR.SC +* Date/Publication: 2024-03-19 08:40:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "CRMetrics")` for more info +Run `revdepcheck::cloud_details(, "DR.SC")` for more info
-## Error before installation +## In both + +* checking whether package ‘DR.SC’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ggpmisc’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/DR.SC’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ggpmisc’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck/DR.SC’ ``` -# csmpv +# DynNom
-* Version: 1.0.3 +* Version: 5.1 * GitHub: NA -* Source code: https://github.com/cran/csmpv -* Date/Publication: 2024-03-01 18:12:44 UTC -* Number of recursive dependencies: 175 +* Source code: https://github.com/cran/DynNom +* Date/Publication: 2024-06-07 12:20:21 UTC +* Number of recursive dependencies: 104 -Run `revdepcheck::cloud_details(, "csmpv")` for more info +Run `revdepcheck::cloud_details(, "DynNom")` for more info
## In both -* checking whether package ‘csmpv’ can be installed ... ERROR +* checking whether package ‘DynNom’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/00install.out’ for details. ``` ## Installation @@ -2146,64 +1897,57 @@ Run `revdepcheck::cloud_details(, "csmpv")` for more info ### Devel ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DynNom’ ... +** package ‘DynNom’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csmpv’ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ +ERROR: lazy loading failed for package ‘DynNom’ +* removing ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/DynNom’ ``` ### CRAN ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DynNom’ ... +** package ‘DynNom’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ +ERROR: lazy loading failed for package ‘DynNom’ +* removing ‘/tmp/workdir/DynNom/old/DynNom.Rcheck/DynNom’ ``` -# ctsem +# easybgm
-* Version: 3.10.0 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2024-05-09 14:40:03 UTC -* Number of recursive dependencies: 159 +* Version: 0.1.2 +* GitHub: https://github.com/KarolineHuth/easybgm +* Source code: https://github.com/cran/easybgm +* Date/Publication: 2024-03-13 13:40:02 UTC +* Number of recursive dependencies: 174 -Run `revdepcheck::cloud_details(, "ctsem")` for more info +Run `revdepcheck::cloud_details(, "easybgm")` for more info
## In both -* checking whether package ‘ctsem’ can be installed ... ERROR +* checking whether package ‘easybgm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. ``` ## Installation @@ -2211,153 +1955,117 @@ Run `revdepcheck::cloud_details(, "ctsem")` for more info ### Devel ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ ``` ### CRAN ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ ``` -# CytoSimplex +# ecolottery
-* Version: 0.1.1 -* GitHub: https://github.com/welch-lab/CytoSimplex -* Source code: https://github.com/cran/CytoSimplex -* Date/Publication: 2023-12-15 09:30:06 UTC -* Number of recursive dependencies: 177 +* Version: 1.0.0 +* GitHub: https://github.com/frmunoz/ecolottery +* Source code: https://github.com/cran/ecolottery +* Date/Publication: 2017-07-03 11:01:29 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "CytoSimplex")` for more info +Run `revdepcheck::cloud_details(, "ecolottery")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/CytoSimplex/new/CytoSimplex.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs +* checking whether package ‘ecolottery’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CytoSimplex/old/CytoSimplex.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CytoSimplex/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘CytoSimplex.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ ``` -# DepthProc +# EpiEstim
-* Version: 2.1.5 -* GitHub: https://github.com/zzawadz/DepthProc -* Source code: https://github.com/cran/DepthProc -* Date/Publication: 2022-02-03 20:30:02 UTC -* Number of recursive dependencies: 134 +* Version: 2.2-4 +* GitHub: https://github.com/mrc-ide/EpiEstim +* Source code: https://github.com/cran/EpiEstim +* Date/Publication: 2021-01-07 16:20:10 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "DepthProc")` for more info +Run `revdepcheck::cloud_details(, "EpiEstim")` for more info
## In both -* checking whether package ‘DepthProc’ can be installed ... ERROR +* checking whether package ‘EpiEstim’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. ``` ## Installation @@ -2365,305 +2073,203 @@ Run `revdepcheck::cloud_details(, "DepthProc")` for more info ### Devel ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ ``` ### CRAN ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ ``` -# DIscBIO +# evolqg
-* Version: 1.2.2 -* GitHub: https://github.com/ocbe-uio/DIscBIO -* Source code: https://github.com/cran/DIscBIO -* Date/Publication: 2023-11-06 10:50:02 UTC -* Number of recursive dependencies: 209 +* Version: 0.3-4 +* GitHub: https://github.com/lem-usp/evolqg +* Source code: https://github.com/cran/evolqg +* Date/Publication: 2023-12-05 15:20:12 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "DIscBIO")` for more info +Run `revdepcheck::cloud_details(, "evolqg")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/DIscBIO/new/DIscBIO.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DIscBIO/DESCRIPTION’ ... OK -... -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* DONE -Status: 1 NOTE +* checking whether package ‘evolqg’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/DIscBIO/old/DIscBIO.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DIscBIO/DESCRIPTION’ ... OK -... -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ ``` -# DR.SC +# ForecastComb
-* Version: 3.4 -* GitHub: https://github.com/feiyoung/DR.SC -* Source code: https://github.com/cran/DR.SC -* Date/Publication: 2024-03-19 08:40:02 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "DR.SC")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DR.SC/DESCRIPTION’ ... OK -... -* this is package ‘DR.SC’ version ‘3.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DR.SC/DESCRIPTION’ ... OK -... -* this is package ‘DR.SC’ version ‘3.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# dyngen +* Version: 1.3.1 +* GitHub: https://github.com/ceweiss/ForecastComb +* Source code: https://github.com/cran/ForecastComb +* Date/Publication: 2018-08-07 13:50:08 UTC +* Number of recursive dependencies: 74 -
+Run `revdepcheck::cloud_details(, "ForecastComb")` for more info -* Version: 1.0.5 -* GitHub: https://github.com/dynverse/dyngen -* Source code: https://github.com/cran/dyngen -* Date/Publication: 2022-10-12 15:22:39 UTC -* Number of recursive dependencies: 209 +
-Run `revdepcheck::cloud_details(, "dyngen")` for more info +## In both -
+* checking whether package ‘ForecastComb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/dyngen/new/dyngen.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘dyngen/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting_started.html.asis’ using ‘UTF-8’... OK - ‘installation.html.asis’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/dyngen/old/dyngen.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘dyngen/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘getting_started.html.asis’ using ‘UTF-8’... OK - ‘installation.html.asis’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ ``` -# EcoEnsemble +# gapfill
-* Version: 1.0.5 -* GitHub: NA -* Source code: https://github.com/cran/EcoEnsemble -* Date/Publication: 2023-09-18 11:50:02 UTC -* Number of recursive dependencies: 91 +* Version: 0.9.6-1 +* GitHub: https://github.com/florafauna/gapfill +* Source code: https://github.com/cran/gapfill +* Date/Publication: 2021-02-12 10:10:05 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info +Run `revdepcheck::cloud_details(, "gapfill")` for more info
## In both -* checking whether package ‘EcoEnsemble’ can be installed ... ERROR +* checking whether package ‘gapfill’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'raster', 'doParallel', 'doMPI' ``` ## Installation @@ -2671,77 +2277,77 @@ Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info ### Devel ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R ... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_ensemble_model_hierarchical.cc:32:1: fatal error: error writing to /tmp/ccqp74mc.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ ``` ### CRAN ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ ``` -# ecolottery +# GeomComb
-* Version: 1.0.0 -* GitHub: https://github.com/frmunoz/ecolottery -* Source code: https://github.com/cran/ecolottery -* Date/Publication: 2017-07-03 11:01:29 UTC -* Number of recursive dependencies: 88 +* Version: 1.0 +* GitHub: https://github.com/ceweiss/GeomComb +* Source code: https://github.com/cran/GeomComb +* Date/Publication: 2016-11-27 16:02:26 +* Number of recursive dependencies: 75 -Run `revdepcheck::cloud_details(, "ecolottery")` for more info +Run `revdepcheck::cloud_details(, "GeomComb")` for more info
## In both -* checking whether package ‘ecolottery’ can be installed ... ERROR +* checking whether package ‘GeomComb’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. ``` ## Installation @@ -2749,59 +2355,57 @@ Run `revdepcheck::cloud_details(, "ecolottery")` for more info ### Devel ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ ``` ### CRAN ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ ``` -# EpiEstim +# ggrcs
-* Version: 2.2-4 -* GitHub: https://github.com/mrc-ide/EpiEstim -* Source code: https://github.com/cran/EpiEstim -* Date/Publication: 2021-01-07 16:20:10 UTC -* Number of recursive dependencies: 91 +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/ggrcs +* Date/Publication: 2024-06-29 02:40:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "EpiEstim")` for more info +Run `revdepcheck::cloud_details(, "ggrcs")` for more info
## In both -* checking whether package ‘EpiEstim’ can be installed ... ERROR +* checking whether package ‘ggrcs’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. ``` ## Installation @@ -2809,61 +2413,63 @@ Run `revdepcheck::cloud_details(, "EpiEstim")` for more info ### Devel ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ ``` ### CRAN ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrcs’ ... +** package ‘ggrcs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ +ERROR: lazy loading failed for package ‘ggrcs’ +* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ ``` -# evolqg +# ggrisk
-* Version: 0.3-4 -* GitHub: https://github.com/lem-usp/evolqg -* Source code: https://github.com/cran/evolqg -* Date/Publication: 2023-12-05 15:20:12 UTC -* Number of recursive dependencies: 111 +* Version: 1.3 +* GitHub: https://github.com/yikeshu0611/ggrisk +* Source code: https://github.com/cran/ggrisk +* Date/Publication: 2021-08-09 07:40:06 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "evolqg")` for more info +Run `revdepcheck::cloud_details(, "ggrisk")` for more info
## In both -* checking whether package ‘evolqg’ can be installed ... ERROR +* checking whether package ‘ggrisk’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. ``` ## Installation @@ -2871,73 +2477,61 @@ Run `revdepcheck::cloud_details(, "evolqg")` for more info ### Devel ``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -** inst +*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ ``` ### CRAN ``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ggrisk’ ... +** package ‘ggrisk’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -** inst +*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ +ERROR: lazy loading failed for package ‘ggrisk’ +* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ ``` -# ForecastComb +# gJLS2
-* Version: 1.3.1 -* GitHub: https://github.com/ceweiss/ForecastComb -* Source code: https://github.com/cran/ForecastComb -* Date/Publication: 2018-08-07 13:50:08 UTC -* Number of recursive dependencies: 73 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/gJLS2 +* Date/Publication: 2021-09-30 09:00:05 UTC +* Number of recursive dependencies: 45 -Run `revdepcheck::cloud_details(, "ForecastComb")` for more info +Run `revdepcheck::cloud_details(, "gJLS2")` for more info
## In both -* checking whether package ‘ForecastComb’ can be installed ... ERROR +* checking whether package ‘gJLS2’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. ``` ## Installation @@ -2945,67 +2539,63 @@ Run `revdepcheck::cloud_details(, "ForecastComb")` for more info ### Devel ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ ``` ### CRAN ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ ``` -# gapfill +# Greg
-* Version: 0.9.6-1 -* GitHub: https://github.com/florafauna/gapfill -* Source code: https://github.com/cran/gapfill -* Date/Publication: 2021-02-12 10:10:05 UTC -* Number of recursive dependencies: 71 +* Version: 2.0.2 +* GitHub: https://github.com/gforge/Greg +* Source code: https://github.com/cran/Greg +* Date/Publication: 2024-01-29 13:30:21 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "gapfill")` for more info +Run `revdepcheck::cloud_details(, "Greg")` for more info
## In both -* checking whether package ‘gapfill’ can be installed ... ERROR +* checking whether package ‘Greg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages which this enhances but not available for checking: - 'raster', 'doParallel', 'doMPI' + See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. ``` ## Installation @@ -3013,77 +2603,59 @@ Run `revdepcheck::cloud_details(, "gapfill")` for more info ### Devel ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ ``` ### CRAN ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Greg’ ... +** package ‘Greg’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘Greg’ +* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ ``` -# GeomComb +# greport
-* Version: 1.0 -* GitHub: https://github.com/ceweiss/GeomComb -* Source code: https://github.com/cran/GeomComb -* Date/Publication: 2016-11-27 16:02:26 -* Number of recursive dependencies: 74 +* Version: 0.7-4 +* GitHub: https://github.com/harrelfe/greport +* Source code: https://github.com/cran/greport +* Date/Publication: 2023-09-02 22:20:02 UTC +* Number of recursive dependencies: 84 -Run `revdepcheck::cloud_details(, "GeomComb")` for more info +Run `revdepcheck::cloud_details(, "greport")` for more info
## In both -* checking whether package ‘GeomComb’ can be installed ... ERROR +* checking whether package ‘greport’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. ``` ## Installation @@ -3091,78 +2663,59 @@ Run `revdepcheck::cloud_details(, "GeomComb")` for more info ### Devel ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ ``` ### CRAN ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘greport’ ... +** package ‘greport’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ +ERROR: lazy loading failed for package ‘greport’ +* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ ``` -# geostan +# hettx
-* Version: 0.6.1 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-05-10 22:23:01 UTC -* Number of recursive dependencies: 108 +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 85 -Run `revdepcheck::cloud_details(, "geostan")` for more info +Run `revdepcheck::cloud_details(, "hettx")` for more info
-## Newly broken +## In both -* checking whether package ‘geostan’ can be installed ... ERROR +* checking whether package ‘hettx’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking installed package size ... NOTE - ``` - installed size is 129.8Mb - sub-directories of 1Mb or more: - libs 127.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. ``` ## Installation @@ -3170,77 +2723,63 @@ Run `revdepcheck::cloud_details(, "geostan")` for more info ### Devel ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ ``` ### CRAN ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -** help -*** installing help indices -*** copying figures -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (geostan) +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# ggrcs +# hIRT
-* Version: 0.3.8 -* GitHub: NA -* Source code: https://github.com/cran/ggrcs -* Date/Publication: 2024-01-30 03:20:08 UTC -* Number of recursive dependencies: 78 +* Version: 0.3.0 +* GitHub: https://github.com/xiangzhou09/hIRT +* Source code: https://github.com/cran/hIRT +* Date/Publication: 2020-03-26 17:10:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "ggrcs")` for more info +Run `revdepcheck::cloud_details(, "hIRT")` for more info
## In both -* checking whether package ‘ggrcs’ can be installed ... ERROR +* checking whether package ‘hIRT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. ``` ## Installation @@ -3248,63 +2787,61 @@ Run `revdepcheck::cloud_details(, "ggrcs")` for more info ### Devel ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ ``` ### CRAN ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hIRT’ ... +** package ‘hIRT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ +ERROR: lazy loading failed for package ‘hIRT’ +* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ ``` -# ggrisk +# Hmsc
-* Version: 1.3 -* GitHub: https://github.com/yikeshu0611/ggrisk -* Source code: https://github.com/cran/ggrisk -* Date/Publication: 2021-08-09 07:40:06 UTC -* Number of recursive dependencies: 115 +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "ggrisk")` for more info +Run `revdepcheck::cloud_details(, "Hmsc")` for more info
## In both -* checking whether package ‘ggrisk’ can be installed ... ERROR +* checking whether package ‘Hmsc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3312,137 +2849,123 @@ Run `revdepcheck::cloud_details(, "ggrisk")` for more info ### Devel ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ ``` ### CRAN ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ ``` -# ggsector +# inventorize
-* Version: 1.6.6 -* GitHub: https://github.com/yanpd01/ggsector -* Source code: https://github.com/cran/ggsector -* Date/Publication: 2022-12-05 15:20:02 UTC -* Number of recursive dependencies: 159 +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "ggsector")` for more info +Run `revdepcheck::cloud_details(, "inventorize")` for more info
-## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/ggsector/new/ggsector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ggsector/DESCRIPTION’ ... OK -... -* this is package ‘ggsector’ version ‘1.6.6’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ +## Newly broken -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking whether package ‘inventorize’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in pm[[2]] : subscript out of bounds +Error: unable to load R code in package ‘inventorize’ +Execution halted +ERROR: lazy loading failed for package ‘inventorize’ +* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ggsector/old/ggsector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ggsector/DESCRIPTION’ ... OK -... -* this is package ‘ggsector’ version ‘1.6.6’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Warning in qgamma(service_level, alpha, beta) : NaNs produced +Warning in qgamma(service_level, alpha, beta) : NaNs produced +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (inventorize) ``` -# gJLS2 +# iNZightPlots
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/gJLS2 -* Date/Publication: 2021-09-30 09:00:05 UTC -* Number of recursive dependencies: 45 +* Version: 2.15.3 +* GitHub: https://github.com/iNZightVIT/iNZightPlots +* Source code: https://github.com/cran/iNZightPlots +* Date/Publication: 2023-10-14 05:00:02 UTC +* Number of recursive dependencies: 162 -Run `revdepcheck::cloud_details(, "gJLS2")` for more info +Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info
## In both -* checking whether package ‘gJLS2’ can be installed ... ERROR +* checking whether package ‘iNZightPlots’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/00install.out’ for details. ``` ## Installation @@ -3450,139 +2973,59 @@ Run `revdepcheck::cloud_details(, "gJLS2")` for more info ### Devel ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/iNZightPlots’ ``` ### CRAN ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightPlots’ ... +** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ - - -``` -# grandR - -
- -* Version: 0.2.5 -* GitHub: https://github.com/erhard-lab/grandR -* Source code: https://github.com/cran/grandR -* Date/Publication: 2024-02-15 15:30:02 UTC -* Number of recursive dependencies: 265 - -Run `revdepcheck::cloud_details(, "grandR")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘grandR/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘getting-started.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +ERROR: lazy loading failed for package ‘iNZightPlots’ +* removing ‘/tmp/workdir/iNZightPlots/old/iNZightPlots.Rcheck/iNZightPlots’ ``` -# Greg +# iNZightRegression
-* Version: 2.0.2 -* GitHub: https://github.com/gforge/Greg -* Source code: https://github.com/cran/Greg -* Date/Publication: 2024-01-29 13:30:21 UTC -* Number of recursive dependencies: 152 +* Version: 1.3.4 +* GitHub: https://github.com/iNZightVIT/iNZightRegression +* Source code: https://github.com/cran/iNZightRegression +* Date/Publication: 2024-04-05 02:32:59 UTC +* Number of recursive dependencies: 158 -Run `revdepcheck::cloud_details(, "Greg")` for more info +Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info
## In both -* checking whether package ‘Greg’ can be installed ... ERROR +* checking whether package ‘iNZightRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -3590,8 +3033,8 @@ Run `revdepcheck::cloud_details(, "Greg")` for more info ### Devel ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -3600,16 +3043,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/iNZightRegression’ ``` ### CRAN ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iNZightRegression’ ... +** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -3618,31 +3061,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘iNZightRegression’ +* removing ‘/tmp/workdir/iNZightRegression/old/iNZightRegression.Rcheck/iNZightRegression’ ``` -# greport +# IRexamples
-* Version: 0.7-4 -* GitHub: https://github.com/harrelfe/greport -* Source code: https://github.com/cran/greport -* Date/Publication: 2023-09-02 22:20:02 UTC -* Number of recursive dependencies: 84 +* Version: 0.0.4 +* GitHub: https://github.com/vinhdizzo/IRexamples +* Source code: https://github.com/cran/IRexamples +* Date/Publication: 2023-10-06 06:40:02 UTC +* Number of recursive dependencies: 177 -Run `revdepcheck::cloud_details(, "greport")` for more info +Run `revdepcheck::cloud_details(, "IRexamples")` for more info
## In both -* checking whether package ‘greport’ can be installed ... ERROR +* checking whether package ‘IRexamples’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. ``` ## Installation @@ -3650,135 +3093,73 @@ Run `revdepcheck::cloud_details(, "greport")` for more info ### Devel ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ ``` ### CRAN ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ ``` -# harmony +# jmBIG
-* Version: 1.2.0 +* Version: 0.1.2 * GitHub: NA -* Source code: https://github.com/cran/harmony -* Date/Publication: 2023-11-29 08:30:04 UTC -* Number of recursive dependencies: 214 - -Run `revdepcheck::cloud_details(, "harmony")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/harmony/new/harmony.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘harmony/DESCRIPTION’ ... OK -... ---- finished re-building ‘quickstart.Rmd’ - -SUMMARY: processing the following file failed: - ‘Seurat.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 WARNING, 3 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/harmony/old/harmony.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘harmony/DESCRIPTION’ ... OK -... ---- finished re-building ‘quickstart.Rmd’ - -SUMMARY: processing the following file failed: - ‘Seurat.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 WARNING, 3 NOTEs - - - - - -``` -# hettx - -
- -* Version: 0.1.3 -* GitHub: https://github.com/bfifield/hettx -* Source code: https://github.com/cran/hettx -* Date/Publication: 2023-08-19 22:22:34 UTC -* Number of recursive dependencies: 85 +* Source code: https://github.com/cran/jmBIG +* Date/Publication: 2024-03-20 23:40:02 UTC +* Number of recursive dependencies: 184 -Run `revdepcheck::cloud_details(, "hettx")` for more info +Run `revdepcheck::cloud_details(, "jmBIG")` for more info
## In both -* checking whether package ‘hettx’ can be installed ... ERROR +* checking whether package ‘jmBIG’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/00install.out’ for details. ``` ## Installation @@ -3786,63 +3167,61 @@ Run `revdepcheck::cloud_details(, "hettx")` for more info ### Devel ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked +* installing *source* package ‘jmBIG’ ... +** package ‘jmBIG’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ +ERROR: lazy loading failed for package ‘jmBIG’ +* removing ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/jmBIG’ ``` ### CRAN ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked +* installing *source* package ‘jmBIG’ ... +** package ‘jmBIG’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ +ERROR: lazy loading failed for package ‘jmBIG’ +* removing ‘/tmp/workdir/jmBIG/old/jmBIG.Rcheck/jmBIG’ ``` -# hIRT +# joineRML
-* Version: 0.3.0 -* GitHub: https://github.com/xiangzhou09/hIRT -* Source code: https://github.com/cran/hIRT -* Date/Publication: 2020-03-26 17:10:02 UTC -* Number of recursive dependencies: 88 +* Version: 0.4.6 +* GitHub: https://github.com/graemeleehickey/joineRML +* Source code: https://github.com/cran/joineRML +* Date/Publication: 2023-01-20 04:50:02 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "hIRT")` for more info +Run `revdepcheck::cloud_details(, "joineRML")` for more info
## In both -* checking whether package ‘hIRT’ can be installed ... ERROR +* checking whether package ‘joineRML’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. ``` ## Installation @@ -3850,61 +3229,77 @@ Run `revdepcheck::cloud_details(, "hIRT")` for more info ### Devel ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ ``` ### CRAN ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ ``` -# Hmsc +# JWileymisc
-* Version: 3.0-13 -* GitHub: https://github.com/hmsc-r/HMSC -* Source code: https://github.com/cran/Hmsc -* Date/Publication: 2022-08-11 14:10:14 UTC -* Number of recursive dependencies: 76 +* Version: 1.4.1 +* GitHub: https://github.com/JWiley/JWileymisc +* Source code: https://github.com/cran/JWileymisc +* Date/Publication: 2023-10-05 04:50:02 UTC +* Number of recursive dependencies: 167 -Run `revdepcheck::cloud_details(, "Hmsc")` for more info +Run `revdepcheck::cloud_details(, "JWileymisc")` for more info
## In both -* checking whether package ‘Hmsc’ can be installed ... ERROR +* checking whether package ‘JWileymisc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3912,63 +3307,73 @@ Run `revdepcheck::cloud_details(, "Hmsc")` for more info ### Devel ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ ``` ### CRAN ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘JWileymisc’ ... +** package ‘JWileymisc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘JWileymisc’ +* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ ``` -# iNZightPlots +# kmc
-* Version: 2.15.3 -* GitHub: https://github.com/iNZightVIT/iNZightPlots -* Source code: https://github.com/cran/iNZightPlots -* Date/Publication: 2023-10-14 05:00:02 UTC -* Number of recursive dependencies: 162 +* Version: 0.4-2 +* GitHub: https://github.com/yfyang86/kmc +* Source code: https://github.com/cran/kmc +* Date/Publication: 2022-11-22 08:30:02 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info +Run `revdepcheck::cloud_details(, "kmc")` for more info
## In both -* checking whether package ‘iNZightPlots’ can be installed ... ERROR +* checking whether package ‘kmc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3976,59 +3381,73 @@ Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info ### Devel ``` -* installing *source* package ‘iNZightPlots’ ... -** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R -** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightPlots’ -* removing ‘/tmp/workdir/iNZightPlots/new/iNZightPlots.Rcheck/iNZightPlots’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ ``` ### CRAN ``` -* installing *source* package ‘iNZightPlots’ ... -** package ‘iNZightPlots’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs +** R +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightPlots’ -* removing ‘/tmp/workdir/iNZightPlots/old/iNZightPlots.Rcheck/iNZightPlots’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ ``` -# iNZightRegression +# L2E
-* Version: 1.3.4 -* GitHub: https://github.com/iNZightVIT/iNZightRegression -* Source code: https://github.com/cran/iNZightRegression -* Date/Publication: 2024-04-05 02:32:59 UTC -* Number of recursive dependencies: 154 +* Version: 2.0 +* GitHub: NA +* Source code: https://github.com/cran/L2E +* Date/Publication: 2022-09-08 21:13:00 UTC +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info +Run `revdepcheck::cloud_details(, "L2E")` for more info
## In both -* checking whether package ‘iNZightRegression’ can be installed ... ERROR +* checking whether package ‘L2E’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. ``` ## Installation @@ -4036,59 +3455,61 @@ Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info ### Devel ``` -* installing *source* package ‘iNZightRegression’ ... -** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightRegression’ -* removing ‘/tmp/workdir/iNZightRegression/new/iNZightRegression.Rcheck/iNZightRegression’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ ``` ### CRAN ``` -* installing *source* package ‘iNZightRegression’ ... -** package ‘iNZightRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘iNZightRegression’ -* removing ‘/tmp/workdir/iNZightRegression/old/iNZightRegression.Rcheck/iNZightRegression’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ ``` -# IRexamples +# llbayesireg
-* Version: 0.0.4 -* GitHub: https://github.com/vinhdizzo/IRexamples -* Source code: https://github.com/cran/IRexamples -* Date/Publication: 2023-10-06 06:40:02 UTC -* Number of recursive dependencies: 185 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/llbayesireg +* Date/Publication: 2019-04-04 16:20:03 UTC +* Number of recursive dependencies: 60 -Run `revdepcheck::cloud_details(, "IRexamples")` for more info +Run `revdepcheck::cloud_details(, "llbayesireg")` for more info
## In both -* checking whether package ‘IRexamples’ can be installed ... ERROR +* checking whether package ‘llbayesireg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/00install.out’ for details. ``` ## Installation @@ -4096,63 +3517,61 @@ Run `revdepcheck::cloud_details(, "IRexamples")` for more info ### Devel ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/llbayesireg’ ``` ### CRAN ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘llbayesireg’ ... +** package ‘llbayesireg’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘llbayesireg’ +* removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ ``` -# joineRML +# LorenzRegression
-* Version: 0.4.6 -* GitHub: https://github.com/graemeleehickey/joineRML -* Source code: https://github.com/cran/joineRML -* Date/Publication: 2023-01-20 04:50:02 UTC -* Number of recursive dependencies: 91 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/LorenzRegression +* Date/Publication: 2023-02-28 17:32:34 UTC +* Number of recursive dependencies: 63 -Run `revdepcheck::cloud_details(, "joineRML")` for more info +Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info
## In both -* checking whether package ‘joineRML’ can be installed ... ERROR +* checking whether package ‘LorenzRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -4160,16 +3579,16 @@ Run `revdepcheck::cloud_details(, "joineRML")` for more info ### Devel ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4179,24 +3598,24 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/LorenzRegression’ ``` ### CRAN ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘LorenzRegression’ ... +** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4206,31 +3625,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘LorenzRegression’ +* removing ‘/tmp/workdir/LorenzRegression/old/LorenzRegression.Rcheck/LorenzRegression’ ``` -# JWileymisc +# lsirm12pl
-* Version: 1.4.1 -* GitHub: https://github.com/JWiley/JWileymisc -* Source code: https://github.com/cran/JWileymisc -* Date/Publication: 2023-10-05 04:50:02 UTC -* Number of recursive dependencies: 164 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/lsirm12pl +* Date/Publication: 2023-06-22 14:12:35 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "JWileymisc")` for more info +Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info
## In both -* checking whether package ‘JWileymisc’ can be installed ... ERROR +* checking whether package ‘lsirm12pl’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/00install.out’ for details. ``` ## Installation @@ -4238,63 +3657,77 @@ Run `revdepcheck::cloud_details(, "JWileymisc")` for more info ### Devel ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/lsirm12pl’ ``` ### CRAN ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘lsirm12pl’ ... +** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +... ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ ``` -# kmc +# mbsts
-* Version: 0.4-2 -* GitHub: https://github.com/yfyang86/kmc -* Source code: https://github.com/cran/kmc -* Date/Publication: 2022-11-22 08:30:02 UTC -* Number of recursive dependencies: 61 +* Version: 3.0 +* GitHub: NA +* Source code: https://github.com/cran/mbsts +* Date/Publication: 2023-01-07 01:10:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "kmc")` for more info +Run `revdepcheck::cloud_details(, "mbsts")` for more info
## In both -* checking whether package ‘kmc’ can be installed ... ERROR +* checking whether package ‘mbsts’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/00install.out’ for details. ``` ## Installation @@ -4302,73 +3735,59 @@ Run `revdepcheck::cloud_details(, "kmc")` for more info ### Devel ``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/mbsts’ ``` ### CRAN ``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mbsts’ ... +** package ‘mbsts’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ ``` -# L2E +# MendelianRandomization
-* Version: 2.0 +* Version: 0.10.0 * GitHub: NA -* Source code: https://github.com/cran/L2E -* Date/Publication: 2022-09-08 21:13:00 UTC -* Number of recursive dependencies: 65 +* Source code: https://github.com/cran/MendelianRandomization +* Date/Publication: 2024-04-12 10:10:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "L2E")` for more info +Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info
## In both -* checking whether package ‘L2E’ can be installed ... ERROR +* checking whether package ‘MendelianRandomization’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. ``` ## Installation @@ -4376,61 +3795,71 @@ Run `revdepcheck::cloud_details(, "L2E")` for more info ### Devel ``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ ``` ### CRAN ``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ ``` -# llbayesireg +# MetabolicSurv
-* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/llbayesireg -* Date/Publication: 2019-04-04 16:20:03 UTC -* Number of recursive dependencies: 61 +* Version: 1.1.2 +* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv +* Source code: https://github.com/cran/MetabolicSurv +* Date/Publication: 2021-06-11 08:30:02 UTC +* Number of recursive dependencies: 131 -Run `revdepcheck::cloud_details(, "llbayesireg")` for more info +Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info
## In both -* checking whether package ‘llbayesireg’ can be installed ... ERROR +* checking whether package ‘MetabolicSurv’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. ``` ## Installation @@ -4438,61 +3867,63 @@ Run `revdepcheck::cloud_details(, "llbayesireg")` for more info ### Devel ``` -* installing *source* package ‘llbayesireg’ ... -** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘llbayesireg’ -* removing ‘/tmp/workdir/llbayesireg/new/llbayesireg.Rcheck/llbayesireg’ +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ ``` ### CRAN ``` -* installing *source* package ‘llbayesireg’ ... -** package ‘llbayesireg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MetabolicSurv’ ... +** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘llbayesireg’ -* removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ +ERROR: lazy loading failed for package ‘MetabolicSurv’ +* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ ``` -# LorenzRegression +# miWQS
-* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/LorenzRegression -* Date/Publication: 2023-02-28 17:32:34 UTC -* Number of recursive dependencies: 63 +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info +Run `revdepcheck::cloud_details(, "miWQS")` for more info
## In both -* checking whether package ‘LorenzRegression’ can be installed ... ERROR +* checking whether package ‘miWQS’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. ``` ## Installation @@ -4500,17 +3931,10 @@ Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info ### Devel ``` -* installing *source* package ‘LorenzRegression’ ... -** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -... +** R ** data *** moving datasets to lazyload DB ** inst @@ -4519,25 +3943,18 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘LorenzRegression’ -* removing ‘/tmp/workdir/LorenzRegression/new/LorenzRegression.Rcheck/LorenzRegression’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ ``` ### CRAN ``` -* installing *source* package ‘LorenzRegression’ ... -** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -... +** R ** data *** moving datasets to lazyload DB ** inst @@ -4546,31 +3963,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘LorenzRegression’ -* removing ‘/tmp/workdir/LorenzRegression/old/LorenzRegression.Rcheck/LorenzRegression’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ ``` -# lsirm12pl +# MRZero
-* Version: 1.3.1 +* Version: 0.2.0 * GitHub: NA -* Source code: https://github.com/cran/lsirm12pl -* Date/Publication: 2023-06-22 14:12:35 UTC -* Number of recursive dependencies: 123 +* Source code: https://github.com/cran/MRZero +* Date/Publication: 2024-04-14 09:30:03 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info +Run `revdepcheck::cloud_details(, "MRZero")` for more info
## In both -* checking whether package ‘lsirm12pl’ can be installed ... ERROR +* checking whether package ‘MRZero’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. ``` ## Installation @@ -4578,77 +3995,57 @@ Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info ### Devel ``` -* installing *source* package ‘lsirm12pl’ ... -** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o -... ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/new/lsirm12pl.Rcheck/lsirm12pl’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ ``` ### CRAN ``` -* installing *source* package ‘lsirm12pl’ ... -** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o -... ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ ``` -# mbsts +# Multiaovbay
-* Version: 3.0 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/mbsts -* Date/Publication: 2023-01-07 01:10:02 UTC -* Number of recursive dependencies: 82 +* Source code: https://github.com/cran/Multiaovbay +* Date/Publication: 2023-03-17 17:20:02 UTC +* Number of recursive dependencies: 153 -Run `revdepcheck::cloud_details(, "mbsts")` for more info +Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info
## In both -* checking whether package ‘mbsts’ can be installed ... ERROR +* checking whether package ‘Multiaovbay’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. ``` ## Installation @@ -4656,59 +4053,57 @@ Run `revdepcheck::cloud_details(, "mbsts")` for more info ### Devel ``` -* installing *source* package ‘mbsts’ ... -** package ‘mbsts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘mbsts’ -* removing ‘/tmp/workdir/mbsts/new/mbsts.Rcheck/mbsts’ +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ ``` ### CRAN ``` -* installing *source* package ‘mbsts’ ... -** package ‘mbsts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Multiaovbay’ ... +** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘mbsts’ -* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ +ERROR: lazy loading failed for package ‘Multiaovbay’ +* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ ``` -# MendelianRandomization +# multilevelTools
-* Version: 0.10.0 -* GitHub: NA -* Source code: https://github.com/cran/MendelianRandomization -* Date/Publication: 2024-04-12 10:10:02 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info - +* Version: 0.1.1 +* GitHub: https://github.com/JWiley/multilevelTools +* Source code: https://github.com/cran/multilevelTools +* Date/Publication: 2020-03-04 09:50:02 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "multilevelTools")` for more info +
## In both -* checking whether package ‘MendelianRandomization’ can be installed ... ERROR +* checking whether package ‘multilevelTools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/00install.out’ for details. ``` ## Installation @@ -4716,71 +4111,69 @@ Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info ### Devel ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/multilevelTools’ ``` ### CRAN ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multilevelTools’ ... +** package ‘multilevelTools’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs ** R ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ +ERROR: lazy loading failed for package ‘multilevelTools’ +* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ ``` -# MetabolicSurv +# multinma
-* Version: 1.1.2 -* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv -* Source code: https://github.com/cran/MetabolicSurv -* Date/Publication: 2021-06-11 08:30:02 UTC -* Number of recursive dependencies: 142 +* Version: 0.7.1 +* GitHub: https://github.com/dmphillippo/multinma +* Source code: https://github.com/cran/multinma +* Date/Publication: 2024-06-11 12:20:06 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info +Run `revdepcheck::cloud_details(, "multinma")` for more info
## In both -* checking whether package ‘MetabolicSurv’ can be installed ... ERROR +* checking whether package ‘multinma’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. ``` ## Installation @@ -4788,63 +4181,77 @@ Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info ### Devel ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ ``` ### CRAN ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ ``` -# miWQS +# NCA
-* Version: 0.4.4 -* GitHub: https://github.com/phargarten2/miWQS -* Source code: https://github.com/cran/miWQS -* Date/Publication: 2021-04-02 21:50:02 UTC -* Number of recursive dependencies: 152 +* Version: 4.0.1 +* GitHub: NA +* Source code: https://github.com/cran/NCA +* Date/Publication: 2024-02-23 09:30:15 UTC +* Number of recursive dependencies: 99 -Run `revdepcheck::cloud_details(, "miWQS")` for more info +Run `revdepcheck::cloud_details(, "NCA")` for more info
## In both -* checking whether package ‘miWQS’ can be installed ... ERROR +* checking whether package ‘NCA’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NCA/new/NCA.Rcheck/00install.out’ for details. ``` ## Installation @@ -4852,63 +4259,59 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info ### Devel ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/new/NCA.Rcheck/NCA’ ``` ### CRAN ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NCA’ ... +** package ‘NCA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘NCA’ +* removing ‘/tmp/workdir/NCA/old/NCA.Rcheck/NCA’ ``` -# mlmts +# netcmc
-* Version: 1.1.1 +* Version: 1.0.2 * GitHub: NA -* Source code: https://github.com/cran/mlmts -* Date/Publication: 2023-01-22 21:30:02 UTC -* Number of recursive dependencies: 241 +* Source code: https://github.com/cran/netcmc +* Date/Publication: 2022-11-08 22:30:15 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "mlmts")` for more info +Run `revdepcheck::cloud_details(, "netcmc")` for more info
## In both -* checking whether package ‘mlmts’ can be installed ... ERROR +* checking whether package ‘netcmc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details. ``` ## Installation @@ -4916,63 +4319,77 @@ Run `revdepcheck::cloud_details(, "mlmts")` for more info ### Devel ``` -* installing *source* package ‘mlmts’ ... -** package ‘mlmts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘mlmts’ -* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’ +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’ ``` ### CRAN ``` -* installing *source* package ‘mlmts’ ... -** package ‘mlmts’ successfully unpacked and MD5 sums checked +* installing *source* package ‘netcmc’ ... +** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +... +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading -Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘mlmts’ -* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’ +ERROR: lazy loading failed for package ‘netcmc’ +* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’ ``` -# MRZero +# NetworkChange
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/MRZero -* Date/Publication: 2024-04-14 09:30:03 UTC -* Number of recursive dependencies: 82 +* Version: 0.8 +* GitHub: https://github.com/jongheepark/NetworkChange +* Source code: https://github.com/cran/NetworkChange +* Date/Publication: 2022-03-04 07:30:02 UTC +* Number of recursive dependencies: 132 -Run `revdepcheck::cloud_details(, "MRZero")` for more info +Run `revdepcheck::cloud_details(, "NetworkChange")` for more info
## In both -* checking whether package ‘MRZero’ can be installed ... ERROR +* checking whether package ‘NetworkChange’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details. ``` ## Installation @@ -4980,57 +4397,57 @@ Run `revdepcheck::cloud_details(, "MRZero")` for more info ### Devel ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’ ``` ### CRAN ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NetworkChange’ ... +** package ‘NetworkChange’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ +ERROR: lazy loading failed for package ‘NetworkChange’ +* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’ ``` -# Multiaovbay +# nlmeVPC
-* Version: 0.1.0 +* Version: 2.6 * GitHub: NA -* Source code: https://github.com/cran/Multiaovbay -* Date/Publication: 2023-03-17 17:20:02 UTC -* Number of recursive dependencies: 161 +* Source code: https://github.com/cran/nlmeVPC +* Date/Publication: 2022-12-22 05:20:02 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info +Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info
## In both -* checking whether package ‘Multiaovbay’ can be installed ... ERROR +* checking whether package ‘nlmeVPC’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00install.out’ for details. ``` ## Installation @@ -5038,57 +4455,73 @@ Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info ### Devel ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R +** data ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/nlmeVPC’ ``` ### CRAN ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘nlmeVPC’ ... +** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R +** data ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘nlmeVPC’ +* removing ‘/tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/nlmeVPC’ ``` -# multilevelTools +# NMADiagT
-* Version: 0.1.1 -* GitHub: https://github.com/JWiley/multilevelTools -* Source code: https://github.com/cran/multilevelTools -* Date/Publication: 2020-03-04 09:50:02 UTC -* Number of recursive dependencies: 164 +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/NMADiagT +* Date/Publication: 2020-02-26 07:00:02 UTC +* Number of recursive dependencies: 79 -Run `revdepcheck::cloud_details(, "multilevelTools")` for more info +Run `revdepcheck::cloud_details(, "NMADiagT")` for more info
## In both -* checking whether package ‘multilevelTools’ can be installed ... ERROR +* checking whether package ‘NMADiagT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/00install.out’ for details. ``` ## Installation @@ -5096,8 +4529,8 @@ Run `revdepcheck::cloud_details(, "multilevelTools")` for more info ### Devel ``` -* installing *source* package ‘multilevelTools’ ... -** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -5106,16 +4539,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelTools’ -* removing ‘/tmp/workdir/multilevelTools/new/multilevelTools.Rcheck/multilevelTools’ +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/NMADiagT’ ``` ### CRAN ``` -* installing *source* package ‘multilevelTools’ ... -** package ‘multilevelTools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMADiagT’ ... +** package ‘NMADiagT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -5124,31 +4557,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘multilevelTools’ -* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ +ERROR: lazy loading failed for package ‘NMADiagT’ +* removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ ``` -# multinma +# optweight
-* Version: 0.7.0 -* GitHub: https://github.com/dmphillippo/multinma -* Source code: https://github.com/cran/multinma -* Date/Publication: 2024-05-07 15:40:02 UTC -* Number of recursive dependencies: 152 +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/optweight +* Date/Publication: 2019-09-16 15:40:02 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "multinma")` for more info +Run `revdepcheck::cloud_details(, "optweight")` for more info
## In both -* checking whether package ‘multinma’ can be installed ... ERROR +* checking whether package ‘optweight’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. ``` ## Installation @@ -5156,77 +4589,57 @@ Run `revdepcheck::cloud_details(, "multinma")` for more info ### Devel ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ ``` ### CRAN ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ ``` -# NCA +# OVtool
-* Version: 4.0.1 +* Version: 1.0.3 * GitHub: NA -* Source code: https://github.com/cran/NCA -* Date/Publication: 2024-02-23 09:30:15 UTC -* Number of recursive dependencies: 99 +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 157 -Run `revdepcheck::cloud_details(, "NCA")` for more info +Run `revdepcheck::cloud_details(, "OVtool")` for more info
## In both -* checking whether package ‘NCA’ can be installed ... ERROR +* checking whether package ‘OVtool’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NCA/new/NCA.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. ``` ## Installation @@ -5234,59 +4647,61 @@ Run `revdepcheck::cloud_details(, "NCA")` for more info ### Devel ``` -* installing *source* package ‘NCA’ ... -** package ‘NCA’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘NCA’ -* removing ‘/tmp/workdir/NCA/new/NCA.Rcheck/NCA’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ ``` ### CRAN ``` -* installing *source* package ‘NCA’ ... -** package ‘NCA’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘NCA’ -* removing ‘/tmp/workdir/NCA/old/NCA.Rcheck/NCA’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ ``` -# netcmc +# paths
-* Version: 1.0.2 +* Version: 0.1.1 * GitHub: NA -* Source code: https://github.com/cran/netcmc -* Date/Publication: 2022-11-08 22:30:15 UTC -* Number of recursive dependencies: 61 +* Source code: https://github.com/cran/paths +* Date/Publication: 2021-06-18 08:40:02 UTC +* Number of recursive dependencies: 102 -Run `revdepcheck::cloud_details(, "netcmc")` for more info +Run `revdepcheck::cloud_details(, "paths")` for more info
## In both -* checking whether package ‘netcmc’ can be installed ... ERROR +* checking whether package ‘paths’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. ``` ## Installation @@ -5294,77 +4709,63 @@ Run `revdepcheck::cloud_details(, "netcmc")` for more info ### Devel ``` -* installing *source* package ‘netcmc’ ... -** package ‘netcmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o -... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘netcmc’ -* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ ``` ### CRAN ``` -* installing *source* package ‘netcmc’ ... -** package ‘netcmc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o -... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘netcmc’ -* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ ``` -# NetworkChange +# PLMIX
-* Version: 0.8 -* GitHub: https://github.com/jongheepark/NetworkChange -* Source code: https://github.com/cran/NetworkChange -* Date/Publication: 2022-03-04 07:30:02 UTC -* Number of recursive dependencies: 132 +* Version: 2.1.1 +* GitHub: NA +* Source code: https://github.com/cran/PLMIX +* Date/Publication: 2019-09-04 11:50:02 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "NetworkChange")` for more info +Run `revdepcheck::cloud_details(, "PLMIX")` for more info
## In both -* checking whether package ‘NetworkChange’ can be installed ... ERROR +* checking whether package ‘PLMIX’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/00install.out’ for details. ``` ## Installation @@ -5372,57 +4773,77 @@ Run `revdepcheck::cloud_details(, "NetworkChange")` for more info ### Devel ``` -* installing *source* package ‘NetworkChange’ ... -** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NetworkChange’ -* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’ +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/PLMIX’ ``` ### CRAN ``` -* installing *source* package ‘NetworkChange’ ... -** package ‘NetworkChange’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PLMIX’ ... +** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +... ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NetworkChange’ -* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’ +ERROR: lazy loading failed for package ‘PLMIX’ +* removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ ``` -# nlmeVPC +# popstudy
-* Version: 2.6 +* Version: 1.0.1 * GitHub: NA -* Source code: https://github.com/cran/nlmeVPC -* Date/Publication: 2022-12-22 05:20:02 UTC -* Number of recursive dependencies: 91 +* Source code: https://github.com/cran/popstudy +* Date/Publication: 2023-10-17 23:50:02 UTC +* Number of recursive dependencies: 240 -Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info +Run `revdepcheck::cloud_details(, "popstudy")` for more info
## In both -* checking whether package ‘nlmeVPC’ can be installed ... ERROR +* checking whether package ‘popstudy’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/00install.out’ for details. ``` ## Installation @@ -5430,73 +4851,63 @@ Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info ### Devel ``` -* installing *source* package ‘nlmeVPC’ ... -** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘nlmeVPC’ -* removing ‘/tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/nlmeVPC’ +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/popstudy’ ``` ### CRAN ``` -* installing *source* package ‘nlmeVPC’ ... -** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked +* installing *source* package ‘popstudy’ ... +** package ‘popstudy’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R ** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘nlmeVPC’ -* removing ‘/tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/nlmeVPC’ +ERROR: lazy loading failed for package ‘popstudy’ +* removing ‘/tmp/workdir/popstudy/old/popstudy.Rcheck/popstudy’ ``` -# NMADiagT +# pould
-* Version: 0.1.2 +* Version: 1.0.1 * GitHub: NA -* Source code: https://github.com/cran/NMADiagT -* Date/Publication: 2020-02-26 07:00:02 UTC -* Number of recursive dependencies: 79 +* Source code: https://github.com/cran/pould +* Date/Publication: 2020-10-16 13:50:03 UTC +* Number of recursive dependencies: 104 -Run `revdepcheck::cloud_details(, "NMADiagT")` for more info +Run `revdepcheck::cloud_details(, "pould")` for more info
## In both -* checking whether package ‘NMADiagT’ can be installed ... ERROR +* checking whether package ‘pould’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. ``` ## Installation @@ -5504,59 +4915,63 @@ Run `revdepcheck::cloud_details(, "NMADiagT")` for more info ### Devel ``` -* installing *source* package ‘NMADiagT’ ... -** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NMADiagT’ -* removing ‘/tmp/workdir/NMADiagT/new/NMADiagT.Rcheck/NMADiagT’ +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ ``` ### CRAN ``` -* installing *source* package ‘NMADiagT’ ... -** package ‘NMADiagT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pould’ ... +** package ‘pould’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘NMADiagT’ -* removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ +ERROR: lazy loading failed for package ‘pould’ +* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ ``` -# optweight +# powerly
-* Version: 0.2.5 -* GitHub: NA -* Source code: https://github.com/cran/optweight -* Date/Publication: 2019-09-16 15:40:02 UTC -* Number of recursive dependencies: 55 +* Version: 1.8.6 +* GitHub: https://github.com/mihaiconstantin/powerly +* Source code: https://github.com/cran/powerly +* Date/Publication: 2022-09-09 14:10:01 UTC +* Number of recursive dependencies: 181 -Run `revdepcheck::cloud_details(, "optweight")` for more info +Run `revdepcheck::cloud_details(, "powerly")` for more info
## In both -* checking whether package ‘optweight’ can be installed ... ERROR +* checking whether package ‘powerly’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/powerly/new/powerly.Rcheck/00install.out’ for details. ``` ## Installation @@ -5564,57 +4979,69 @@ Run `revdepcheck::cloud_details(, "optweight")` for more info ### Devel ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/new/powerly.Rcheck/powerly’ ``` ### CRAN ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘powerly’ ... +** package ‘powerly’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘powerly’ +* removing ‘/tmp/workdir/powerly/old/powerly.Rcheck/powerly’ ``` -# OVtool +# pre
-* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 158 +* Version: 1.0.7 +* GitHub: https://github.com/marjoleinF/pre +* Source code: https://github.com/cran/pre +* Date/Publication: 2024-01-12 19:30:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "OVtool")` for more info +Run `revdepcheck::cloud_details(, "pre")` for more info
## In both -* checking whether package ‘OVtool’ can be installed ... ERROR +* checking whether package ‘pre’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pre/new/pre.Rcheck/00install.out’ for details. ``` ## Installation @@ -5622,125 +5049,139 @@ Run `revdepcheck::cloud_details(, "OVtool")` for more info ### Devel ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/new/pre.Rcheck/pre’ ``` ### CRAN ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pre’ ... +** package ‘pre’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘pre’ +* removing ‘/tmp/workdir/pre/old/pre.Rcheck/pre’ ``` -# paths +# ProFAST
-* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/paths -* Date/Publication: 2021-06-18 08:40:02 UTC -* Number of recursive dependencies: 103 +* Version: 1.4 +* GitHub: https://github.com/feiyoung/ProFAST +* Source code: https://github.com/cran/ProFAST +* Date/Publication: 2024-03-18 08:10:06 UTC +* Number of recursive dependencies: 245 -Run `revdepcheck::cloud_details(, "paths")` for more info +Run `revdepcheck::cloud_details(, "ProFAST")` for more info
-## In both - -* checking whether package ‘paths’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ +* using log directory ‘/tmp/workdir/ProFAST/new/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ +* using log directory ‘/tmp/workdir/ProFAST/old/ProFAST.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ProFAST/DESCRIPTION’ ... OK +... +* this is package ‘ProFAST’ version ‘1.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'DR.SC', 'PRECAST' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# PLMIX +# psbcSpeedUp
-* Version: 2.1.1 -* GitHub: NA -* Source code: https://github.com/cran/PLMIX -* Date/Publication: 2019-09-04 11:50:02 UTC -* Number of recursive dependencies: 151 +* Version: 2.0.7 +* GitHub: https://github.com/ocbe-uio/psbcSpeedUp +* Source code: https://github.com/cran/psbcSpeedUp +* Date/Publication: 2024-07-01 09:00:02 UTC +* Number of recursive dependencies: 129 -Run `revdepcheck::cloud_details(, "PLMIX")` for more info +Run `revdepcheck::cloud_details(, "psbcSpeedUp")` for more info
## In both -* checking whether package ‘PLMIX’ can be installed ... ERROR +* checking whether package ‘psbcSpeedUp’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/00install.out’ for details. ``` ## Installation @@ -5748,16 +5189,16 @@ Run `revdepcheck::cloud_details(, "PLMIX")` for more info ### Devel ``` -* installing *source* package ‘PLMIX’ ... -** package ‘PLMIX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psbcSpeedUp’ ... +** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes ... ** data *** moving datasets to lazyload DB @@ -5767,24 +5208,24 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PLMIX’ -* removing ‘/tmp/workdir/PLMIX/new/PLMIX.Rcheck/PLMIX’ +ERROR: lazy loading failed for package ‘psbcSpeedUp’ +* removing ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/psbcSpeedUp’ ``` ### CRAN ``` -* installing *source* package ‘PLMIX’ ... -** package ‘PLMIX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psbcSpeedUp’ ... +** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +checking whether the C++ compiler works... yes +checking for C++ compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether the compiler supports GNU C++... yes +checking whether g++ -std=gnu++17 accepts -g... yes ... ** data *** moving datasets to lazyload DB @@ -5794,31 +5235,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PLMIX’ -* removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ +ERROR: lazy loading failed for package ‘psbcSpeedUp’ +* removing ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck/psbcSpeedUp’ ``` -# popstudy +# pscore
-* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/popstudy -* Date/Publication: 2023-10-17 23:50:02 UTC -* Number of recursive dependencies: 236 +* Version: 0.4.0 +* GitHub: https://github.com/JWiley/score-project +* Source code: https://github.com/cran/pscore +* Date/Publication: 2022-05-13 22:30:02 UTC +* Number of recursive dependencies: 169 -Run `revdepcheck::cloud_details(, "popstudy")` for more info +Run `revdepcheck::cloud_details(, "pscore")` for more info
## In both -* checking whether package ‘popstudy’ can be installed ... ERROR +* checking whether package ‘pscore’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/pscore/new/pscore.Rcheck/00install.out’ for details. ``` ## Installation @@ -5826,63 +5267,71 @@ Run `revdepcheck::cloud_details(, "popstudy")` for more info ### Devel ``` -* installing *source* package ‘popstudy’ ... -** package ‘popstudy’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘popstudy’ -* removing ‘/tmp/workdir/popstudy/new/popstudy.Rcheck/popstudy’ +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/new/pscore.Rcheck/pscore’ ``` ### CRAN ``` -* installing *source* package ‘popstudy’ ... -** package ‘popstudy’ successfully unpacked and MD5 sums checked +* installing *source* package ‘pscore’ ... +** package ‘pscore’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘popstudy’ -* removing ‘/tmp/workdir/popstudy/old/popstudy.Rcheck/popstudy’ +ERROR: lazy loading failed for package ‘pscore’ +* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ ``` -# pould +# psfmi
-* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/pould -* Date/Publication: 2020-10-16 13:50:03 UTC -* Number of recursive dependencies: 104 +* Version: 1.4.0 +* GitHub: https://github.com/mwheymans/psfmi +* Source code: https://github.com/cran/psfmi +* Date/Publication: 2023-06-17 22:40:02 UTC +* Number of recursive dependencies: 164 -Run `revdepcheck::cloud_details(, "pould")` for more info +Run `revdepcheck::cloud_details(, "psfmi")` for more info
## In both -* checking whether package ‘pould’ can be installed ... ERROR +* checking whether package ‘psfmi’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. ``` ## Installation @@ -5890,8 +5339,8 @@ Run `revdepcheck::cloud_details(, "pould")` for more info ### Devel ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -5902,16 +5351,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ ``` ### CRAN ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked +* installing *source* package ‘psfmi’ ... +** package ‘psfmi’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -5922,31 +5371,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ +ERROR: lazy loading failed for package ‘psfmi’ +* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ ``` -# powerly +# qPCRtools
-* Version: 1.8.6 -* GitHub: https://github.com/mihaiconstantin/powerly -* Source code: https://github.com/cran/powerly -* Date/Publication: 2022-09-09 14:10:01 UTC -* Number of recursive dependencies: 176 +* Version: 1.0.1 +* GitHub: https://github.com/lixiang117423/qPCRtools +* Source code: https://github.com/cran/qPCRtools +* Date/Publication: 2023-11-02 13:10:05 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "powerly")` for more info +Run `revdepcheck::cloud_details(, "qPCRtools")` for more info
## In both -* checking whether package ‘powerly’ can be installed ... ERROR +* checking whether package ‘qPCRtools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/powerly/new/powerly.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qPCRtools/new/qPCRtools.Rcheck/00install.out’ for details. ``` ## Installation @@ -5954,59 +5403,59 @@ Run `revdepcheck::cloud_details(, "powerly")` for more info ### Devel ``` -* installing *source* package ‘powerly’ ... -** package ‘powerly’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qPCRtools’ ... +** package ‘qPCRtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘powerly’ -* removing ‘/tmp/workdir/powerly/new/powerly.Rcheck/powerly’ +ERROR: lazy loading failed for package ‘qPCRtools’ +* removing ‘/tmp/workdir/qPCRtools/new/qPCRtools.Rcheck/qPCRtools’ ``` ### CRAN ``` -* installing *source* package ‘powerly’ ... -** package ‘powerly’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qPCRtools’ ... +** package ‘qPCRtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘powerly’ -* removing ‘/tmp/workdir/powerly/old/powerly.Rcheck/powerly’ +ERROR: lazy loading failed for package ‘qPCRtools’ +* removing ‘/tmp/workdir/qPCRtools/old/qPCRtools.Rcheck/qPCRtools’ ``` -# pre +# qreport
-* Version: 1.0.7 -* GitHub: https://github.com/marjoleinF/pre -* Source code: https://github.com/cran/pre -* Date/Publication: 2024-01-12 19:30:02 UTC -* Number of recursive dependencies: 152 +* Version: 1.0-1 +* GitHub: NA +* Source code: https://github.com/cran/qreport +* Date/Publication: 2024-05-26 21:50:03 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "pre")` for more info +Run `revdepcheck::cloud_details(, "qreport")` for more info
## In both -* checking whether package ‘pre’ can be installed ... ERROR +* checking whether package ‘qreport’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pre/new/pre.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. ``` ## Installation @@ -6014,215 +5463,135 @@ Run `revdepcheck::cloud_details(, "pre")` for more info ### Devel ``` -* installing *source* package ‘pre’ ... -** package ‘pre’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pre’ -* removing ‘/tmp/workdir/pre/new/pre.Rcheck/pre’ +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ ``` ### CRAN ``` -* installing *source* package ‘pre’ ... -** package ‘pre’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qreport’ ... +** package ‘qreport’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pre’ -* removing ‘/tmp/workdir/pre/old/pre.Rcheck/pre’ +ERROR: lazy loading failed for package ‘qreport’ +* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ ``` -# PRECAST +# qris
-* Version: 1.6.5 -* GitHub: https://github.com/feiyoung/PRECAST -* Source code: https://github.com/cran/PRECAST -* Date/Publication: 2024-03-19 08:30:02 UTC -* Number of recursive dependencies: 225 +* Version: 1.1.1 +* GitHub: https://github.com/Kyuhyun07/qris +* Source code: https://github.com/cran/qris +* Date/Publication: 2024-03-05 14:40:03 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "PRECAST")` for more info +Run `revdepcheck::cloud_details(, "qris")` for more info
-## Error before installation +## In both -### Devel - -``` -* using log directory ‘/tmp/workdir/PRECAST/new/PRECAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PRECAST/DESCRIPTION’ ... OK -... -* this is package ‘PRECAST’ version ‘1.6.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'DR.SC' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/PRECAST/old/PRECAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PRECAST/DESCRIPTION’ ... OK -... -* this is package ‘PRECAST’ version ‘1.6.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'DR.SC' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# ProFAST - -
- -* Version: 1.4 -* GitHub: https://github.com/feiyoung/ProFAST -* Source code: https://github.com/cran/ProFAST -* Date/Publication: 2024-03-18 08:10:06 UTC -* Number of recursive dependencies: 253 - -Run `revdepcheck::cloud_details(, "ProFAST")` for more info - -
+* checking whether package ‘qris’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/ProFAST/new/ProFAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ProFAST/DESCRIPTION’ ... OK +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... -* this is package ‘ProFAST’ version ‘1.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/ProFAST/old/ProFAST.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ProFAST/DESCRIPTION’ ... OK +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... -* this is package ‘ProFAST’ version ‘1.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ ``` -# pscore +# qte
-* Version: 0.4.0 -* GitHub: https://github.com/JWiley/score-project -* Source code: https://github.com/cran/pscore -* Date/Publication: 2022-05-13 22:30:02 UTC -* Number of recursive dependencies: 165 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/qte +* Date/Publication: 2022-09-01 14:30:02 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "pscore")` for more info +Run `revdepcheck::cloud_details(, "qte")` for more info
## In both -* checking whether package ‘pscore’ can be installed ... ERROR +* checking whether package ‘qte’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pscore/new/pscore.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. ``` ## Installation @@ -6230,61 +5599,63 @@ Run `revdepcheck::cloud_details(, "pscore")` for more info ### Devel ``` -* installing *source* package ‘pscore’ ... -** package ‘pscore’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pscore’ -* removing ‘/tmp/workdir/pscore/new/pscore.Rcheck/pscore’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ ``` ### CRAN ``` -* installing *source* package ‘pscore’ ... -** package ‘pscore’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pscore’ -* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ ``` -# psfmi +# quid
-* Version: 1.4.0 -* GitHub: https://github.com/mwheymans/psfmi -* Source code: https://github.com/cran/psfmi -* Date/Publication: 2023-06-17 22:40:02 UTC -* Number of recursive dependencies: 160 +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/quid +* Date/Publication: 2021-12-09 09:00:02 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "psfmi")` for more info +Run `revdepcheck::cloud_details(, "quid")` for more info
## In both -* checking whether package ‘psfmi’ can be installed ... ERROR +* checking whether package ‘quid’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/quid/new/quid.Rcheck/00install.out’ for details. ``` ## Installation @@ -6292,8 +5663,8 @@ Run `revdepcheck::cloud_details(, "psfmi")` for more info ### Devel ``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -6304,16 +5675,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/new/quid.Rcheck/quid’ ``` ### CRAN ``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quid’ ... +** package ‘quid’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -6324,31 +5695,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ +ERROR: lazy loading failed for package ‘quid’ +* removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ ``` -# qreport +# RATest
-* Version: 1.0-0 -* GitHub: NA -* Source code: https://github.com/cran/qreport -* Date/Publication: 2023-09-12 22:10:02 UTC -* Number of recursive dependencies: 77 +* Version: 0.1.10 +* GitHub: https://github.com/ignaciomsarmiento/RATest +* Source code: https://github.com/cran/RATest +* Date/Publication: 2022-09-29 04:30:02 UTC +* Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "qreport")` for more info +Run `revdepcheck::cloud_details(, "RATest")` for more info
## In both -* checking whether package ‘qreport’ can be installed ... ERROR +* checking whether package ‘RATest’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. ``` ## Installation @@ -6356,57 +5727,63 @@ Run `revdepcheck::cloud_details(, "qreport")` for more info ### Devel ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ ``` ### CRAN ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RATest’ ... +** package ‘RATest’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** byte-compile and prepare package for lazy loading +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘RATest’ +* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ ``` -# qris +# RcmdrPlugin.RiskDemo
-* Version: 1.1.1 -* GitHub: https://github.com/Kyuhyun07/qris -* Source code: https://github.com/cran/qris -* Date/Publication: 2024-03-05 14:40:03 UTC -* Number of recursive dependencies: 55 +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 200 -Run `revdepcheck::cloud_details(, "qris")` for more info +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info
## In both -* checking whether package ‘qris’ can be installed ... ERROR +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. ``` ## Installation @@ -6414,77 +5791,71 @@ Run `revdepcheck::cloud_details(, "qris")` for more info ### Devel ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` ### CRAN ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` -# qte +# rddtools
-* Version: 1.3.1 -* GitHub: NA -* Source code: https://github.com/cran/qte -* Date/Publication: 2022-09-01 14:30:02 UTC -* Number of recursive dependencies: 87 +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "qte")` for more info +Run `revdepcheck::cloud_details(, "rddtools")` for more info
## In both -* checking whether package ‘qte’ can be installed ... ERROR +* checking whether package ‘rddtools’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. ``` ## Installation @@ -6492,63 +5863,59 @@ Run `revdepcheck::cloud_details(, "qte")` for more info ### Devel ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ ``` ### CRAN ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ ``` -# quid +# riskRegression
-* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/quid -* Date/Publication: 2021-12-09 09:00:02 UTC -* Number of recursive dependencies: 95 +* Version: 2023.12.21 +* GitHub: https://github.com/tagteam/riskRegression +* Source code: https://github.com/cran/riskRegression +* Date/Publication: 2023-12-19 17:00:02 UTC +* Number of recursive dependencies: 186 -Run `revdepcheck::cloud_details(, "quid")` for more info +Run `revdepcheck::cloud_details(, "riskRegression")` for more info
## In both -* checking whether package ‘quid’ can be installed ... ERROR +* checking whether package ‘riskRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/quid/new/quid.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -6556,63 +5923,82 @@ Run `revdepcheck::cloud_details(, "quid")` for more info ### Devel ``` -* installing *source* package ‘quid’ ... -** package ‘quid’ successfully unpacked and MD5 sums checked +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘quid’ -* removing ‘/tmp/workdir/quid/new/quid.Rcheck/quid’ +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ ``` ### CRAN ``` -* installing *source* package ‘quid’ ... -** package ‘quid’ successfully unpacked and MD5 sums checked +* installing *source* package ‘riskRegression’ ... +** package ‘riskRegression’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o +... ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘quid’ -* removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ +ERROR: lazy loading failed for package ‘riskRegression’ +* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ ``` -# RATest +# rms
-* Version: 0.1.10 -* GitHub: https://github.com/ignaciomsarmiento/RATest -* Source code: https://github.com/cran/RATest -* Date/Publication: 2022-09-29 04:30:02 UTC -* Number of recursive dependencies: 54 +* Version: 6.8-1 +* GitHub: https://github.com/harrelfe/rms +* Source code: https://github.com/cran/rms +* Date/Publication: 2024-05-27 12:00:02 UTC +* Number of recursive dependencies: 145 -Run `revdepcheck::cloud_details(, "RATest")` for more info +Run `revdepcheck::cloud_details(, "rms")` for more info
## In both -* checking whether package ‘RATest’ can be installed ... ERROR +* checking whether package ‘rms’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘rmsb’ ``` ## Installation @@ -6620,63 +6006,77 @@ Run `revdepcheck::cloud_details(, "RATest")` for more info ### Devel ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... ** R -** data -*** moving datasets to lazyload DB +** demo ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ ``` ### CRAN ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rms’ ... +** package ‘rms’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o +gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o +gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o +gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o +... ** R -** data -*** moving datasets to lazyload DB +** demo ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘rms’ +* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ ``` -# RcmdrPlugin.RiskDemo +# rmsb
-* Version: 3.2 +* Version: 1.1-1 * GitHub: NA -* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo -* Date/Publication: 2024-02-06 09:20:02 UTC -* Number of recursive dependencies: 208 +* Source code: https://github.com/cran/rmsb +* Date/Publication: 2024-07-08 11:10:03 UTC +* Number of recursive dependencies: 135 -Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info +Run `revdepcheck::cloud_details(, "rmsb")` for more info
## In both -* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR +* checking whether package ‘rmsb’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. ``` ## Installation @@ -6684,61 +6084,51 @@ Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info ### Devel ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ ``` ### CRAN ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rmsb’ ... +** package ‘rmsb’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: configuration failed for package ‘rmsb’ +* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ ``` -# rddtools +# robmed
-* Version: 1.6.0 -* GitHub: https://github.com/bquast/rddtools -* Source code: https://github.com/cran/rddtools -* Date/Publication: 2022-01-10 12:42:49 UTC -* Number of recursive dependencies: 102 +* Version: 1.0.2 +* GitHub: https://github.com/aalfons/robmed +* Source code: https://github.com/cran/robmed +* Date/Publication: 2023-06-16 23:00:02 UTC +* Number of recursive dependencies: 60 -Run `revdepcheck::cloud_details(, "rddtools")` for more info +Run `revdepcheck::cloud_details(, "robmed")` for more info
## In both -* checking whether package ‘rddtools’ can be installed ... ERROR +* checking whether package ‘robmed’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. ``` ## Installation @@ -6746,59 +6136,63 @@ Run `revdepcheck::cloud_details(, "rddtools")` for more info ### Devel ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ ``` ### CRAN ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ ``` -# riskRegression +# robmedExtra
-* Version: 2023.12.21 -* GitHub: https://github.com/tagteam/riskRegression -* Source code: https://github.com/cran/riskRegression -* Date/Publication: 2023-12-19 17:00:02 UTC -* Number of recursive dependencies: 186 +* Version: 0.1.0 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2023-06-02 14:40:02 UTC +* Number of recursive dependencies: 96 -Run `revdepcheck::cloud_details(, "riskRegression")` for more info +Run `revdepcheck::cloud_details(, "robmedExtra")` for more info
## In both -* checking whether package ‘riskRegression’ can be installed ... ERROR +* checking whether package ‘robmedExtra’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. ``` ## Installation @@ -6806,158 +6200,119 @@ Run `revdepcheck::cloud_details(, "riskRegression")` for more info ### Devel ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ ``` ### CRAN ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ ``` -# rliger +# RPPanalyzer
-* Version: 2.0.1 -* GitHub: https://github.com/welch-lab/liger -* Source code: https://github.com/cran/rliger -* Date/Publication: 2024-04-04 23:20:02 UTC -* Number of recursive dependencies: 218 +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/RPPanalyzer +* Date/Publication: 2024-01-25 11:00:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "rliger")` for more info +Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/rliger/new/rliger.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘rliger/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘liger-vignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 ERRORs, 2 NOTEs +* checking whether package ‘RPPanalyzer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/rliger/old/rliger.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘rliger/DESCRIPTION’ ... OK -... - [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1234 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘liger-vignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 ERRORs, 2 NOTEs - - - +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ ``` -# rms +# RQdeltaCT
-* Version: 6.8-0 -* GitHub: https://github.com/harrelfe/rms -* Source code: https://github.com/cran/rms -* Date/Publication: 2024-03-11 16:20:02 UTC -* Number of recursive dependencies: 154 +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/RQdeltaCT +* Date/Publication: 2024-04-17 15:50:02 UTC +* Number of recursive dependencies: 165 -Run `revdepcheck::cloud_details(, "rms")` for more info +Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info
## In both -* checking whether package ‘rms’ can be installed ... ERROR +* checking whether package ‘RQdeltaCT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rmsb’ + See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. ``` ## Installation @@ -6965,77 +6320,68 @@ Run `revdepcheck::cloud_details(, "rms")` for more info ### Devel ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ ``` ### CRAN ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ ``` -# rmsb +# scCustomize
-* Version: 1.1-0 -* GitHub: NA -* Source code: https://github.com/cran/rmsb -* Date/Publication: 2024-03-12 15:50:02 UTC -* Number of recursive dependencies: 144 +* Version: 2.1.2 +* GitHub: https://github.com/samuel-marsh/scCustomize +* Source code: https://github.com/cran/scCustomize +* Date/Publication: 2024-02-28 19:40:02 UTC +* Number of recursive dependencies: 267 -Run `revdepcheck::cloud_details(, "rmsb")` for more info +Run `revdepcheck::cloud_details(, "scCustomize")` for more info
## In both -* checking whether package ‘rmsb’ can be installed ... ERROR +* checking whether package ‘scCustomize’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘Nebulosa’ ``` ## Installation @@ -7043,51 +6389,59 @@ Run `revdepcheck::cloud_details(, "rmsb")` for more info ### Devel ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ ``` ### CRAN ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked ** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ ``` -# robmed +# SCdeconR
-* Version: 1.0.2 -* GitHub: https://github.com/aalfons/robmed -* Source code: https://github.com/cran/robmed -* Date/Publication: 2023-06-16 23:00:02 UTC -* Number of recursive dependencies: 60 +* Version: 1.0.0 +* GitHub: https://github.com/Liuy12/SCdeconR +* Source code: https://github.com/cran/SCdeconR +* Date/Publication: 2024-03-22 19:20:02 UTC +* Number of recursive dependencies: 236 -Run `revdepcheck::cloud_details(, "robmed")` for more info +Run `revdepcheck::cloud_details(, "SCdeconR")` for more info
## In both -* checking whether package ‘robmed’ can be installed ... ERROR +* checking whether package ‘SCdeconR’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck/00install.out’ for details. ``` ## Installation @@ -7095,63 +6449,57 @@ Run `revdepcheck::cloud_details(, "robmed")` for more info ### Devel ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCdeconR’ ... +** package ‘SCdeconR’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘SCdeconR’ +* removing ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck/SCdeconR’ ``` ### CRAN ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCdeconR’ ... +** package ‘SCdeconR’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘SCdeconR’ +* removing ‘/tmp/workdir/SCdeconR/old/SCdeconR.Rcheck/SCdeconR’ ``` -# robmedExtra +# scGate
-* Version: 0.1.0 -* GitHub: https://github.com/aalfons/robmedExtra -* Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2023-06-02 14:40:02 UTC -* Number of recursive dependencies: 96 +* Version: 1.6.2 +* GitHub: https://github.com/carmonalab/scGate +* Source code: https://github.com/cran/scGate +* Date/Publication: 2024-04-23 08:50:02 UTC +* Number of recursive dependencies: 179 -Run `revdepcheck::cloud_details(, "robmedExtra")` for more info +Run `revdepcheck::cloud_details(, "scGate")` for more info
## In both -* checking whether package ‘robmedExtra’ can be installed ... ERROR +* checking whether package ‘scGate’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scGate/new/scGate.Rcheck/00install.out’ for details. ``` ## Installation @@ -7159,57 +6507,71 @@ Run `revdepcheck::cloud_details(, "robmedExtra")` for more info ### Devel ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scGate’ ... +** package ‘scGate’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ +ERROR: lazy loading failed for package ‘scGate’ +* removing ‘/tmp/workdir/scGate/new/scGate.Rcheck/scGate’ ``` ### CRAN ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scGate’ ... +** package ‘scGate’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘query.seurat’ ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ +ERROR: lazy loading failed for package ‘scGate’ +* removing ‘/tmp/workdir/scGate/old/scGate.Rcheck/scGate’ ``` -# RPPanalyzer +# SCIntRuler
-* Version: 1.4.9 -* GitHub: NA -* Source code: https://github.com/cran/RPPanalyzer -* Date/Publication: 2024-01-25 11:00:02 UTC -* Number of recursive dependencies: 82 +* Version: 0.99.6 +* GitHub: https://github.com/yuelyu21/SCIntRuler +* Source code: https://github.com/cran/SCIntRuler +* Date/Publication: 2024-07-12 15:20:08 UTC +* Number of recursive dependencies: 202 -Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info +Run `revdepcheck::cloud_details(, "SCIntRuler")` for more info
## In both -* checking whether package ‘RPPanalyzer’ can be installed ... ERROR +* checking whether package ‘SCIntRuler’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/00install.out’ for details. ``` ## Installation @@ -7217,61 +6579,77 @@ Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info ### Devel ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCIntRuler’ ... +** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/SCIntRuler’ ``` ### CRAN ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SCIntRuler’ ... +** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ ``` -# rstanarm +# scMappR
-* Version: 2.32.1 -* GitHub: https://github.com/stan-dev/rstanarm -* Source code: https://github.com/cran/rstanarm -* Date/Publication: 2024-01-18 23:00:03 UTC -* Number of recursive dependencies: 138 +* Version: 1.0.11 +* GitHub: NA +* Source code: https://github.com/cran/scMappR +* Date/Publication: 2023-06-30 08:40:08 UTC +* Number of recursive dependencies: 234 -Run `revdepcheck::cloud_details(, "rstanarm")` for more info +Run `revdepcheck::cloud_details(, "scMappR")` for more info
## In both -* checking whether package ‘rstanarm’ can be installed ... ERROR +* checking whether package ‘scMappR’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/scMappR/new/scMappR.Rcheck/00install.out’ for details. ``` ## Installation @@ -7279,662 +6657,118 @@ Run `revdepcheck::cloud_details(, "rstanarm")` for more info ### Devel ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scMappR’ ... +** package ‘scMappR’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 -rm stan_files/bernoulli.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scMappR’ +* removing ‘/tmp/workdir/scMappR/new/scMappR.Rcheck/scMappR’ ``` ### CRAN ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘scMappR’ ... +** package ‘scMappR’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/bernoulli.o] Error 1 -rm stan_files/bernoulli.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scMappR’ +* removing ‘/tmp/workdir/scMappR/old/scMappR.Rcheck/scMappR’ ``` -# scCustomize +# scpi
-* Version: 2.1.2 -* GitHub: https://github.com/samuel-marsh/scCustomize -* Source code: https://github.com/cran/scCustomize -* Date/Publication: 2024-02-28 19:40:02 UTC -* Number of recursive dependencies: 274 +* Version: 2.2.5 +* GitHub: NA +* Source code: https://github.com/cran/scpi +* Date/Publication: 2023-11-01 06:10:07 UTC +* Number of recursive dependencies: 98 -Run `revdepcheck::cloud_details(, "scCustomize")` for more info +Run `revdepcheck::cloud_details(, "scpi")` for more info
-## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -Package suggested but not available for checking: ‘Nebulosa’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -Package suggested but not available for checking: ‘Nebulosa’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCdeconR - -
- -* Version: 1.0.0 -* GitHub: https://github.com/Liuy12/SCdeconR -* Source code: https://github.com/cran/SCdeconR -* Date/Publication: 2024-03-22 19:20:02 UTC -* Number of recursive dependencies: 235 - -Run `revdepcheck::cloud_details(, "SCdeconR")` for more info +## In both -
+* checking whether package ‘scpi’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/scpi/new/scpi.Rcheck/00install.out’ for details. + ``` -## Error before installation +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/SCdeconR/new/SCdeconR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCdeconR/DESCRIPTION’ ... OK -... -* this is package ‘SCdeconR’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCdeconR/old/SCdeconR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCdeconR/DESCRIPTION’ ... OK -... -* this is package ‘SCdeconR’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scDiffCom - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/scDiffCom -* Date/Publication: 2023-11-03 18:40:02 UTC -* Number of recursive dependencies: 259 - -Run `revdepcheck::cloud_details(, "scDiffCom")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scGate - -
- -* Version: 1.6.2 -* GitHub: https://github.com/carmonalab/scGate -* Source code: https://github.com/cran/scGate -* Date/Publication: 2024-04-23 08:50:02 UTC -* Number of recursive dependencies: 178 - -Run `revdepcheck::cloud_details(, "scGate")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scGate/new/scGate.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scGate/DESCRIPTION’ ... OK -... -* this is package ‘scGate’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scGate/old/scGate.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scGate/DESCRIPTION’ ... OK -... -* this is package ‘scGate’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# scMappR - -
- -* Version: 1.0.11 -* GitHub: NA -* Source code: https://github.com/cran/scMappR -* Date/Publication: 2023-06-30 08:40:08 UTC -* Number of recursive dependencies: 233 - -Run `revdepcheck::cloud_details(, "scMappR")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scMappR/new/scMappR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scMappR/DESCRIPTION’ ... OK -... -* this is package ‘scMappR’ version ‘1.0.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scMappR/old/scMappR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scMappR/DESCRIPTION’ ... OK -... -* this is package ‘scMappR’ version ‘1.0.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCORPIUS - -
- -* Version: 1.0.9 -* GitHub: https://github.com/rcannood/SCORPIUS -* Source code: https://github.com/cran/SCORPIUS -* Date/Publication: 2023-08-07 17:30:05 UTC -* Number of recursive dependencies: 202 - -Run `revdepcheck::cloud_details(, "SCORPIUS")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SCORPIUS/new/SCORPIUS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK -... -Run `reticulate::py_last_error()` for details. -Execution halted - - ‘anndata.Rmd’ using ‘UTF-8’... failed - ‘ginhoux.Rmd’ using ‘UTF-8’... OK - ‘simulated-data.Rmd’ using ‘UTF-8’... OK - ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCORPIUS/old/SCORPIUS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCORPIUS/DESCRIPTION’ ... OK -... -Run `reticulate::py_last_error()` for details. -Execution halted - - ‘anndata.Rmd’ using ‘UTF-8’... failed - ‘ginhoux.Rmd’ using ‘UTF-8’... OK - ‘simulated-data.Rmd’ using ‘UTF-8’... OK - ‘singlecellexperiment.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -# scpoisson - -
- -* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/scpoisson -* Date/Publication: 2022-08-17 06:50:02 UTC -* Number of recursive dependencies: 203 - -Run `revdepcheck::cloud_details(, "scpoisson")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scpoisson/new/scpoisson.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scpoisson/DESCRIPTION’ ... OK -... -* this is package ‘scpoisson’ version ‘0.0.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scpoisson/old/scpoisson.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scpoisson/DESCRIPTION’ ... OK -... -* this is package ‘scpoisson’ version ‘0.0.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'Seurat', 'SeuratObject' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SCpubr - -
- -* Version: 2.0.2 -* GitHub: https://github.com/enblacar/SCpubr -* Source code: https://github.com/cran/SCpubr -* Date/Publication: 2023-10-11 09:50:02 UTC -* Number of recursive dependencies: 306 - -Run `revdepcheck::cloud_details(, "SCpubr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SCpubr/new/SCpubr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCpubr/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘reference_manual.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SCpubr/old/SCpubr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SCpubr/DESCRIPTION’ ... OK +* installing *source* package ‘scpi’ ... +** package ‘scpi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstVal"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : ... -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘reference_manual.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORExpr"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORNULL"; definition not updated +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scpi’ +* removing ‘/tmp/workdir/scpi/new/scpi.Rcheck/scpi’ +``` +### CRAN +``` +* installing *source* package ‘scpi’ ... +** package ‘scpi’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstVal"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : +... +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORExpr"; definition not updated +Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "ConstValORNULL"; definition not updated +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scpi’ +* removing ‘/tmp/workdir/scpi/old/scpi.Rcheck/scpi’ ``` @@ -7946,71 +6780,73 @@ Status: 2 NOTEs * GitHub: NA * Source code: https://github.com/cran/scRNAstat * Date/Publication: 2021-09-22 08:10:02 UTC -* Number of recursive dependencies: 155 +* Number of recursive dependencies: 156 Run `revdepcheck::cloud_details(, "scRNAstat")` for more info -## Error before installation +## In both + +* checking whether package ‘scRNAstat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +* installing *source* package ‘scRNAstat’ ... +** package ‘scRNAstat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘SeuratObject’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ ... -* this is package ‘scRNAstat’ version ‘0.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘DBI’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scRNAstat’ +* removing ‘/tmp/workdir/scRNAstat/new/scRNAstat.Rcheck/scRNAstat’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/scRNAstat/old/scRNAstat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scRNAstat/DESCRIPTION’ ... OK +* installing *source* package ‘scRNAstat’ ... +** package ‘scRNAstat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘Seurat’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘SeuratObject’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ ... -* this is package ‘scRNAstat’ version ‘0.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +Warning: namespace ‘DBI’ is not available and has been replaced +by .GlobalEnv when processing object ‘AJ064_small_last_sce’ +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘scRNAstat’ +* removing ‘/tmp/workdir/scRNAstat/old/scRNAstat.Rcheck/scRNAstat’ ``` @@ -8086,7 +6922,7 @@ ERROR: lazy loading failed for package ‘sectorgap’ * GitHub: NA * Source code: https://github.com/cran/SEERaBomb * Date/Publication: 2019-12-12 18:50:03 UTC -* Number of recursive dependencies: 184 +* Number of recursive dependencies: 185 Run `revdepcheck::cloud_details(, "SEERaBomb")` for more info @@ -8160,22 +6996,222 @@ ERROR: lazy loading failed for package ‘SEERaBomb’
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/semicmprskcoxmsm -* Date/Publication: 2022-04-29 23:40:02 UTC -* Number of recursive dependencies: 70 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/semicmprskcoxmsm +* Date/Publication: 2022-04-29 23:40:02 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info + +
+ +## In both + +* checking whether package ‘semicmprskcoxmsm’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +### CRAN + +``` +* installing *source* package ‘semicmprskcoxmsm’ ... +** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ +* removing ‘/tmp/workdir/semicmprskcoxmsm/old/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ + + +``` +# SensMap + +
+ +* Version: 0.7 +* GitHub: https://github.com/IbtihelRebhi/SensMap +* Source code: https://github.com/cran/SensMap +* Date/Publication: 2022-07-04 19:00:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "SensMap")` for more info + +
+ +## In both + +* checking whether package ‘SensMap’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/SensMap’ + + +``` +### CRAN + +``` +* installing *source* package ‘SensMap’ ... +** package ‘SensMap’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SensMap’ +* removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ + + +``` +# Seurat + +
+ +* Version: 5.1.0 +* GitHub: https://github.com/satijalab/seurat +* Source code: https://github.com/cran/Seurat +* Date/Publication: 2024-05-10 17:23:17 UTC +* Number of recursive dependencies: 266 + +Run `revdepcheck::cloud_details(, "Seurat")` for more info + +
+ +## In both + +* checking whether package ‘Seurat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’ + + +``` +### CRAN + +``` +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ + + +``` +# shinyTempSignal + +
+ +* Version: 0.0.8 +* GitHub: https://github.com/YuLab-SMU/shinyTempSignal +* Source code: https://github.com/cran/shinyTempSignal +* Date/Publication: 2024-03-06 08:00:02 UTC +* Number of recursive dependencies: 137 -Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info +Run `revdepcheck::cloud_details(, "shinyTempSignal")` for more info
## In both -* checking whether package ‘semicmprskcoxmsm’ can be installed ... ERROR +* checking whether package ‘shinyTempSignal’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/00install.out’ for details. ``` ## Installation @@ -8183,57 +7219,59 @@ Run `revdepcheck::cloud_details(, "semicmprskcoxmsm")` for more info ### Devel ``` -* installing *source* package ‘semicmprskcoxmsm’ ... -** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘shinyTempSignal’ ... +** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ -* removing ‘/tmp/workdir/semicmprskcoxmsm/new/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ +ERROR: lazy loading failed for package ‘shinyTempSignal’ +* removing ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/shinyTempSignal’ ``` ### CRAN ``` -* installing *source* package ‘semicmprskcoxmsm’ ... -** package ‘semicmprskcoxmsm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘shinyTempSignal’ ... +** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ -* removing ‘/tmp/workdir/semicmprskcoxmsm/old/semicmprskcoxmsm.Rcheck/semicmprskcoxmsm’ +ERROR: lazy loading failed for package ‘shinyTempSignal’ +* removing ‘/tmp/workdir/shinyTempSignal/old/shinyTempSignal.Rcheck/shinyTempSignal’ ``` -# SensMap +# sievePH
-* Version: 0.7 -* GitHub: https://github.com/IbtihelRebhi/SensMap -* Source code: https://github.com/cran/SensMap -* Date/Publication: 2022-07-04 19:00:02 UTC -* Number of recursive dependencies: 146 +* Version: 1.1 +* GitHub: https://github.com/mjuraska/sievePH +* Source code: https://github.com/cran/sievePH +* Date/Publication: 2024-05-17 23:40:02 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "SensMap")` for more info +Run `revdepcheck::cloud_details(, "sievePH")` for more info
## In both -* checking whether package ‘SensMap’ can be installed ... ERROR +* checking whether package ‘sievePH’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/00install.out’ for details. ``` ## Installation @@ -8241,40 +7279,46 @@ Run `revdepcheck::cloud_details(, "SensMap")` for more info ### Devel ``` -* installing *source* package ‘SensMap’ ... -** package ‘SensMap’ successfully unpacked and MD5 sums checked +* installing *source* package ‘sievePH’ ... +** package ‘sievePH’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/new/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SensMap’ -* removing ‘/tmp/workdir/SensMap/new/SensMap.Rcheck/SensMap’ +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/sievePH’ ``` ### CRAN ``` -* installing *source* package ‘SensMap’ ... -** package ‘SensMap’ successfully unpacked and MD5 sums checked +* installing *source* package ‘sievePH’ ... +** package ‘sievePH’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/old/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs ** R -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SensMap’ -* removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ ``` @@ -8286,71 +7330,73 @@ ERROR: lazy loading failed for package ‘SensMap’ * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac * Date/Publication: 2024-04-04 02:42:57 UTC -* Number of recursive dependencies: 249 +* Number of recursive dependencies: 250 Run `revdepcheck::cloud_details(, "Signac")` for more info -## Error before installation +## In both + +* checking whether package ‘Signac’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SeuratObject’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/new/Signac.Rcheck/Signac’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SeuratObject’ - -Package suggested but not available for checking: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/old/Signac.Rcheck/Signac’ ``` @@ -8362,7 +7408,7 @@ Status: 1 ERROR * GitHub: https://github.com/arcaldwell49/SimplyAgree * Source code: https://github.com/cran/SimplyAgree * Date/Publication: 2024-03-21 14:20:06 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 115 Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info @@ -8389,6 +7435,11 @@ Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace @@ -8409,6 +7460,11 @@ ERROR: lazy loading failed for package ‘SimplyAgree’ *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace @@ -8550,7 +7606,7 @@ ERROR: lazy loading failed for package ‘SNPassoc’ * GitHub: NA * Source code: https://github.com/cran/snplinkage * Date/Publication: 2023-05-04 08:10:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "snplinkage")` for more info @@ -8626,94 +7682,18 @@ Status: 1 ERROR * GitHub: https://github.com/constantAmateur/SoupX * Source code: https://github.com/cran/SoupX * Date/Publication: 2022-11-01 14:00:03 UTC -* Number of recursive dependencies: 200 +* Number of recursive dependencies: 201 Run `revdepcheck::cloud_details(, "SoupX")` for more info -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SoupX/new/SoupX.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SoupX/DESCRIPTION’ ... OK -... -* this is package ‘SoupX’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SoupX/old/SoupX.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SoupX/DESCRIPTION’ ... OK -... -* this is package ‘SoupX’ version ‘1.6.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# SpaDES.core - -
- -* Version: 2.0.5 -* GitHub: https://github.com/PredictiveEcology/SpaDES.core -* Source code: https://github.com/cran/SpaDES.core -* Date/Publication: 2024-04-25 17:20:02 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info - -
- ## In both -* checking whether package ‘SpaDES.core’ can be installed ... ERROR +* checking whether package ‘SoupX’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/00install.out’ for details. ``` ## Installation @@ -8721,38 +7701,40 @@ Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info ### Devel ``` -* installing *source* package ‘SpaDES.core’ ... -** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ -Error in get(x, envir = ns, inherits = FALSE) : - object '.addingToMemoisedMsg' not found -Error: unable to load R code in package ‘SpaDES.core’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SpaDES.core’ -* removing ‘/tmp/workdir/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core’ +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/SoupX’ ``` ### CRAN ``` -* installing *source* package ‘SpaDES.core’ ... -** package ‘SpaDES.core’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Creating a new generic function for ‘citation’ in package ‘SpaDES.core’ -Error in get(x, envir = ns, inherits = FALSE) : - object '.addingToMemoisedMsg' not found -Error: unable to load R code in package ‘SpaDES.core’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SpaDES.core’ -* removing ‘/tmp/workdir/SpaDES.core/old/SpaDES.core.Rcheck/SpaDES.core’ +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/old/SoupX.Rcheck/SoupX’ ``` @@ -8797,112 +7779,36 @@ installing to /tmp/workdir/sparsereg/new/sparsereg.Rcheck/00LOCK-sparsereg/00new ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sparsereg’ -* removing ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/sparsereg’ - - -``` -### CRAN - -``` -* installing *source* package ‘sparsereg’ ... -** package ‘sparsereg’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sparsereg’ -* removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ - - -``` -# SPECK - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SPECK -* Date/Publication: 2023-11-17 17:30:02 UTC -* Number of recursive dependencies: 161 - -Run `revdepcheck::cloud_details(, "SPECK")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SPECK/new/SPECK.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SPECK/DESCRIPTION’ ... OK -... -Package required but not available: ‘Seurat’ - -Package required and available but unsuitable version: ‘Matrix’ - -Package suggested but not available for checking: ‘SeuratObject’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/new/sparsereg.Rcheck/sparsereg’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/SPECK/old/SPECK.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SPECK/DESCRIPTION’ ... OK -... -Package required but not available: ‘Seurat’ - -Package required and available but unsuitable version: ‘Matrix’ - -Package suggested but not available for checking: ‘SeuratObject’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘sparsereg’ ... +** package ‘sparsereg’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sparsereg’ +* removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ ``` @@ -8986,7 +7892,7 @@ ERROR: lazy loading failed for package ‘spikeSlabGAM’ * GitHub: https://github.com/StatsWithR/statsr * Source code: https://github.com/cran/statsr * Date/Publication: 2021-01-22 20:40:03 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 97 Run `revdepcheck::cloud_details(, "statsr")` for more info @@ -9048,7 +7954,7 @@ ERROR: lazy loading failed for package ‘statsr’ * GitHub: NA * Source code: https://github.com/cran/streamDAG * Date/Publication: 2023-10-06 18:50:02 UTC -* Number of recursive dependencies: 133 +* Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "streamDAG")` for more info @@ -9326,7 +8232,7 @@ ERROR: lazy loading failed for package ‘tempted’ * GitHub: https://github.com/YuLab-SMU/tidydr * Source code: https://github.com/cran/tidydr * Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 71 +* Number of recursive dependencies: 74 Run `revdepcheck::cloud_details(, "tidydr")` for more info @@ -9388,7 +8294,7 @@ ERROR: lazy loading failed for package ‘tidydr’ * GitHub: NA * Source code: https://github.com/cran/tidyEdSurvey * Date/Publication: 2024-05-14 20:20:03 UTC -* Number of recursive dependencies: 107 +* Number of recursive dependencies: 111 Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info @@ -9412,8 +8318,13 @@ Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info ** using staged installation ** R ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +In addition: Warning message: +In check_dep_version() : ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Execution halted ERROR: lazy loading failed for package ‘tidyEdSurvey’ * removing ‘/tmp/workdir/tidyEdSurvey/new/tidyEdSurvey.Rcheck/tidyEdSurvey’ @@ -9428,8 +8339,13 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1.1 is required +Error: package or namespace load failed for ‘EdSurvey’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +In addition: Warning message: +In check_dep_version() : ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Execution halted ERROR: lazy loading failed for package ‘tidyEdSurvey’ * removing ‘/tmp/workdir/tidyEdSurvey/old/tidyEdSurvey.Rcheck/tidyEdSurvey’ @@ -9444,71 +8360,57 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ * GitHub: https://github.com/stemangiola/tidyseurat * Source code: https://github.com/cran/tidyseurat * Date/Publication: 2024-01-10 04:50:02 UTC -* Number of recursive dependencies: 206 +* Number of recursive dependencies: 207 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidyseurat/DESCRIPTION’ ... OK -... -* this is package ‘tidyseurat’ version ‘0.8.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'SeuratObject', 'Seurat' +## In both -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking whether package ‘tidyseurat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘tidyseurat’ ... +** package ‘tidyseurat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyseurat’ +* removing ‘/tmp/workdir/tidyseurat/new/tidyseurat.Rcheck/tidyseurat’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidyseurat/DESCRIPTION’ ... OK -... -* this is package ‘tidyseurat’ version ‘0.8.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'SeuratObject', 'Seurat' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘tidyseurat’ ... +** package ‘tidyseurat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyseurat’ +* removing ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck/tidyseurat’ ``` @@ -9575,82 +8477,6 @@ ERROR: lazy loading failed for package ‘tidyvpc’ * removing ‘/tmp/workdir/tidyvpc/old/tidyvpc.Rcheck/tidyvpc’ -``` -# treefit - -
- -* Version: 1.0.2 -* GitHub: https://github.com/hayamizu-lab/treefit-r -* Source code: https://github.com/cran/treefit -* Date/Publication: 2022-01-18 07:50:02 UTC -* Number of recursive dependencies: 159 - -Run `revdepcheck::cloud_details(, "treefit")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/treefit/new/treefit.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘treefit/DESCRIPTION’ ... OK -... - - When sourcing ‘working-with-seurat.R’: -Error: there is no package called ‘Seurat’ -Execution halted - - ‘treefit.Rmd’ using ‘UTF-8’... OK - ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/treefit/old/treefit.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘treefit/DESCRIPTION’ ... OK -... - - When sourcing ‘working-with-seurat.R’: -Error: there is no package called ‘Seurat’ -Execution halted - - ‘treefit.Rmd’ using ‘UTF-8’... OK - ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - - - ``` # TriDimRegression @@ -9856,26 +8682,26 @@ ERROR: lazy loading failed for package ‘twang’ ``` -# valse +# vdg
-* Version: 0.1-0 +* Version: 1.2.3 * GitHub: NA -* Source code: https://github.com/cran/valse -* Date/Publication: 2021-05-31 08:00:02 UTC -* Number of recursive dependencies: 55 +* Source code: https://github.com/cran/vdg +* Date/Publication: 2024-04-23 13:00:02 UTC +* Number of recursive dependencies: 45 -Run `revdepcheck::cloud_details(, "valse")` for more info +Run `revdepcheck::cloud_details(, "vdg")` for more info
## In both -* checking whether package ‘valse’ can be installed ... ERROR +* checking whether package ‘vdg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/valse/new/valse.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/vdg/new/vdg.Rcheck/00install.out’ for details. ``` ## Installation @@ -9883,77 +8709,71 @@ Run `revdepcheck::cloud_details(, "valse")` for more info ### Devel ``` -* installing *source* package ‘valse’ ... -** package ‘valse’ successfully unpacked and MD5 sums checked +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o -... -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): - unable to load shared object '/tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free -Error: loading failed +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: loading failed -* removing ‘/tmp/workdir/valse/new/valse.Rcheck/valse’ +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/new/vdg.Rcheck/vdg’ ``` ### CRAN ``` -* installing *source* package ‘valse’ ... -** package ‘valse’ successfully unpacked and MD5 sums checked +* installing *source* package ‘vdg’ ... +** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o -... -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...): - unable to load shared object '/tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so': - /tmp/workdir/valse/old/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_permutation_free -Error: loading failed +using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +gfortran -fpic -g -O2 -c FDS.f -o FDS.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: loading failed -* removing ‘/tmp/workdir/valse/old/valse.Rcheck/valse’ +ERROR: lazy loading failed for package ‘vdg’ +* removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ ``` -# vdg +# visa
-* Version: 1.2.3 -* GitHub: NA -* Source code: https://github.com/cran/vdg -* Date/Publication: 2024-04-23 13:00:02 UTC -* Number of recursive dependencies: 45 +* Version: 0.1.0 +* GitHub: https://github.com/kang-yu/visa +* Source code: https://github.com/cran/visa +* Date/Publication: 2021-04-20 07:20:02 UTC +* Number of recursive dependencies: 140 -Run `revdepcheck::cloud_details(, "vdg")` for more info +Run `revdepcheck::cloud_details(, "visa")` for more info
## In both -* checking whether package ‘vdg’ can be installed ... ERROR +* checking whether package ‘visa’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/vdg/new/vdg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/visa/new/visa.Rcheck/00install.out’ for details. ``` ## Installation @@ -9961,48 +8781,40 @@ Run `revdepcheck::cloud_details(, "vdg")` for more info ### Devel ``` -* installing *source* package ‘vdg’ ... -** package ‘vdg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘visa’ ... +** package ‘visa’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gfortran -fpic -g -O2 -c FDS.f -o FDS.o -gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘vdg’ -* removing ‘/tmp/workdir/vdg/new/vdg.Rcheck/vdg’ +ERROR: lazy loading failed for package ‘visa’ +* removing ‘/tmp/workdir/visa/new/visa.Rcheck/visa’ ``` ### CRAN ``` -* installing *source* package ‘vdg’ ... -** package ‘vdg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘visa’ ... +** package ‘visa’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gfortran -fpic -g -O2 -c FDS.f -o FDS.o -gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘quantreg’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘vdg’ -* removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ +ERROR: lazy loading failed for package ‘visa’ +* removing ‘/tmp/workdir/visa/old/visa.Rcheck/visa’ ``` @@ -10014,7 +8826,7 @@ ERROR: lazy loading failed for package ‘vdg’ * GitHub: https://github.com/fawda123/WRTDStidal * Source code: https://github.com/cran/WRTDStidal * Date/Publication: 2023-10-20 09:00:11 UTC -* Number of recursive dependencies: 140 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "WRTDStidal")` for more info diff --git a/revdep/problems.md b/revdep/problems.md index 1280d2fbbb..8e2e437056 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,2640 +1,1317 @@ -# asmbPLS +# activAnalyzer (patchwork) -
+# actxps (thematic) -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/asmbPLS -* Date/Publication: 2023-04-17 09:50:05 UTC -* Number of recursive dependencies: 100 +# AeRobiology (unknown) -Run `revdepcheck::cloud_details(, "asmbPLS")` for more info +``` +#
+# +# * Version: 2.0.1 +# * GitHub: NA +# * Source code: https://github.com/cran/AeRobiology +# * Date/Publication: 2019-06-03 06:20:03 UTC +# * Number of recursive dependencies: 98 +# +# Run `revdepcheck::cloud_details(, "AeRobiology")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘my-vignette.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘my-vignette.Rmd’ +# ... +# + export.plot = FALSE, export.result = FALSE, n.types = 3, +# + y.start = 2011, y.end = .... [TRUNCATED] +# +# > iplot_abundance(munich_pollen, interpolation = FALSE, +# + export.plot = FALSE, export.result = FALSE, n.types = 3, +# + y.start = 2011, y.end = .... [TRUNCATED] +# +# When sourcing ‘my-vignette.R’: +# Error: subscript out of bounds +# Execution halted +# +# ‘my-vignette.Rmd’ using ‘UTF-8’... failed +# ``` +``` -
+# agricolaeplotr (missing labels) -## Newly broken +# AnalysisLin (plotly) -* checking whether package ‘asmbPLS’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘asmbPLS’ - See ‘/tmp/workdir/asmbPLS/new/asmbPLS.Rcheck/00install.out’ for details. - ``` +# animbook (plotly) -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.7Mb - sub-directories of 1Mb or more: - data 2.1Mb - libs 16.5Mb - ``` - -# bdl - -
- -* Version: 1.0.5 -* GitHub: https://github.com/statisticspoland/R_Package_to_API_BDL -* Source code: https://github.com/cran/bdl -* Date/Publication: 2023-02-24 15:00:02 UTC -* Number of recursive dependencies: 144 - -Run `revdepcheck::cloud_details(, "bdl")` for more info - -
- -## Newly broken - -* checking whether package ‘bdl’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bdl’ - See ‘/tmp/workdir/bdl/new/bdl.Rcheck/00install.out’ for details. - ``` - -# bdscale - -
- -* Version: 2.0.0 -* GitHub: https://github.com/dvmlls/bdscale -* Source code: https://github.com/cran/bdscale -* Date/Publication: 2016-03-17 13:27:37 -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "bdscale")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘bdscale.Rmd’ - ... - > options <- as.Date(c("2014-08-15", "2014-09-19")) - - > plot + geom_vline(xintercept = as.numeric(options), - + size = 2, alpha = 0.25) + ggtitle("calendar dates, option expiry") - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - When sourcing ‘bdscale.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘bdscale.Rmd’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘bdscale.Rmd’ using rmarkdown - ``` - -# biclustermd - -
- -* Version: 0.2.3 -* GitHub: https://github.com/jreisner/biclustermd -* Source code: https://github.com/cran/biclustermd -* Date/Publication: 2021-06-17 15:10:06 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "biclustermd")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(biclustermd) - Loading required package: ggplot2 - Loading required package: tidyr - - Attaching package: 'tidyr' - - ... - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── - ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. - Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘nycflights13’ - All declared Imports should be used. - ``` - -# brolgar - -
- -* Version: 1.0.1 -* GitHub: https://github.com/njtierney/brolgar -* Source code: https://github.com/cran/brolgar -* Date/Publication: 2024-05-10 14:50:34 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "brolgar")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘brolgar-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_sample - > ### Title: Facet data into groups to facilitate exploration - > ### Aliases: facet_sample - > - > ### ** Examples - > - > library(ggplot2) - > ggplot(heights, - + aes(x = year, - + y = height_cm, - + group = country)) + - + geom_line() + - + facet_sample() - Error in if (params$as.table) { : argument is of length zero - Calls: ... -> setup -> -> compute_layout - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘getting-started.Rmd’ - ... - > set.seed(2019 - 7 - 23 - 1936) - - > library(ggplot2) - - > ggplot(wages, aes(x = xp, y = ln_wages, group = id)) + - + geom_line() + facet_strata() - - ... - Error: argument is of length zero - Execution halted - - ‘exploratory-modelling.Rmd’ using ‘UTF-8’... OK - ‘finding-features.Rmd’ using ‘UTF-8’... OK - ‘getting-started.Rmd’ using ‘UTF-8’... failed - ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK - ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK - ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed - ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown - ``` - -# bSi - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/bSi -* Date/Publication: 2024-01-24 15:52:57 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "bSi")` for more info - -
- -## Newly broken - -* checking whether package ‘bSi’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘bSi’ - See ‘/tmp/workdir/bSi/new/bSi.Rcheck/00install.out’ for details. - ``` - -# CausalImpact - -
- -* Version: 1.3.0 -* GitHub: NA -* Source code: https://github.com/cran/CausalImpact -* Date/Publication: 2022-11-09 08:40:40 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "CausalImpact")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘CausalImpact_import_test.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # Copyright 2014-2022 Google Inc. All rights reserved. - > # - > # Licensed under the Apache License, Version 2.0 (the "License"); - > # you may not use this file except in compliance with the License. - > # You may obtain a copy of the License at - > # - ... - 20. └─base::lapply(df[aesthetics], self$transform) - 21. └─ggplot2 (local) FUN(X[[i]], ...) - 22. └─ggplot2 (local) transform(..., self = self) - 23. └─transformation$transform(x) - 24. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 25. └─rlang::abort(...) - - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 739 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘CausalImpact.Rmd’ - ... - - > impact <- CausalImpact(data, pre.period, post.period) - - > q <- plot(impact) + theme_bw(base_size = 11) - - > suppressWarnings(plot(q)) - - When sourcing ‘CausalImpact.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘CausalImpact.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘CausalImpact.Rmd’ using rmarkdown - ``` - -# ClusROC - -
- -* Version: 1.0.2 -* GitHub: https://github.com/toduckhanh/ClusROC -* Source code: https://github.com/cran/ClusROC -* Date/Publication: 2022-11-17 15:00:02 UTC -* Number of recursive dependencies: 107 - -Run `revdepcheck::cloud_details(, "ClusROC")` for more info - -
- -## Newly broken - -* checking whether package ‘ClusROC’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ClusROC’ - See ‘/tmp/workdir/ClusROC/new/ClusROC.Rcheck/00install.out’ for details. - ``` - -# clustEff - -
- -* Version: 0.3.1 -* GitHub: NA -* Source code: https://github.com/cran/clustEff -* Date/Publication: 2024-01-23 08:52:55 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "clustEff")` for more info - -
- -## Newly broken - -* checking whether package ‘clustEff’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘clustEff’ - See ‘/tmp/workdir/clustEff/new/clustEff.Rcheck/00install.out’ for details. - ``` - -# CLVTools - -
- -* Version: 0.10.0 -* GitHub: https://github.com/bachmannpatrick/CLVTools -* Source code: https://github.com/cran/CLVTools -* Date/Publication: 2023-10-23 20:10:02 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "CLVTools")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘CLVTools.Rmd’ - ... - 248: 39.95483 2.336902 - 249: 34.28958 38.969738 - 250: 47.35500 7.284870 - - > plot(clv.apparel) - Plotting from 2005-01-03 until 2006-07-16. - - When sourcing ‘CLVTools.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘CLVTools.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘CLVTools.Rmd’ using rmarkdown - - Quitting from lines 270-272 [plot-actual] (CLVTools.Rmd) - Error: processing vignette 'CLVTools.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘CLVTools.Rmd’ - - SUMMARY: processing the following file failed: - ‘CLVTools.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 17.4Mb - sub-directories of 1Mb or more: - libs 15.5Mb - ``` - -# coda4microbiome - -
- -* Version: 0.2.3 -* GitHub: https://github.com/malucalle/coda4microbiome -* Source code: https://github.com/cran/coda4microbiome -* Date/Publication: 2024-02-21 08:30:06 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "coda4microbiome")` for more info - -
- -## Newly broken - -* checking whether package ‘coda4microbiome’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘coda4microbiome’ - See ‘/tmp/workdir/coda4microbiome/new/coda4microbiome.Rcheck/00install.out’ for details. - ``` - -# CompAREdesign - -
- -* Version: 2.3.1 -* GitHub: NA -* Source code: https://github.com/cran/CompAREdesign -* Date/Publication: 2024-02-15 13:00:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "CompAREdesign")` for more info - -
- -## Newly broken - -* checking whether package ‘CompAREdesign’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘CompAREdesign’ - See ‘/tmp/workdir/CompAREdesign/new/CompAREdesign.Rcheck/00install.out’ for details. - ``` - -# covidcast - -
- -* Version: 0.5.2 -* GitHub: https://github.com/cmu-delphi/covidcast -* Source code: https://github.com/cran/covidcast -* Date/Publication: 2023-07-12 23:40:06 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "covidcast")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(covidcast) - We encourage COVIDcast API users to register on our mailing list: - https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api - We'll send announcements about new data sources, package updates, - server maintenance, and new features. - > - ... - • plot/default-county-choropleth.svg - • plot/default-hrr-choropleth-with-include.svg - • plot/default-msa-choropleth-with-include.svg - • plot/default-state-choropleth-with-include.svg - • plot/default-state-choropleth-with-range.svg - • plot/state-choropleth-with-no-metadata.svg - • plot/state-line-graph-with-range.svg - • plot/state-line-graph-with-stderrs.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘plotting-signals.Rmd’ - ... - > plot(inum, choro_col = colors, choro_params = list(breaks = breaks), - + title = "New COVID cases (7-day trailing average) on 2020-07-14") - - When sourcing ‘plotting-signals.R’: - Error: Problem while setting up geom aesthetics. - ℹ Error occurred in the 5th layer. - Caused by error in `check_aesthetics()`: - ! Aesthetics must be either length 1 or the same as the data (3078). - ✖ Fix the following mappings: `fill`. - Execution halted - - ‘correlation-utils.Rmd’ using ‘UTF-8’... OK - ‘covidcast.Rmd’ using ‘UTF-8’... OK - ‘external-data.Rmd’ using ‘UTF-8’... OK - ‘multi-signals.Rmd’ using ‘UTF-8’... OK - ‘plotting-signals.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘correlation-utils.Rmd’ using rmarkdown - --- finished re-building ‘correlation-utils.Rmd’ - - --- re-building ‘covidcast.Rmd’ using rmarkdown - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 20 marked UTF-8 strings - ``` - -# Coxmos - -
- -* Version: 1.0.2 -* GitHub: https://github.com/BiostatOmics/Coxmos -* Source code: https://github.com/cran/Coxmos -* Date/Publication: 2024-03-25 20:32:38 UTC -* Number of recursive dependencies: 204 - -Run `revdepcheck::cloud_details(, "Coxmos")` for more info - -
- -## Newly broken - -* checking Rd files ... WARNING - ``` - prepare_Rd: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Coxmos-pipeline.Rmd’ - ... - Warning in data("X_proteomic") : data set ‘X_proteomic’ not found - - > data("Y_proteomic") - Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found - - > X <- X_proteomic - - When sourcing ‘Coxmos-pipeline.R’: - Error: object 'X_proteomic' not found - Execution halted - - ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... OK - ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - data 2.1Mb - doc 2.9Mb - ``` - -# csa - -
- -* Version: 0.7.1 -* GitHub: https://github.com/imarkonis/csa -* Source code: https://github.com/cran/csa -* Date/Publication: 2023-10-24 13:40:11 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "csa")` for more info - -
- -## Newly broken - -* checking whether package ‘csa’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘csa’ - See ‘/tmp/workdir/csa/new/csa.Rcheck/00install.out’ for details. - ``` - -# deeptime - -
- -* Version: 1.1.1 -* GitHub: https://github.com/willgearty/deeptime -* Source code: https://github.com/cran/deeptime -* Date/Publication: 2024-03-08 17:10:10 UTC -* Number of recursive dependencies: 181 - -Run `revdepcheck::cloud_details(, "deeptime")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘deeptime-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_wrap_color - > ### Title: Wrap a 1d ribbon of panels into 2d with colored strips - > ### Aliases: facet_wrap_color FacetWrapColor - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 6. │ └─ggplot2 (local) setup(..., self = self) - 7. │ └─self$facet$compute_layout(data, self$facet_params) - 8. │ └─ggplot2 (local) compute_layout(..., self = self) - 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 10. │ └─ggplot2:::data_frame0(...) - 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 12. └─vctrs:::stop_recycle_incompatible_size(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(deeptime) - > - > test_check("deeptime") - Scale for y is already present. - Adding another scale for y, which will replace the existing scale. - Scale for y is already present. - ... - • gggeo_scale/gggeo-scale-top-new.svg - • gggeo_scale/gggeo-scale-top-old.svg - • points_range/geom-points-range-aes-new.svg - • points_range/geom-points-range-aes-old.svg - • points_range/geom-points-range-bg-new.svg - • points_range/geom-points-range-bg-old.svg - • points_range/geom-points-range-h-new.svg - • points_range/geom-points-range-h-old.svg - Error: Test failures - Execution halted - ``` - -# DEGRE - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/DEGRE -* Date/Publication: 2022-11-02 09:32:57 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "DEGRE")` for more info - -
- -## Newly broken - -* checking whether package ‘DEGRE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘DEGRE’ - See ‘/tmp/workdir/DEGRE/new/DEGRE.Rcheck/00install.out’ for details. - ``` - -# did - -
- -* Version: 2.1.2 -* GitHub: https://github.com/bcallaway11/did -* Source code: https://github.com/cran/did -* Date/Publication: 2022-07-20 16:00:05 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "did")` for more info - -
- -## Newly broken - -* checking whether package ‘did’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘did’ - See ‘/tmp/workdir/did/new/did.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking running R code from vignettes ... WARNING - ``` - Errors in running code in vignettes: - when running code in ‘TWFE.Rmd’ - ... - - > knitr::opts_chunk$set(collapse = TRUE, comment = "#>", - + echo = TRUE, eval = FALSE) - - > library(tidyverse) - - When sourcing ‘TWFE.R’: - ... - - When sourcing ‘pre-testing.R’: - Error: cannot open the connection - Execution halted - - ‘TWFE.Rmd’ using ‘UTF-8’... failed - ‘did-basics.Rmd’ using ‘UTF-8’... OK - ‘extensions.Rmd’ using ‘UTF-8’... failed - ‘multi-period-did.Rmd’ using ‘UTF-8’... OK - ‘pre-testing.Rmd’ using ‘UTF-8’... failed - ``` - -# EpiCurve - -
- -* Version: 2.4-2 -* GitHub: https://github.com/IamKDO/EpiCurve -* Source code: https://github.com/cran/EpiCurve -* Date/Publication: 2021-07-14 16:20:05 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "EpiCurve")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘EpiCurve.Rmd’ - ... - |2016-11-06 | 6.60| 116| - |2016-11-07 | 7.68| 141| - |2016-11-07 | 10.08| 126| - - > EpiCurve(DF, date = "UTS", period = "day", colors = "#9900ef", - + xlabel = sprintf("From %s to %s", min(DF$UTS), max(DF$UTS))) - - When sourcing ‘EpiCurve.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘EpiCurve.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘EpiCurve.Rmd’ using rmarkdown - - Quitting from lines 103-106 [unnamed-chunk-3] (EpiCurve.Rmd) - Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘EpiCurve.Rmd’ - - SUMMARY: processing the following file failed: - ‘EpiCurve.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘tibble’ - All declared Imports should be used. - ``` - -# epiR - -
- -* Version: 2.0.74 -* GitHub: NA -* Source code: https://github.com/cran/epiR -* Date/Publication: 2024-04-27 12:30:02 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "epiR")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘epiR_descriptive.Rmd’ - ... - + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", - + li .... [TRUNCATED] - - > ggplot(data = dat.df, aes(x = as.Date(odate))) + theme_bw() + - + geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", - + li .... [TRUNCATED] - - When sourcing ‘epiR_descriptive.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘epiR_descriptive.Rmd’... failed - ‘epiR_measures_of_association.Rmd’... OK - ‘epiR_sample_size.Rmd’... OK - ‘epiR_surveillance.Rmd’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘epiR_descriptive.Rmd’ using rmarkdown - ``` - -# FuncNN - -
- -* Version: 1.0 -* GitHub: https://github.com/b-thi/FuncNN -* Source code: https://github.com/cran/FuncNN -* Date/Publication: 2020-09-15 09:40:15 UTC -* Number of recursive dependencies: 170 - -Run `revdepcheck::cloud_details(, "FuncNN")` for more info - -
- -## Newly broken - -* checking whether package ‘FuncNN’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘FuncNN’ - See ‘/tmp/workdir/FuncNN/new/FuncNN.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘foreach’ - All declared Imports should be used. - ``` - -# geostan - -
- -* Version: 0.6.1 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-05-10 22:23:01 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "geostan")` for more info - -
+# ANN2 (missing labels) -## Newly broken +# aplot (patchwork) -* checking whether package ‘geostan’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. - ``` +# applicable (missing labels) -## Newly fixed +# ASRgenomics (factoextra) -* checking installed package size ... NOTE - ``` - installed size is 129.8Mb - sub-directories of 1Mb or more: - libs 127.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -## Installation - -### Devel +# autoplotly (plotly) -``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -stanExports_foundation.cc:32:1: fatal error: error writing to /tmp/cccy6wQ6.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 -ERROR: compilation failed for package ‘geostan’ -* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ +# autoReg (patchwork) + +# bartMan (ggnewscale) + +# bayesAB (missing labels) + +# BayesGrowth (ggdist) + +# BayesianReasoning (missing labels) + +# BayesMallows (missing labels) + +# bayesplot (missing labels) + +# bayestestR (patchwork) + +# beastt (ggdist) +# besthr (patchwork) +# biclustermd (xintercept/yintercept class) + +# biodosetools (missing labels) + +# boxly (plotly) + +# braidReports (annotation_logticks) + +# breathtestcore (plot slots) + +# brolgar (facet params: as.table) + +# cartograflow (plotly) + +# cartographr (unknown) + +``` +#
+# +# * Version: 0.2.2 +# * GitHub: https://github.com/da-wi/cartographr +# * Source code: https://github.com/cran/cartographr +# * Date/Publication: 2024-06-28 14:50:09 UTC +# * Number of recursive dependencies: 99 +# +# Run `revdepcheck::cloud_details(, "cartographr")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > # This file is part of the standard setup for testthat. +# > # It is recommended that you do not modify it. +# > # +# > # Where should you do additional test configuration? +# > # Learn more about the roles of various files in: +# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# > # * https://testthat.r-lib.org/articles/special-files.html +# ... +# 21. │ └─base::stop(...) +# 22. └─base::.handleSimpleError(...) +# 23. └─rlang (local) h(simpleError(msg, call)) +# 24. └─handlers[[1L]](cnd) +# 25. └─cli::cli_abort(...) +# 26. └─rlang::abort(...) +# +# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ] +# Error: Test failures +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 5.3Mb +# sub-directories of 1Mb or more: +# data 3.5Mb +# ``` ``` -### CRAN +# cats (plotly) + +# cheem (plotly) + +# chillR (patchwork) + +# chronicle (plotly) + +# circhelp (patchwork) + +# clifro (missing labels) + +# clinDataReview (plotly) + +# clinUtils (plotly) + +# CohortPlat (plotly) + +# CoreMicrobiomeR (plotly) + +# correlationfunnel (plotly) + +# corrViz (plotly) + +# countfitteR (missing labels) + +# covidcast (unknown) + +``` +#
+# +# * Version: 0.5.2 +# * GitHub: https://github.com/cmu-delphi/covidcast +# * Source code: https://github.com/cran/covidcast +# * Date/Publication: 2023-07-12 23:40:06 UTC +# * Number of recursive dependencies: 93 +# +# Run `revdepcheck::cloud_details(, "covidcast")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(covidcast) +# We encourage COVIDcast API users to register on our mailing list: +# https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api +# We'll send announcements about new data sources, package updates, +# server maintenance, and new features. +# > +# ... +# • plot/default-county-choropleth.svg +# • plot/default-hrr-choropleth-with-include.svg +# • plot/default-msa-choropleth-with-include.svg +# • plot/default-state-choropleth-with-include.svg +# • plot/default-state-choropleth-with-range.svg +# • plot/state-choropleth-with-no-metadata.svg +# • plot/state-line-graph-with-range.svg +# • plot/state-line-graph-with-stderrs.svg +# Error: Test failures +# Execution halted +# ``` +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘plotting-signals.Rmd’ +# ... +# > knitr::opts_chunk$set(fig.width = 6, fig.height = 4) +# +# > plot(dv) +# +# When sourcing ‘plotting-signals.R’: +# Error: Problem while setting up geom aesthetics. +# ℹ Error occurred in the 6th layer. +# Caused by error in `$<-.data.frame`: +# ! replacement has 1 row, data has 0 +# Execution halted +# +# ‘correlation-utils.Rmd’ using ‘UTF-8’... OK +# ‘covidcast.Rmd’ using ‘UTF-8’... OK +# ‘external-data.Rmd’ using ‘UTF-8’... OK +# ‘multi-signals.Rmd’ using ‘UTF-8’... OK +# ‘plotting-signals.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘correlation-utils.Rmd’ using rmarkdown +# --- finished re-building ‘correlation-utils.Rmd’ +# +# --- re-building ‘covidcast.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking data for non-ASCII characters ... NOTE +# ``` +# Note: found 20 marked UTF-8 strings +# ``` ``` -* installing *source* package ‘geostan’ ... -** package ‘geostan’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -** help -*** installing help indices -*** copying figures -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (geostan) +# crosshap (plotly) + +# cubble (patchwork) + +# deeptime (ggnewscale) + +# distributional (ggdist) + +# dittoViz (plotly) + +# EGM (missing labels) + +# entropart (default access) + +# epiCleanr (ggdist) + +# esci (ggdist) +# evalITR (unknown) + +``` +#
+# +# * Version: 1.0.0 +# * GitHub: https://github.com/MichaelLLi/evalITR +# * Source code: https://github.com/cran/evalITR +# * Date/Publication: 2023-08-25 23:10:06 UTC +# * Number of recursive dependencies: 167 +# +# Run `revdepcheck::cloud_details(, "evalITR")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘cv_multiple_alg.Rmd’ +# ... +# intersect, setdiff, setequal, union +# +# +# > load("../data/star.rda") +# Warning in readChar(con, 5L, useBytes = TRUE) : +# cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' +# +# ... +# Execution halted +# +# ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed +# ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed +# ‘install.Rmd’ using ‘UTF-8’... OK +# ‘paper_alg1.Rmd’ using ‘UTF-8’... OK +# ‘sample_split.Rmd’ using ‘UTF-8’... failed +# ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed +# ‘user_itr.Rmd’ using ‘UTF-8’... failed +# ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking dependencies in R code ... NOTE +# ``` +# Namespaces in Imports field not imported from: +# ‘forcats’ ‘rqPen’ ‘utils’ +# All declared Imports should be used. +# ``` ``` -# ggedit - -
- -* Version: 0.4.1 -* GitHub: https://github.com/yonicd/ggedit -* Source code: https://github.com/cran/ggedit -* Date/Publication: 2024-03-04 14:40:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "ggedit")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggedit-Ex.R’ failed - The error most likely occurred in: - - > ### Name: print.ggedit - > ### Title: Print ggedit objects - > ### Aliases: print.ggedit - > - > ### ** Examples - > - > p <- as.gglist(pList[1:2]) - ... - 8. │ └─ggplot2 (local) setup(..., self = self) - 9. │ └─self$facet$compute_layout(data, self$facet_params) - 10. │ └─ggplot2 (local) compute_layout(..., self = self) - 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 12. │ └─ggplot2:::data_frame0(...) - 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 14. └─vctrs:::stop_recycle_incompatible_size(...) - 15. └─vctrs:::stop_vctrs(...) - 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -# ggfixest - -
- -* Version: 0.1.0 -* GitHub: https://github.com/grantmcdermott/ggfixest -* Source code: https://github.com/cran/ggfixest -* Date/Publication: 2023-12-14 08:00:06 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "ggfixest")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. - Complete output: - > ## Throttle CPU threads if R CMD check (for CRAN) - > - > if (any(grepl("_R_CHECK", names(Sys.getenv()), fixed = TRUE))) { - + # fixest - + if (requireNamespace("fixest", quietly = TRUE)) { - + library(fixest) - + setFixest_nthreads(1) - ... - ----- FAILED[]: test_ggcoefplot.R<66--66> - call| expect_snapshot_plot(p_did_iid_summ, label = "ggcoefplot_did_iid") - diff| 7580 - info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png - ----- FAILED[]: test_ggcoefplot.R<67--67> - call| expect_snapshot_plot(p_did_iid, label = "ggcoefplot_did_iid") - diff| 7580 - info| Diff plot saved to: _tinysnapshot_review/ggcoefplot_did_iid.png - Error: 12 out of 101 tests failed - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggiplot.Rmd’ - ... - > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), - + ref.line = -1, main = "Staggered treatment: Split mutli-sample") - The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. - Note that you can provide the argument `df.t` directly. - - When sourcing ‘ggiplot.R’: - Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: - The 1st element of 'object' raises and error: - Error in nb * sd : non-numeric argument to binary operator - Execution halted - - ‘ggiplot.Rmd’ using ‘UTF-8’... failed - ``` - -# ggfortify - -
- -* Version: 0.4.17 -* GitHub: https://github.com/sinhrks/ggfortify -* Source code: https://github.com/cran/ggfortify -* Date/Publication: 2024-04-17 04:30:04 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "ggfortify")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘basics.Rmd’ using knitr - - Attaching package: 'zoo' - - The following objects are masked from 'package:base': - - as.Date, as.Date.numeric - ``` - -# ggh4x - -
- -* Version: 0.2.8 -* GitHub: https://github.com/teunbrand/ggh4x -* Source code: https://github.com/cran/ggh4x -* Date/Publication: 2024-01-23 21:00:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "ggh4x")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggh4x-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_nested_wrap - > ### Title: Ribbon of panels with nested strips. - > ### Aliases: facet_nested_wrap - > - > ### ** Examples - > - > # A standard plot - ... - 6. │ └─ggplot2 (local) setup(..., self = self) - 7. │ └─self$facet$compute_layout(data, self$facet_params) - 8. │ └─ggplot2 (local) compute_layout(..., self = self) - 9. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 10. │ └─ggplot2:::data_frame0(...) - 11. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 12. └─vctrs:::stop_recycle_incompatible_size(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggh4x) - Loading required package: ggplot2 - > - > test_check("ggh4x") - [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] - - ... - 11. │ └─ggplot2:::wrap_layout(id, dims, params$dir) - 12. │ └─ggplot2:::data_frame0(...) - 13. │ └─vctrs::data_frame(..., .name_repair = "minimal") - 14. └─vctrs:::stop_recycle_incompatible_size(...) - 15. └─vctrs:::stop_vctrs(...) - 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - - [ FAIL 8 | WARN 0 | SKIP 18 | PASS 723 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Facets.Rmd’ using rmarkdown - - Quitting from lines 33-39 [wrap_mimick] (Facets.Rmd) - Error: processing vignette 'Facets.Rmd' failed with diagnostics: - Can't recycle `ROW` (size 0) to size 7. - --- failed re-building ‘Facets.Rmd’ - - --- re-building ‘Miscellaneous.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Facets.Rmd’ - ... - Loading required package: ggplot2 - - > p <- ggplot(mpg, aes(displ, hwy, colour = as.factor(cyl))) + - + geom_point() + labs(x = "Engine displacement", y = "Highway miles per gallon") + .... [TRUNCATED] - - > p + facet_wrap2(vars(class)) - - ... - ℹ Error occurred in the 1st layer. - Caused by error in `setup_params()`: - ! A discrete 'nbinom' distribution cannot be fitted to continuous data. - Execution halted - - ‘Facets.Rmd’ using ‘UTF-8’... failed - ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK - ‘PositionGuides.Rmd’ using ‘UTF-8’... OK - ‘Statistics.Rmd’ using ‘UTF-8’... failed - ‘ggh4x.Rmd’ using ‘UTF-8’... OK - ``` - -# ggheatmap - -
- -* Version: 2.2 -* GitHub: NA -* Source code: https://github.com/cran/ggheatmap -* Date/Publication: 2022-09-10 13:32:55 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "ggheatmap")` for more info - -
- -## Newly broken - -* checking whether package ‘ggheatmap’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggheatmap’ - See ‘/tmp/workdir/ggheatmap/new/ggheatmap.Rcheck/00install.out’ for details. - ``` - -# ggScatRidges - -
- -* Version: 0.1.1 -* GitHub: https://github.com/matbou85/ggScatRidges -* Source code: https://github.com/cran/ggScatRidges -* Date/Publication: 2024-03-25 10:20:05 UTC -* Number of recursive dependencies: 117 - -Run `revdepcheck::cloud_details(, "ggScatRidges")` for more info - -
- -## Newly broken - -* checking whether package ‘ggScatRidges’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ggScatRidges’ - See ‘/tmp/workdir/ggScatRidges/new/ggScatRidges.Rcheck/00install.out’ for details. - ``` - -# GimmeMyPlot - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/GimmeMyPlot -* Date/Publication: 2023-10-18 16:10:02 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info - -
- -## Newly broken - -* checking whether package ‘GimmeMyPlot’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘GimmeMyPlot’ - See ‘/tmp/workdir/GimmeMyPlot/new/GimmeMyPlot.Rcheck/00install.out’ for details. - ``` - -# hilldiv - -
- -* Version: 1.5.1 -* GitHub: https://github.com/anttonalberdi/hilldiv -* Source code: https://github.com/cran/hilldiv -* Date/Publication: 2019-10-01 14:40:02 UTC -* Number of recursive dependencies: 153 - -Run `revdepcheck::cloud_details(, "hilldiv")` for more info - -
- -## Newly broken - -* checking whether package ‘hilldiv’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hilldiv’ - See ‘/tmp/workdir/hilldiv/new/hilldiv.Rcheck/00install.out’ for details. - ``` - -# hJAM - -
- -* Version: 1.0.0 -* GitHub: https://github.com/lailylajiang/hJAM -* Source code: https://github.com/cran/hJAM -* Date/Publication: 2020-02-20 14:50:05 UTC -* Number of recursive dependencies: 101 -Run `revdepcheck::cloud_details(, "hJAM")` for more info - -
- -## Newly broken - -* checking whether package ‘hJAM’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘hJAM’ - See ‘/tmp/workdir/hJAM/new/hJAM.Rcheck/00install.out’ for details. - ``` - -# iglu - -
- -* Version: 4.0.0 -* GitHub: https://github.com/irinagain/iglu -* Source code: https://github.com/cran/iglu -* Date/Publication: 2024-02-23 17:50:02 UTC -* Number of recursive dependencies: 125 +# eventstudyr (missing labels) + +# EvoPhylo (patchwork) -Run `revdepcheck::cloud_details(, "iglu")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘iglu-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mage_ma_single - > ### Title: Calculates Mean Amplitude of Glycemic Excursions (see "mage") - > ### Aliases: mage_ma_single - > - > ### ** Examples - > - > data(example_data_1_subject) - ... - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) - 17. └─ggplot2 (local) transform(..., self = self) - 18. └─transformation$transform(x) - 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") - 20. └─rlang::abort(...) - Execution halted - ``` +# expirest (missing labels) -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘MAGE.Rmd’ - ... - - > fig1data <- example_data_1_subject[1:200, ] - - > mage(fig1data, plot = TRUE, show_ma = TRUE, title = "Glucose Trace - Subject 1") - - When sourcing ‘MAGE.R’: - Error: ℹ In index: 1. - Caused by error in `transformation$transform()`: - ! `transform_time()` works with objects of class only - Execution halted - - ‘AGP_and_Episodes.Rmd’ using ‘UTF-8’... OK - ‘MAGE.Rmd’ using ‘UTF-8’... failed - ‘iglu.Rmd’ using ‘UTF-8’... OK - ‘lasagna_plots.Rmd’ using ‘UTF-8’... OK - ‘metrics_list.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘AGP_and_Episodes.Rmd’ using rmarkdown - ``` - -# ImFoR - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/ImFoR -* Date/Publication: 2023-09-21 18:50:02 UTC -* Number of recursive dependencies: 173 - -Run `revdepcheck::cloud_details(, "ImFoR")` for more info - -
- -## Newly broken - -* checking whether package ‘ImFoR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘ImFoR’ - See ‘/tmp/workdir/ImFoR/new/ImFoR.Rcheck/00install.out’ for details. - ``` - -# iNEXT.4steps - -
- -* Version: 1.0.0 -* GitHub: https://github.com/KaiHsiangHu/iNEXT.4steps -* Source code: https://github.com/cran/iNEXT.4steps -* Date/Publication: 2024-04-10 20:00:05 UTC -* Number of recursive dependencies: 107 - -Run `revdepcheck::cloud_details(, "iNEXT.4steps")` for more info - -
- -## Newly broken - -* checking whether package ‘iNEXT.4steps’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘iNEXT.4steps’ - See ‘/tmp/workdir/iNEXT.4steps/new/iNEXT.4steps.Rcheck/00install.out’ for details. - ``` - -# insane - -
- -* Version: 1.0.3 -* GitHub: https://github.com/mcanouil/insane -* Source code: https://github.com/cran/insane -* Date/Publication: 2023-11-14 21:50:02 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "insane")` for more info - -
- -## Newly broken - -* checking whether package ‘insane’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘insane’ - See ‘/tmp/workdir/insane/new/insane.Rcheck/00install.out’ for details. - ``` - -# MarketMatching - -
- -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/MarketMatching -* Date/Publication: 2024-01-31 09:40:02 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "MarketMatching")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle - - Quitting from lines 114-115 [unnamed-chunk-3] (MarketMatching-Vignette.Rmd) - Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘MarketMatching-Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘MarketMatching-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# mc2d - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/mc2d -* Date/Publication: 2023-07-17 16:00:02 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "mc2d")` for more info - -
- -## Newly broken - -* checking whether package ‘mc2d’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ - See ‘/tmp/workdir/mc2d/new/mc2d.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘docmcEnglish.Rnw’ using Sweave - Loading required package: mvtnorm - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘mc2d’ - - Attaching package: ‘mc2d’ - - The following objects are masked from ‘package:base’: - - pmax, pmin - ... - l.179 \RequirePackage{grfext}\relax - ^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘mc2dLmEnglish.rnw’ - - SUMMARY: processing the following files failed: - ‘docmcEnglish.Rnw’ ‘mc2dLmEnglish.rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MetaIntegrator - -
- -* Version: 2.1.3 -* GitHub: NA -* Source code: https://github.com/cran/MetaIntegrator -* Date/Publication: 2020-02-26 13:00:11 UTC -* Number of recursive dependencies: 178 - -Run `revdepcheck::cloud_details(, "MetaIntegrator")` for more info - -
- -## Newly broken - -* checking whether package ‘MetaIntegrator’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MetaIntegrator’ - See ‘/tmp/workdir/MetaIntegrator/new/MetaIntegrator.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - data 3.9Mb - doc 2.1Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’ - ‘readr’ - All declared Imports should be used. - ``` - -# MF.beta4 - -
- -* Version: 1.0.3 -* GitHub: https://github.com/AnneChao/MF.beta4 -* Source code: https://github.com/cran/MF.beta4 -* Date/Publication: 2024-04-16 16:30:02 UTC -* Number of recursive dependencies: 173 - -Run `revdepcheck::cloud_details(, "MF.beta4")` for more info - -
- -## Newly broken - -* checking whether package ‘MF.beta4’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MF.beta4’ - See ‘/tmp/workdir/MF.beta4/new/MF.beta4.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Introduction.Rnw’ using Sweave - Error: processing vignette 'Introduction.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'Introduction.tex' failed. - LaTeX errors: - ! LaTeX Error: File `pdfpages.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.4 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘Introduction.Rnw’ - - SUMMARY: processing the following file failed: - ‘Introduction.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MIMSunit - -
- -* Version: 0.11.2 -* GitHub: https://github.com/mhealthgroup/MIMSunit -* Source code: https://github.com/cran/MIMSunit -* Date/Publication: 2022-06-21 11:00:09 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "MIMSunit")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MIMSunit-Ex.R’ failed - The error most likely occurred in: - - > ### Name: illustrate_extrapolation - > ### Title: Plot illustrations about extrapolation in illustration style. - > ### Aliases: illustrate_extrapolation - > - > ### ** Examples - > - > # Use the maxed-out data for the conceptual diagram - ... - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─ggproto_parent(ScaleContinuous, self)$transform(x) - 17. └─ggplot2 (local) transform(..., self = self) - 18. └─transformation$transform(x) - 19. └─cli::cli_abort("{.fun transform_time} works with objects of class {.cls POSIXct} only") - 20. └─rlang::abort(...) - Execution halted - ``` - -# missingHE - -
- -* Version: 1.5.0 -* GitHub: NA -* Source code: https://github.com/cran/missingHE -* Date/Publication: 2023-03-21 08:50:02 UTC -* Number of recursive dependencies: 151 - -Run `revdepcheck::cloud_details(, "missingHE")` for more info - -
- -## Newly broken - -* checking whether package ‘missingHE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘missingHE’ - See ‘/tmp/workdir/missingHE/new/missingHE.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘mcmcr’ - All declared Imports should be used. - ``` - -# MSPRT - -
- -* Version: 3.0 -* GitHub: NA -* Source code: https://github.com/cran/MSPRT -* Date/Publication: 2020-11-13 10:20:05 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "MSPRT")` for more info - -
- -## Newly broken - -* checking whether package ‘MSPRT’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘MSPRT’ - See ‘/tmp/workdir/MSPRT/new/MSPRT.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’ - All declared Imports should be used. - ``` - -# nzelect - -
- -* Version: 0.4.0 -* GitHub: NA -* Source code: https://github.com/cran/nzelect -* Date/Publication: 2017-10-02 20:35:23 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "nzelect")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nzelect-Ex.R’ failed - The error most likely occurred in: - - > ### Name: polls - > ### Title: New Zealand Opinion Polls - > ### Aliases: polls - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - data 5.6Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6409 marked UTF-8 strings - ``` - -# OenoKPM - -
- -* Version: 2.4.1 -* GitHub: NA -* Source code: https://github.com/cran/OenoKPM -* Date/Publication: 2024-04-08 19:20:10 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "OenoKPM")` for more info - -
- -## Newly broken - -* checking whether package ‘OenoKPM’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘OenoKPM’ - See ‘/tmp/workdir/OenoKPM/new/OenoKPM.Rcheck/00install.out’ for details. - ``` - -# posologyr - -
- -* Version: 1.2.4 -* GitHub: https://github.com/levenc/posologyr -* Source code: https://github.com/cran/posologyr -* Date/Publication: 2024-02-09 11:50:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "posologyr")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘a_priori_dosing.Rmd’ - ... - 16: source(output, echo = TRUE) - 17: doTryCatch(return(expr), name, parentenv, handler) - 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 19: tryCatchList(expr, classes, parentenv, handlers) - 20: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)}) - 21: tools:::.run_one_vignette("a_priori_dosing.Rmd", "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr/vignettes", encoding = "UTF-8", pkgdir = "/tmp/workdir/posologyr/new/posologyr.Rcheck/00_pkg_src/posologyr") - An irrecoverable exception occurred. R is aborting now ... - ... - Segmentation fault - - ... incomplete output. Crash? - - ‘a_posteriori_dosing.Rmd’ using ‘UTF-8’... OK - ‘a_priori_dosing.Rmd’ using ‘UTF-8’... failed to complete the test - ‘auc_based_dosing.Rmd’ using ‘UTF-8’... OK - ‘multiple_endpoints.Rmd’ using ‘UTF-8’... OK - ‘patient_data_input.Rmd’ using ‘UTF-8’... OK - ‘posologyr_user_defined_models.Rmd’ using ‘UTF-8’... OK - ``` - -# qicharts - -
- -* Version: 0.5.8 -* GitHub: NA -* Source code: https://github.com/cran/qicharts -* Date/Publication: 2021-04-20 12:20:03 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "qicharts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘qicharts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tcc - > ### Title: Trellis Control Charts - > ### Aliases: tcc - > - > ### ** Examples - > - > # Run chart of 24 random normal variables - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -# qicharts2 - -
- -* Version: 0.7.5 -* GitHub: https://github.com/anhoej/qicharts2 -* Source code: https://github.com/cran/qicharts2 -* Date/Publication: 2024-05-09 06:20:03 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "qicharts2")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘qicharts2.Rmd’ - ... - > qic(month, n, notes = notes, data = cdi, decimals = 0, - + title = "Hospital acquired Clostridium difficile infections", - + ylab = "Count", x .... [TRUNCATED] - - > qic(month, n, data = cdi, decimals = 0, freeze = 24, - + part.labels = c("Baseline", "Intervention"), title = "Hospital acquired Clostridium diff ..." ... [TRUNCATED] - - When sourcing ‘qicharts2.R’: - Error: `transform_time()` works with objects of class only - Execution halted - - ‘qicharts2.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘qicharts2.Rmd’ using rmarkdown - ``` - -# QuadratiK - -
- -* Version: 1.1.0 -* GitHub: https://github.com/giovsaraceno/QuadratiK-package -* Source code: https://github.com/cran/QuadratiK -* Date/Publication: 2024-05-14 13:50:06 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "QuadratiK")` for more info - -
- -## Newly broken - -* checking whether package ‘QuadratiK’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘QuadratiK’ - See ‘/tmp/workdir/QuadratiK/new/QuadratiK.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 14.6Mb - sub-directories of 1Mb or more: - libs 12.9Mb - ``` - -# RCTrep - -
- -* Version: 1.2.0 -* GitHub: https://github.com/duolajiang/RCTrep -* Source code: https://github.com/cran/RCTrep -* Date/Publication: 2023-11-02 14:40:02 UTC -* Number of recursive dependencies: 166 - -Run `revdepcheck::cloud_details(, "RCTrep")` for more info - -
- -## Newly broken - -* checking whether package ‘RCTrep’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘RCTrep’ - See ‘/tmp/workdir/RCTrep/new/RCTrep.Rcheck/00install.out’ for details. - ``` +# explainer (plotly) -# scdtb +# ezEDA (missing labels) -
+# ezplot (0-length width) -* Version: 0.1.0 -* GitHub: https://github.com/mightymetrika/scdtb -* Source code: https://github.com/cran/scdtb -* Date/Publication: 2024-04-30 08:50:02 UTC -* Number of recursive dependencies: 97 +# fable.prophet (ggdist) -Run `revdepcheck::cloud_details(, "scdtb")` for more info +# fabletools (ggdist) -
+# factoextra (0-length width) -## Newly broken +# fairmodels (missing labels) -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - Error in `nlme::gls(model = mod_form, data = .df, method = "REML", correlation = nlme::corAR1(form = re_form), - ...)`: false convergence (8) - Backtrace: - ▆ - 1. └─scdtb::mixed_model_analysis(...) at test-mixed_model_analysis.R:114:3 - 2. └─nlme::gls(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ] - Error: Test failures - Execution halted - ``` +# fddm (ggforce) -# SCOUTer +# feasts (missing labels) -
+# ffp (ggdist) -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SCOUTer -* Date/Publication: 2020-06-30 09:30:03 UTC -* Number of recursive dependencies: 99 +# fido (ggdist) -Run `revdepcheck::cloud_details(, "SCOUTer")` for more info +# flipr (unknown) + +``` +#
+# +# * Version: 0.3.3 +# * GitHub: https://github.com/LMJL-Alea/flipr +# * Source code: https://github.com/cran/flipr +# * Date/Publication: 2023-08-23 09:00:02 UTC +# * Number of recursive dependencies: 106 +# +# Run `revdepcheck::cloud_details(, "flipr")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘alternative.Rmd’ using rmarkdown +# --- finished re-building ‘alternative.Rmd’ +# +# --- re-building ‘exactness.Rmd’ using rmarkdown +# +# Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) +# Error: processing vignette 'exactness.Rmd' failed with diagnostics: +# subscript out of bounds +# --- failed re-building ‘exactness.Rmd’ +# +# --- re-building ‘flipr.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘exactness.Rmd’ +# ... +# +# > library(flipr) +# +# > load("../R/sysdata.rda") +# Warning in readChar(con, 5L, useBytes = TRUE) : +# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' +# +# ... +# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' +# +# When sourcing ‘plausibility.R’: +# Error: cannot open the connection +# Execution halted +# +# ‘alternative.Rmd’ using ‘UTF-8’... OK +# ‘exactness.Rmd’ using ‘UTF-8’... failed +# ‘flipr.Rmd’ using ‘UTF-8’... failed +# ‘plausibility.Rmd’ using ‘UTF-8’... failed +# ``` +# +# * checking installed package size ... NOTE +# ``` +# installed size is 11.0Mb +# sub-directories of 1Mb or more: +# doc 9.1Mb +# libs 1.2Mb +# ``` +``` -
+# foqat (ggnewscale) -## Newly broken +# forestly (patchwork) -* checking whether package ‘SCOUTer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SCOUTer’ - See ‘/tmp/workdir/SCOUTer/new/SCOUTer.Rcheck/00install.out’ for details. - ``` - -# sievePH - -
+# frailtyEM (plotly) -* Version: 1.0.4 -* GitHub: https://github.com/mjuraska/sievePH -* Source code: https://github.com/cran/sievePH -* Date/Publication: 2023-02-03 18:40:02 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "sievePH")` for more info - -
- -## Newly broken - -* checking whether package ‘sievePH’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘sievePH’ - See ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/00install.out’ for details. - ``` +# funcharts (patchwork) -# SouthParkRshiny +# geomtextpath (default access) -
+# GGally (missing labels) -* Version: 1.0.0 -* GitHub: https://github.com/Amalan-ConStat/SouthParkRshiny -* Source code: https://github.com/cran/SouthParkRshiny -* Date/Publication: 2024-03-09 11:10:08 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "SouthParkRshiny")` for more info - -
- -## Newly broken - -* checking whether package ‘SouthParkRshiny’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SouthParkRshiny’ - See ‘/tmp/workdir/SouthParkRshiny/new/SouthParkRshiny.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.6Mb - sub-directories of 1Mb or more: - data 8.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1562 marked UTF-8 strings - ``` +# gganimate (gganimate) -# SqueakR +# ggbrain (ggnewscale) -
+# ggbreak (patchwork) -* Version: 1.3.0 -* GitHub: https://github.com/osimon81/SqueakR -* Source code: https://github.com/cran/SqueakR -* Date/Publication: 2022-06-28 09:20:04 UTC -* Number of recursive dependencies: 142 +# ggdark (default access) -Run `revdepcheck::cloud_details(, "SqueakR")` for more info +# ggdist (ggdist) -
+# ggDoubleHeat (ggnewscale) -## Newly broken +# ggeasy (missing labels) -* checking whether package ‘SqueakR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘SqueakR’ - See ‘/tmp/workdir/SqueakR/new/SqueakR.Rcheck/00install.out’ for details. - ``` +# ggedit (saved to disk) -## In both +# ggESDA (passing NULL aesthetic mapping) -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘SqueakR.Rmd’ - ... - $ experimenters : NULL - $ experimental_data: list() - - > my_new_data <- add_timepoint_data(data_path = "../inst/extdata/Example_Mouse_Data.xlsx", - + t1 = 5, t2 = 25) - Adding call features Excel file to workspace... - - When sourcing ‘SqueakR.R’: - Error: `path` does not exist: ‘../inst/extdata/Example_Mouse_Data.xlsx’ - Execution halted - - ‘SqueakR.Rmd’ using ‘UTF-8’... failed - ``` +# ggfixest (visual differences) -* checking installed package size ... NOTE - ``` - installed size is 8.8Mb - sub-directories of 1Mb or more: - doc 8.2Mb - ``` +# ggforce (ggforce) -# survminer +Note: facet_zoom/facet_col/facet_row -
+# ggformula (docs) -* Version: 0.4.9 -* GitHub: https://github.com/kassambara/survminer -* Source code: https://github.com/cran/survminer -* Date/Publication: 2021-03-09 09:50:03 UTC -* Number of recursive dependencies: 130 +# ggfortify (tests) + +# gggenomes (patchwork) + +# ggh4x (unknown) + +``` +#
+# +# * Version: 0.2.8 +# * GitHub: https://github.com/teunbrand/ggh4x +# * Source code: https://github.com/cran/ggh4x +# * Date/Publication: 2024-01-23 21:00:02 UTC +# * Number of recursive dependencies: 77 +# +# Run `revdepcheck::cloud_details(, "ggh4x")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggh4x-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: guide_stringlegend +# > ### Title: String legend +# > ### Aliases: guide_stringlegend +# > +# > ### ** Examples +# > +# > p <- ggplot(mpg, aes(displ, hwy)) + +# + geom_point(aes(colour = manufacturer)) +# > +# > # String legend can be set in the `guides()` function +# > p + guides(colour = guide_stringlegend(ncol = 2)) +# Error in (function (layer, df) : +# argument "theme" is missing, with no default +# Calls: ... use_defaults -> eval_from_theme -> %||% -> calc_element +# Execution halted +# ``` +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(ggh4x) +# Loading required package: ggplot2 +# > +# > test_check("ggh4x") +# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] +# +# ... +# 25. └─ggplot2 (local) compute_geom_2(..., self = self) +# 26. └─self$geom$use_defaults(...) +# 27. └─ggplot2 (local) use_defaults(..., self = self) +# 28. └─ggplot2:::eval_from_theme(default_aes, theme) +# 29. ├─calc_element("geom", theme) %||% .default_geom_element +# 30. └─ggplot2::calc_element("geom", theme) +# +# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] +# Error: Test failures +# Execution halted +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘Facets.Rmd’ using rmarkdown +# ``` +# +# ## In both +# +# * checking running R code from vignettes ... ERROR +# ``` +# Errors in running code in vignettes: +# when running code in ‘Miscellaneous.Rmd’ +# ... +# +# > ggplot(diamonds, aes(price, carat, colour = clarity)) + +# + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", +# + guide = "stri ..." ... [TRUNCATED] +# Warning: The S3 guide system was deprecated in ggplot2 3.5.0. +# ℹ It has been replaced by a ggproto system that can be extended. +# +# ... +# ℹ Error occurred in the 1st layer. +# Caused by error in `setup_params()`: +# ! A discrete 'nbinom' distribution cannot be fitted to continuous data. +# Execution halted +# +# ‘Facets.Rmd’ using ‘UTF-8’... OK +# ‘Miscellaneous.Rmd’ using ‘UTF-8’... failed +# ‘PositionGuides.Rmd’ using ‘UTF-8’... OK +# ‘Statistics.Rmd’ using ‘UTF-8’... failed +# ‘ggh4x.Rmd’ using ‘UTF-8’... OK +# ``` +``` + +# gghighlight (default access) + +# ggHoriPlot (patchwork) + +# ggiraph (additional params) + +# ggiraphExtra (additional params) + +# ggmice (plotly) + +# ggmulti (custom use_defaults) + +# ggnewscale (ggnewscale) + +# ggparallel (unknown) + +``` +#
+# +# * Version: 0.4.0 +# * GitHub: https://github.com/heike/ggparallel +# * Source code: https://github.com/cran/ggparallel +# * Date/Publication: 2024-03-09 22:00:02 UTC +# * Number of recursive dependencies: 51 +# +# Run `revdepcheck::cloud_details(, "ggparallel")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > # This file is part of the standard setup for testthat. +# > # It is recommended that you do not modify it. +# > # +# > # Where should you do additional test configuration? +# > # Learn more about the roles of various files in: +# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# > # * https://testthat.r-lib.org/articles/special-files.html +# ... +# 12. └─self$get_layer_key(params, layers[include], data[include], theme) +# 13. └─ggplot2 (local) get_layer_key(...) +# 14. └─base::Map(...) +# 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) +# 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) +# 17. └─layer$compute_geom_2(key, single_params, theme) +# +# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] +# Error: Test failures +# Execution halted +# ``` +``` -Run `revdepcheck::cloud_details(, "survminer")` for more info +# ggpicrust2 (patchwork) -
+# ggpie (ggnewscale) -## Newly broken +# ggplotlyExtra (plotly) -* checking whether package ‘survminer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘survminer’ - See ‘/tmp/workdir/survminer/new/survminer.Rcheck/00install.out’ for details. - ``` +# ggpol (default access) -## In both +# ggpubr (update tests) -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - doc 5.5Mb - ``` +# ggraph (guide theme passing) -# symptomcheckR +# ggredist (unknown) -
+``` +#
+# +# * Version: 0.0.2 +# * GitHub: https://github.com/alarm-redist/ggredist +# * Source code: https://github.com/cran/ggredist +# * Date/Publication: 2022-11-23 11:20:02 UTC +# * Number of recursive dependencies: 67 +# +# Run `revdepcheck::cloud_details(, "ggredist")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggredist-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: geom_district_text +# > ### Title: Label Map Regions +# > ### Aliases: geom_district_text geom_district_label +# > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText +# > ### Keywords: datasets +# > +# > ### ** Examples +# ... +# 22. │ └─coord$transform(data, panel_params) +# 23. │ └─ggplot2 (local) transform(..., self = self) +# 24. │ └─ggplot2:::sf_rescale01(...) +# 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) +# 26. └─base::.handleSimpleError(...) +# 27. └─rlang (local) h(simpleError(msg, call)) +# 28. └─handlers[[1L]](cnd) +# 29. └─cli::cli_abort(...) +# 30. └─rlang::abort(...) +# Execution halted +# ``` +``` -* Version: 0.1.3 -* GitHub: https://github.com/ma-kopka/symptomcheckR -* Source code: https://github.com/cran/symptomcheckR -* Date/Publication: 2024-04-16 20:40:06 UTC -* Number of recursive dependencies: 101 +# ggRtsy (missing labels) -Run `revdepcheck::cloud_details(, "symptomcheckR")` for more info +# ggseqplot (length 0 width) -
+# ggside (unknown) -## Newly broken +``` +#
+# +# * Version: 0.3.1 +# * GitHub: https://github.com/jtlandis/ggside +# * Source code: https://github.com/cran/ggside +# * Date/Publication: 2024-03-01 09:12:37 UTC +# * Number of recursive dependencies: 76 +# +# Run `revdepcheck::cloud_details(, "ggside")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(ggplot2) +# > library(ggside) +# Registered S3 method overwritten by 'ggside': +# method from +# +.gg ggplot2 +# > +# ... +# • ops_meaningful/alpha-0-5-from-function.svg +# • side_layers/boxplot2.svg +# • vdiff_irisScatter/collapsed-histo.svg +# • vdiff_irisScatter/facetgrid-collapsed-density.svg +# • vdiff_irisScatter/facetgrid-histo.svg +# • vdiff_irisScatter/facetgrid-side-density.svg +# • vdiff_irisScatter/stacked-side-density.svg +# • vdiff_irisScatter/yside-histo.svg +# Error: Test failures +# Execution halted +# ``` +# +# * checking for code/documentation mismatches ... WARNING +# ``` +# Codoc mismatches from documentation object 'geom_xsideabline': +# geom_xsidehline +# Code: function(mapping = NULL, data = NULL, position = "identity", +# ..., yintercept, na.rm = FALSE, show.legend = NA) +# Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = +# FALSE, show.legend = NA) +# Argument names in code not in docs: +# position +# Mismatches in argument names (first 3): +# Position: 3 Code: position Docs: ... +# ... +# Docs: function(mapping = NULL, data = NULL, stat = "identity", +# position = "identity", ..., lineend = "butt", linejoin +# = "round", linemitre = 10, arrow = NULL, na.rm = +# FALSE, show.legend = NA, inherit.aes = TRUE) +# Argument names in code not in docs: +# arrow.fill +# Mismatches in argument names: +# Position: 10 Code: arrow.fill Docs: na.rm +# Position: 11 Code: na.rm Docs: show.legend +# Position: 12 Code: show.legend Docs: inherit.aes +# ``` +``` -* checking whether package ‘symptomcheckR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘symptomcheckR’ - See ‘/tmp/workdir/symptomcheckR/new/symptomcheckR.Rcheck/00install.out’ for details. - ``` +# ggspatial (missing defaults) -# tcgaViz +# ggtern (ggtern) -
+# ggupset (unknown) -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/tcgaViz -* Date/Publication: 2023-04-04 15:40:02 UTC -* Number of recursive dependencies: 139 +``` +#
+# +# * Version: 0.4.0 +# * GitHub: https://github.com/const-ae/ggupset +# * Source code: https://github.com/cran/ggupset +# * Date/Publication: 2024-06-24 10:10:04 UTC +# * Number of recursive dependencies: 46 +# +# Run `revdepcheck::cloud_details(, "ggupset")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘ggupset-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: axis_combmatrix +# > ### Title: Convert delimited text labels into a combination matrix axis +# > ### Aliases: axis_combmatrix +# > +# > ### ** Examples +# > +# > library(ggplot2) +# ... +# Datsun 710 Cyl: 4_Gears: 4 +# Hornet 4 Drive Cyl: 6_Gears: 3 +# Hornet Sportabout Cyl: 8_Gears: 3 +# Valiant Cyl: 6_Gears: 3 +# > ggplot(mtcars, aes(x=combined)) + +# + geom_bar() + +# + axis_combmatrix(sep = "_") +# Error in as.unit(e2) : object is not coercible to a unit +# Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit +# Execution halted +# ``` +``` -Run `revdepcheck::cloud_details(, "tcgaViz")` for more info +# ggVennDiagram (plotly) -
+# greatR (patchwork) -## Newly broken +# Greymodels (plotly) -* checking whether package ‘tcgaViz’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘tcgaViz’ - See ‘/tmp/workdir/tcgaViz/new/tcgaViz.Rcheck/00install.out’ for details. - ``` +# gtExtras (unknown) -# TestGardener +``` +#
+# +# * Version: 0.5.0 +# * GitHub: https://github.com/jthomasmock/gtExtras +# * Source code: https://github.com/cran/gtExtras +# * Date/Publication: 2023-09-15 22:32:06 UTC +# * Number of recursive dependencies: 105 +# +# Run `revdepcheck::cloud_details(, "gtExtras")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(gtExtras) +# Loading required package: gt +# +# Attaching package: 'gt' +# +# The following object is masked from 'package:testthat': +# ... +# ══ Failed tests ════════════════════════════════════════════════════════════════ +# ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── +# `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). +# +# `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" +# `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" +# +# [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] +# Error: Test failures +# Execution halted +# ``` +``` -
+# HaploCatcher (patchwork) -* Version: 3.3.3 -* GitHub: NA -* Source code: https://github.com/cran/TestGardener -* Date/Publication: 2024-03-20 13:50:02 UTC -* Number of recursive dependencies: 131 +# healthyR (plotly) -Run `revdepcheck::cloud_details(, "TestGardener")` for more info +# healthyR.ts (plotly) -
+# heatmaply (plotly) -## Newly broken +# hermiter (patchwork) -* checking whether package ‘TestGardener’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘TestGardener’ - See ‘/tmp/workdir/TestGardener/new/TestGardener.Rcheck/00install.out’ for details. - ``` +# hesim (missing labels) -# tidydr +# hidecan (ggnewscale) -
+# HVT (plotly) -* Version: 0.0.5 -* GitHub: https://github.com/YuLab-SMU/tidydr -* Source code: https://github.com/cran/tidydr -* Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 71 +# hypsoLoop (namespace conflict) -Run `revdepcheck::cloud_details(, "tidydr")` for more info +# ICvectorfields (ggnewscale) -
+# idopNetwork (patchwork) -## Newly broken +# inferCSN (plotly) -* checking whether package ‘tidydr’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. - ``` +# insurancerating (patchwork) -## Installation +# inTextSummaryTable (default access) -### Devel +# inventorize (unknown) ``` -* installing *source* package ‘tidydr’ ... -** package ‘tidydr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in get(x, envir = ns, inherits = FALSE) : - object 'len0_null' not found -Error: unable to load R code in package ‘tidydr’ -Execution halted -ERROR: lazy loading failed for package ‘tidydr’ -* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ +#
+# +# * Version: 1.1.1 +# * GitHub: NA +# * Source code: https://github.com/cran/inventorize +# * Date/Publication: 2022-05-31 22:20:09 UTC +# * Number of recursive dependencies: 71 +# +# Run `revdepcheck::cloud_details(, "inventorize")` for more info +# +#
+# +# ## Newly broken +# +# * checking whether package ‘inventorize’ can be installed ... ERROR +# ``` +# Installation failed. +# See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. +# ``` +# +# ## Installation +# +# ### Devel +# +# ``` +# * installing *source* package ‘inventorize’ ... +# ** package ‘inventorize’ successfully unpacked and MD5 sums checked +# ** using staged installation +# ** R +# ** byte-compile and prepare package for lazy loading +# Error in pm[[2]] : subscript out of bounds +# Error: unable to load R code in package ‘inventorize’ +# Execution halted +# ERROR: lazy loading failed for package ‘inventorize’ +# * removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ +# +# +# ``` +# ### CRAN +# +# ``` +# * installing *source* package ‘inventorize’ ... +# ** package ‘inventorize’ successfully unpacked and MD5 sums checked +# ** using staged installation +# ** R +# ** byte-compile and prepare package for lazy loading +# Warning in qgamma(service_level, alpha, beta) : NaNs produced +# Warning in qgamma(service_level, alpha, beta) : NaNs produced +# ** help +# *** installing help indices +# ** building package indices +# ** testing if installed package can be loaded from temporary location +# ** testing if installed package can be loaded from final location +# ** testing if installed package keeps a record of temporary installation path +# * DONE (inventorize) +# +# +# ``` +``` +# karel (gganimate) + +# kDGLM (plotly) + +# latentcor (plotly) + +# lcars (device issue) + +# lemon (resolve theme) + +# lfproQC (plotly) + +# LMoFit (saved to disk) + +# manydata (plot slots) + +# MARVEL (ggnewscale) + +# MBNMAdose (cannot reproduce) + +# MBNMAtime (ggdist) + +# MetaNet (ggnewscale) +# metR (fixed in dev) +# migraph (missing labels) + +# MiMIR (plotly) + +# miRetrieve (plotly) + +# misspi (plotly) + +# mizer (cannot reproduce) + +# mlr3spatiotempcv (patchwork) + +# mlr3viz (patchwork) + +# modeltime.resample (plotly) + +# move (false positive) + +# mtb (missing labels) + +# neatmaps (plotly) + +# NetFACS (false positive) + +# NeuralSens (ggnewscale) + +# NHSRplotthedots (missing labels) + +# NIMAA (plotly) + +# OBIC (patchwork) + +# OmicNavigator (plotly) + +# oncomsm (patchwork) + +# pafr (missing labels) + +# patchwork (patchwork) + +# pathviewr (missing labels) + +# pcutils (patchwork) + +# pdxTrees (gganimate) + +# personalized (plotly) + +# phylepic (ggnewscale) + +# Plasmidprofiler (plotly) + +# platetools (faulty tests) + +# plotDK (missing labels) + +# plotly (plotly) + +# pmartR (unknown) + +``` +#
+# +# * Version: 2.4.5 +# * GitHub: https://github.com/pmartR/pmartR +# * Source code: https://github.com/cran/pmartR +# * Date/Publication: 2024-05-21 15:50:02 UTC +# * Number of recursive dependencies: 149 +# +# Run `revdepcheck::cloud_details(, "pmartR")` for more info +# +#
+# +# ## Newly broken +# +# * checking tests ... ERROR +# ``` +# Running ‘testthat.R’ +# Running the tests in ‘tests/testthat.R’ failed. +# Complete output: +# > library(testthat) +# > library(pmartR) +# > +# > test_check("pmartR") +# [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] +# +# ══ Skipped tests (11) ══════════════════════════════════════════════════════════ +# ... +# • plots/plot-spansres-color-high-color-low.svg +# • plots/plot-spansres.svg +# • plots/plot-statres-anova-volcano.svg +# • plots/plot-statres-anova.svg +# • plots/plot-statres-combined-volcano.svg +# • plots/plot-statres-combined.svg +# • plots/plot-statres-gtest.svg +# • plots/plot-totalcountfilt.svg +# Error: Test failures +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 10.4Mb +# sub-directories of 1Mb or more: +# R 1.5Mb +# help 1.5Mb +# libs 6.3Mb +# ``` ``` -### CRAN + +# pmxTools (ggdist) + +# posterior (ggdist) + +# PPQplan (plotly) + +# ppseq (plotly) + +# precrec (patchwork) + +# priorsense (ggdist) + +# ProAE (ggnewscale) + +# probably (missing labels) + +# processmapR (plotly) + +# psborrow (missing labels) + +# r2dii.plot (missing labels) + +# Radviz (accessing defaults) + +# rassta (plotly) + +# REddyProc (false positive) + +# redist (patchwork) + +# reReg (length 0 width) + +# reservr (patchwork) + +# rKOMICS (unknown) ``` -* installing *source* package ‘tidydr’ ... -** package ‘tidydr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (tidydr) +#
+# +# * Version: 1.3 +# * GitHub: NA +# * Source code: https://github.com/cran/rKOMICS +# * Date/Publication: 2023-06-29 22:40:03 UTC +# * Number of recursive dependencies: 128 +# +# Run `revdepcheck::cloud_details(, "rKOMICS")` for more info +# +#
+# +# ## Newly broken +# +# * checking examples ... ERROR +# ``` +# Running examples in ‘rKOMICS-Ex.R’ failed +# The error most likely occurred in: +# +# > ### Name: msc.pca +# > ### Title: Prinicple Component Analysis based on MSC +# > ### Aliases: msc.pca +# > +# > ### ** Examples +# > +# > data(matrices) +# ... +# 11. │ └─base::withCallingHandlers(...) +# 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) +# 13. └─l$compute_geom_2(d, theme = plot$theme) +# 14. └─ggplot2 (local) compute_geom_2(..., self = self) +# 15. └─self$geom$use_defaults(...) +# 16. └─ggplot2 (local) use_defaults(..., self = self) +# 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) +# 18. └─cli::cli_abort(...) +# 19. └─rlang::abort(...) +# Execution halted +# ``` +# +# ## In both +# +# * checking installed package size ... NOTE +# ``` +# installed size is 24.8Mb +# sub-directories of 1Mb or more: +# extdata 24.0Mb +# ``` +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘example.Rnw’ using Sweave +# Loading required package: viridisLite +# Warning: Removed 95 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 89 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 149 rows containing non-finite outside the scale range +# (`stat_boxplot()`). +# Warning: Removed 286 rows containing non-finite outside the scale range +# ... +# l.5 \usepackage +# {xcolor}^^M +# ! ==> Fatal error occurred, no output PDF file produced! +# --- failed re-building ‘example.Rnw’ +# +# SUMMARY: processing the following file failed: +# ‘example.Rnw’ +# +# Error: Vignette re-building failed. +# Execution halted +# ``` +``` + +# RKorAPClient (missing labels) + +# RNAseqQC (patchwork) + +# roahd (plotly) + +# romic (plotly) + +# roptions (plotly) + +# santaR (plot slots) + +# scdtb (missing labels) + +# scoringutils (ggdist) + +# scUtils (missing labels) + +# SCVA (plotly) + +# SDMtune (missing labels) + +# SeaVal (plotly) + +# sgsR (missing labels) + +# SHAPforxgboost (ggforce) +# SHELF (unknown) ``` -# tis - -
- -* Version: 1.39 -* GitHub: NA -* Source code: https://github.com/cran/tis -* Date/Publication: 2021-09-28 19:50:02 UTC -* Number of recursive dependencies: 15 +#
+# +# * Version: 1.10.0 +# * GitHub: https://github.com/OakleyJ/SHELF +# * Source code: https://github.com/cran/SHELF +# * Date/Publication: 2024-05-07 14:20:03 UTC +# * Number of recursive dependencies: 126 +# +# Run `revdepcheck::cloud_details(, "SHELF")` for more info +# +#
+# +# ## Newly broken +# +# * checking re-building of vignette outputs ... NOTE +# ``` +# Error(s) in re-building vignettes: +# --- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown +# ``` +``` + +# shinipsum (plot slots) + +# SimNPH (missing labels) + +# smallsets (patchwork) + +# spbal (empty sf) + +# spinifex (plotly) + +# sport (missing labels) + +# SqueakR (false positive) + +# statgenGWAS (device issue) + +# surveyexplorer (ggupset) + +# Sysrecon (patchwork) + +# tabledown (plotly) + +# TCIU (plotly) + +# tensorEVD (ggnewscale) + +# thematic (thematic) + +# tidybayes (ggdist) + +# tidycat (ggforce) + +# tidyCDISC (plotly) + +# tidydr (uses internals) + +# tidysdm (patchwork) + +# tidytreatment (ggdist) -Run `revdepcheck::cloud_details(, "tis")` for more info - -
+# timetk (plotly) -## Newly broken +# tinyarray (patchwork) -* checking examples ... ERROR - ``` - Running examples in ‘tis-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fortify.tis - > ### Title: Fortify a tis object - > ### Aliases: fortify.tis - > - > ### ** Examples - > - > if(require("ggplot2") && require("reshape")) { - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` +# tornado (length 0 width) -## In both +# TOSTER (ggdist) -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘zoo’ - ``` +# TreatmentPatterns (plotly) -# UniprotR +# trelliscopejs (plotly) -
+# tricolore (ggtern) -* Version: 2.4.0 -* GitHub: https://github.com/Proteomicslab57357/UniprotR -* Source code: https://github.com/cran/UniprotR -* Date/Publication: 2024-03-05 15:10:02 UTC -* Number of recursive dependencies: 192 +# triptych (patchwork) -Run `revdepcheck::cloud_details(, "UniprotR")` for more info +# tsnet (ggdist) -
+# umiAnalyzer (plotly) -## Newly broken +# valr (missing labels) -* checking whether package ‘UniprotR’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘UniprotR’ - See ‘/tmp/workdir/UniprotR/new/UniprotR.Rcheck/00install.out’ for details. - ``` +# vivaldi (plotly) -# VALERIE +# vivid (ggnewscale) -
+# vvshiny (plotly) -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/VALERIE -* Date/Publication: 2020-07-10 10:20:13 UTC -* Number of recursive dependencies: 133 +# wilson (plotly) -Run `revdepcheck::cloud_details(, "VALERIE")` for more info +# xaringanthemer (default access) -
- -## Newly broken - -* checking whether package ‘VALERIE’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘VALERIE’ - See ‘/tmp/workdir/VALERIE/new/VALERIE.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.6Mb - sub-directories of 1Mb or more: - extdata 8.7Mb - ``` - -# vannstats - -
- -* Version: 1.3.4.14 -* GitHub: NA -* Source code: https://github.com/cran/vannstats -* Date/Publication: 2023-04-15 04:30:02 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "vannstats")` for more info - -
- -## Newly broken - -* checking whether package ‘vannstats’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vannstats’ - See ‘/tmp/workdir/vannstats/new/vannstats.Rcheck/00install.out’ for details. - ``` - -# vici - -
- -* Version: 0.7.3 -* GitHub: https://github.com/sistm/vici -* Source code: https://github.com/cran/vici -* Date/Publication: 2024-02-02 16:20:02 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "vici")` for more info - -
- -## Newly broken - -* checking whether package ‘vici’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::ggpar’ by ‘ggpubr::ggpar’ when loading ‘vici’ - See ‘/tmp/workdir/vici/new/vici.Rcheck/00install.out’ for details. - ``` - -# Wats - -
- -* Version: 1.0.1 -* GitHub: https://github.com/OuhscBbmc/Wats -* Source code: https://github.com/cran/Wats -* Date/Publication: 2023-03-10 22:50:05 UTC -* Number of recursive dependencies: 122 - -Run `revdepcheck::cloud_details(, "Wats")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Wats-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cartesian_periodic - > ### Title: Linear Plot with Periodic Elements - > ### Aliases: cartesian_periodic - > ### Keywords: Cartesian - > - > ### ** Examples - > - ... - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. └─scale$transform_df(df = df) - 12. └─ggplot2 (local) transform_df(..., self = self) - 13. └─base::lapply(df[aesthetics], self$transform) - 14. └─ggplot2 (local) FUN(X[[i]], ...) - 15. └─ggplot2 (local) transform(..., self = self) - 16. └─transformation$transform(x) - 17. └─cli::cli_abort("{.fun transform_date} works with objects of class {.cls Date} only") - 18. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘mbr-figures.Rmd’ - ... - + dv_name = "birth_rate", center_function = stats::median, - + spread_function = h_sprea .... [TRUNCATED] - - > cartesian_rolling(ds_linear = portfolio_cartesian$ds_linear, - + x_name = "date", y_name = "birth_rate", stage_id_name = "stage_id", - + chang .... [TRUNCATED] - - When sourcing ‘mbr-figures.R’: - Error: `transform_date()` works with objects of class only - Execution halted - - ‘mbr-figures.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mbr-figures.Rmd’ using rmarkdown - - Quitting from lines 135-165 [fig-2-individual-basic] (mbr-figures.Rmd) - Error: processing vignette 'mbr-figures.Rmd' failed with diagnostics: - `transform_date()` works with objects of class only - --- failed re-building ‘mbr-figures.Rmd’ - - SUMMARY: processing the following file failed: - ‘mbr-figures.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# xaringanthemer - -
- -* Version: 0.4.2 -* GitHub: https://github.com/gadenbuie/xaringanthemer -* Source code: https://github.com/cran/xaringanthemer -* Date/Publication: 2022-08-20 18:40:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "xaringanthemer")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(xaringanthemer) - > - > test_check("xaringanthemer") - [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] - - ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-ggplot2.R:267:3'): theme_xaringan_restore_defaults() restores defaults ── - res$after_restore$line_colour (`actual`) not equal to res$original$colour (`expected`). - - `actual`: "#0088ff" - `expected`: "black" - - [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘xaringanthemer.Rmd’ - ... - Warning in file(con, "r") : - cannot open file './../man/fragments/_quick-intro.Rmd': No such file or directory - - Quitting from lines 43-43 [unnamed-chunk-2] (xaringanthemer.Rmd) - - When tangling ‘xaringanthemer.Rmd’: - Error: cannot open the connection - Execution halted - - ‘ggplot2-themes.Rmd’ using ‘UTF-8’... OK - ‘template-variables.Rmd’ using ‘UTF-8’... OK - ‘xaringanthemer.Rmd’ using ‘UTF-8’... failed - ``` +# yamlet (missing labels) diff --git a/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg b/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg index 6f424b0c4a..8532b083e3 100644 --- a/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg +++ b/tests/testthat/_snaps/coord-cartesian/clip-on-by-default-only-inside-visible.svg @@ -27,14 +27,14 @@ -inside -inside -inside -inside -outside -outside -outside -outside +inside +inside +inside +inside +outside +outside +outside +outside clip on by default, only 'inside' visible diff --git a/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg b/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg index 89932b9196..b2120e5e14 100644 --- a/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg +++ b/tests/testthat/_snaps/coord-cartesian/clip-turned-off-both-inside-and-outside-visible.svg @@ -20,14 +20,14 @@ -inside -inside -inside -inside -outside -outside -outside -outside +inside +inside +inside +inside +outside +outside +outside +outside clip turned off, both 'inside' and 'outside' visible diff --git a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg index 30c4b0fc24..caa297b3f5 100644 --- a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg +++ b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg @@ -40,18 +40,18 @@ -cat -strawberry -cake -coffee -window -fluid -cat -strawberry -cake -coffee -window -fluid +cat +strawberry +cake +coffee +window +fluid +cat +strawberry +cake +coffee +window +fluid 1 2 3 diff --git a/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg b/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg index cf5ffdbbf2..f11f41251b 100644 --- a/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg +++ b/tests/testthat/_snaps/geom-sf/labels-for-north-carolina.svg @@ -27,8 +27,8 @@ - -ashe + +ashe diff --git a/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg b/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg index 96ffe43109..ec2184a425 100644 --- a/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg +++ b/tests/testthat/_snaps/geom-sf/texts-for-north-carolina.svg @@ -27,7 +27,7 @@ -ashe +ashe diff --git a/tests/testthat/_snaps/theme/theme-bw-large.svg b/tests/testthat/_snaps/theme/theme-bw-large.svg index 148d1a93ca..cbffb819ac 100644 --- a/tests/testthat/_snaps/theme/theme-bw-large.svg +++ b/tests/testthat/_snaps/theme/theme-bw-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_bw_large diff --git a/tests/testthat/_snaps/theme/theme-classic-large.svg b/tests/testthat/_snaps/theme/theme-classic-large.svg index 8a4643dba1..7105d5474b 100644 --- a/tests/testthat/_snaps/theme/theme-classic-large.svg +++ b/tests/testthat/_snaps/theme/theme-classic-large.svg @@ -27,9 +27,9 @@ - - - + + + @@ -70,9 +70,9 @@ z - + - + a b theme_classic_large diff --git a/tests/testthat/_snaps/theme/theme-dark-large.svg b/tests/testthat/_snaps/theme/theme-dark-large.svg index 9bad950947..f6f9c1058f 100644 --- a/tests/testthat/_snaps/theme/theme-dark-large.svg +++ b/tests/testthat/_snaps/theme/theme-dark-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -86,9 +86,9 @@ z - + - + a b theme_dark_large diff --git a/tests/testthat/_snaps/theme/theme-gray-large.svg b/tests/testthat/_snaps/theme/theme-gray-large.svg index a827864db6..4348638185 100644 --- a/tests/testthat/_snaps/theme/theme-gray-large.svg +++ b/tests/testthat/_snaps/theme/theme-gray-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -86,9 +86,9 @@ z - + - + a b theme_gray_large diff --git a/tests/testthat/_snaps/theme/theme-light-large.svg b/tests/testthat/_snaps/theme/theme-light-large.svg index 727f55ae02..29fc210917 100644 --- a/tests/testthat/_snaps/theme/theme-light-large.svg +++ b/tests/testthat/_snaps/theme/theme-light-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_light_large diff --git a/tests/testthat/_snaps/theme/theme-linedraw-large.svg b/tests/testthat/_snaps/theme/theme-linedraw-large.svg index 66998cd898..e2aadff6e7 100644 --- a/tests/testthat/_snaps/theme/theme-linedraw-large.svg +++ b/tests/testthat/_snaps/theme/theme-linedraw-large.svg @@ -45,9 +45,9 @@ - - - + + + @@ -87,9 +87,9 @@ z - + - + a b theme_linedraw_large diff --git a/tests/testthat/_snaps/theme/theme-minimal-large.svg b/tests/testthat/_snaps/theme/theme-minimal-large.svg index 4673e9cc60..8ec3b18625 100644 --- a/tests/testthat/_snaps/theme/theme-minimal-large.svg +++ b/tests/testthat/_snaps/theme/theme-minimal-large.svg @@ -43,9 +43,9 @@ - - - + + + @@ -71,8 +71,8 @@ x y z - - + + a b theme_minimal_large diff --git a/tests/testthat/_snaps/utilities-break.md b/tests/testthat/_snaps/utilities-break.md index c8115c4c48..31563a6cd7 100644 --- a/tests/testthat/_snaps/utilities-break.md +++ b/tests/testthat/_snaps/utilities-break.md @@ -1,4 +1,4 @@ -# cut_interval gives the correct +# cut_interval throws the correct error message Specify exactly one of `n` and `length`. diff --git a/tests/testthat/test-geom-.R b/tests/testthat/test-geom-.R index e0a0ca060a..6766178f22 100644 --- a/tests/testthat/test-geom-.R +++ b/tests/testthat/test-geom-.R @@ -6,18 +6,34 @@ test_that("aesthetic checking in geom throws correct errors", { expect_snapshot_error(check_aesthetics(aes, 4)) }) +test_that("get_geom_defaults can use various sources", { + + test <- get_geom_defaults(geom_point) + expect_equal(test$colour, "black") + + test <- get_geom_defaults(geom_point(colour = "red")) + expect_equal(test$colour, "red") + + test <- get_geom_defaults("point") + expect_equal(test$colour, "black") + + test <- get_geom_defaults(GeomPoint, theme(geom = element_geom("red"))) + expect_equal(test$colour, "red") +}) + test_that("geom defaults can be set and reset", { l <- geom_point() - test <- l$geom$use_defaults(data_frame0()) + orig <- l$geom$default_aes$colour + test <- get_geom_defaults(l) expect_equal(test$colour, "black") inv <- update_geom_defaults("point", list(colour = "red")) - test <- l$geom$use_defaults(data_frame0()) + test <- get_geom_defaults(l) expect_equal(test$colour, "red") - expect_equal(inv$colour, "black") + expect_equal(inv$colour, orig) inv <- update_geom_defaults("point", NULL) - test <- l$geom$use_defaults(data_frame0()) + test <- get_geom_defaults(l) expect_equal(test$colour, "black") expect_equal(inv$colour, "red") diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index 0739f78a6d..25c30e2fb1 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -47,7 +47,7 @@ test_that("erroneously dropped aesthetics are found and issue a warning", { # colour is dropped because group a's colour is not constant (GeomBar$default_aes$colour is NA) expect_true(all(is.na(b2$data[[1]]$colour))) # fill is dropped because group b's fill is not constant - expect_true(all(b2$data[[1]]$fill == GeomBar$default_aes$fill)) + expect_true(all(b2$data[[1]]$fill == "#595959FF")) # case 2-1) dropped partially with NA diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 03f2a11d48..9c10202504 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -240,14 +240,12 @@ test_that("complete and non-complete themes interact correctly with ggplot objec expect_identical(pt, tt) p <- ggplot_build(base + theme(text = element_text(colour = 'red', face = 'italic'))) - expect_false(attr(p$plot$theme, "complete")) expect_equal(p$plot$theme$text$colour, "red") expect_equal(p$plot$theme$text$face, "italic") p <- ggplot_build(base + theme(text = element_text(colour = 'red')) + theme(text = element_text(face = 'italic'))) - expect_false(attr(p$plot$theme, "complete")) expect_equal(p$plot$theme$text$colour, "red") expect_equal(p$plot$theme$text$face, "italic") }) From a49bf1eff4491189b2fa1946934afb33c8a28b84 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 28 Aug 2024 09:24:09 +0200 Subject: [PATCH 115/264] Check ellipses in several places (#6031) * helper function to throw error demoted to warning * check `fortify()` dots * check `get_alt_text()` dots * check `deprecated_guide_args()` dots * check for unknown labels * add news bullet --- NEWS.md | 2 ++ R/fortify.R | 7 +++++-- R/guide-legend.R | 1 + R/labels.R | 28 ++++++++++++++++++++++++---- R/utilities.R | 12 ++++++++++++ man/fortify.Rd | 2 +- man/get_alt_text.Rd | 2 +- tests/testthat/_snaps/guides.md | 11 +++++++++++ tests/testthat/_snaps/labels.md | 12 ++++++++++++ tests/testthat/_snaps/plot.md | 7 +++++++ tests/testthat/test-guides.R | 9 +++++++++ tests/testthat/test-labels.R | 9 +++++++++ tests/testthat/test-plot.R | 1 + 13 files changed, 95 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8c5ca3c555..c527454cdd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -168,6 +168,8 @@ * `theme_classic()` now has black ticks and text instead of dark gray. In addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978). * {tibble} is now suggested instead of imported (@teunbrand, #5986) +* The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, + `labs()` and several guides (@teunbrand, #3196). # ggplot2 3.5.1 diff --git a/R/fortify.R b/R/fortify.R index 3a61e3ce49..5b5b7c5171 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -8,9 +8,12 @@ #' @seealso [fortify.lm()] #' @param model model or other R object to convert to data frame #' @param data original dataset, if needed -#' @param ... other arguments passed to methods +#' @inheritParams rlang::args_dots_used #' @export -fortify <- function(model, data, ...) UseMethod("fortify") +fortify <- function(model, data, ...) { + warn_dots_used() + UseMethod("fortify") +} #' @export fortify.data.frame <- function(model, data, ...) model diff --git a/R/guide-legend.R b/R/guide-legend.R index 6f0b98ac33..4dd088f358 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -688,6 +688,7 @@ deprecated_guide_args <- function( default.unit = "line", ..., .call = caller_call()) { + warn_dots_used(call = .call) args <- names(formals(deprecated_guide_args)) args <- setdiff(args, c("theme", "default.unit", "...", ".call")) diff --git a/R/labels.R b/R/labels.R index 7662153e91..20cc929d37 100644 --- a/R/labels.R +++ b/R/labels.R @@ -18,8 +18,8 @@ update_labels <- function(p, labels) { # Called in `ggplot_build()` to set default labels not specified by user. setup_plot_labels <- function(plot, layers, data) { - # Initiate from user-defined labels - labels <- plot$labels + # Initiate empty labels + labels <- list() # Find labels from every layer for (i in seq_along(layers)) { @@ -65,7 +65,26 @@ setup_plot_labels <- function(plot, layers, data) { labels <- defaults(labels, current) } } - labels + + # Warn for spurious labels that don't have a mapping. + # Note: sometimes, 'x' and 'y' might not have a mapping, like in + # `geom_function()`. We can display these labels anyway, so we include them. + plot_labels <- plot$labels + known_labels <- c(names(labels), fn_fmls_names(labs), "x", "y") + extra_labels <- setdiff(names(plot_labels), known_labels) + + if (length(extra_labels) > 0) { + extra_labels <- paste0( + "{.code ", extra_labels, " = \"", plot_labels[extra_labels], "\"}" + ) + names(extra_labels) <- rep("*", length(extra_labels)) + cli::cli_warn(c( + "Ignoring unknown labels:", + extra_labels + )) + } + + defaults(plot_labels, labels) } #' Modify axis, legend, and plot labels @@ -168,7 +187,7 @@ ggtitle <- function(label, subtitle = waiver()) { #' text from the information stored in the plot. #' #' @param p a ggplot object -#' @param ... Currently ignored +#' @inheritParams rlang::args_dots_used #' #' @return A text string #' @@ -191,6 +210,7 @@ ggtitle <- function(label, subtitle = waiver()) { #' get_alt_text(p) #' get_alt_text <- function(p, ...) { + warn_dots_used() UseMethod("get_alt_text") } #' @export diff --git a/R/utilities.R b/R/utilities.R index 2585de5acc..56325e83d9 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -843,6 +843,18 @@ as_unordered_factor <- function(x) { x } +warn_dots_used <- function(env = caller_env(), call = caller_env()) { + check_dots_used( + env = env, call = call, + # Demote from error to warning + error = function(cnd) { + # cli uses \f as newlines, not \n + msg <- gsub("\n", "\f", cnd_message(cnd)) + cli::cli_warn(msg, call = call) + } + ) +} + # Shim for scales/#424 col_mix <- function(a, b, amount = 0.5) { input <- vec_recycle_common(a = a, b = b, amount = amount) diff --git a/man/fortify.Rd b/man/fortify.Rd index 59dcfea9ec..36d1837025 100644 --- a/man/fortify.Rd +++ b/man/fortify.Rd @@ -11,7 +11,7 @@ fortify(model, data, ...) \item{data}{original dataset, if needed} -\item{...}{other arguments passed to methods} +\item{...}{Arguments passed to methods.} } \description{ Rather than using this function, I now recommend using the \pkg{broom} diff --git a/man/get_alt_text.Rd b/man/get_alt_text.Rd index b0da28a783..c9f6bdeb1e 100644 --- a/man/get_alt_text.Rd +++ b/man/get_alt_text.Rd @@ -10,7 +10,7 @@ get_alt_text(p, ...) \arguments{ \item{p}{a ggplot object} -\item{...}{Currently ignored} +\item{...}{Arguments passed to methods.} } \value{ A text string diff --git a/tests/testthat/_snaps/guides.md b/tests/testthat/_snaps/guides.md index 62d1e41d24..be7c84d7f3 100644 --- a/tests/testthat/_snaps/guides.md +++ b/tests/testthat/_snaps/guides.md @@ -1,3 +1,14 @@ +# dots are checked when making guides + + Ignoring unknown argument to `guide_axis()`: `foo`. + +--- + + Arguments in `...` must be used. + x Problematic argument: + * foo = "bar" + i Did you misspell an argument name? + # Using non-position guides for position scales results in an informative error `guide_legend()` cannot be used for x, xmin, xmax, or xend. diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index e1f6ed4140..49efe59a72 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -5,6 +5,18 @@ Output [1] "A plot showing class on a discrete x-axis and count on a continuous y-axis using a bar layer." +# get_alt_text checks dots + + Arguments in `...` must be used. + x Problematic argument: + * foo = "bar" + i Did you misspell an argument name? + +# warnings are thrown for unknown labels + + Ignoring unknown labels: + * `foo = "bar"` + # plot.tag.position rejects invalid input The `plot.tag.position` theme element must be a object. diff --git a/tests/testthat/_snaps/plot.md b/tests/testthat/_snaps/plot.md index 6035364389..157ebb6635 100644 --- a/tests/testthat/_snaps/plot.md +++ b/tests/testthat/_snaps/plot.md @@ -8,6 +8,13 @@ `data` cannot be a function. i Have you misspelled the `data` argument in `ggplot()` +--- + + Arguments in `...` must be used. + x Problematic argument: + * foobar = "nonsense" + i Did you misspell an argument name? + # construction have user friendly errors Cannot use `+` with a single argument. diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index f0057a7452..23df1f75e2 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -87,6 +87,15 @@ test_that("show.legend handles named vectors", { expect_equal(n_legends(p), 1) }) +test_that("dots are checked when making guides", { + expect_snapshot_warning( + new_guide(foo = "bar", super = GuideAxis) + ) + expect_snapshot_warning( + guide_legend(foo = "bar") + ) +}) + test_that("axis_label_overlap_priority always returns the correct number of elements", { expect_identical(axis_label_priority(0), numeric(0)) expect_setequal(axis_label_priority(1), seq_len(1)) diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index c659e39cf5..60f5165c1b 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -104,6 +104,15 @@ test_that("alt text can take a function", { expect_snapshot(get_alt_text(p)) }) +test_that("get_alt_text checks dots", { + expect_snapshot_warning(get_alt_text(ggplot(), foo = "bar")) +}) + +test_that("warnings are thrown for unknown labels", { + p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() + labs(foo = 'bar') + expect_snapshot_warning(ggplot_build(p)) +}) + test_that("plot.tag.position rejects invalid input", { p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() + labs(tag = "Fig. A)") diff --git a/tests/testthat/test-plot.R b/tests/testthat/test-plot.R index dc1b507c13..2cccf79034 100644 --- a/tests/testthat/test-plot.R +++ b/tests/testthat/test-plot.R @@ -1,6 +1,7 @@ test_that("ggplot() throws informative errors", { expect_snapshot_error(ggplot(mapping = letters)) expect_snapshot_error(ggplot(data)) + expect_snapshot_warning(ggplot(foobar = "nonsense")) }) test_that("construction have user friendly errors", { From 7ce155b50fe68c1f57bd3778aebdac71cb13bb98 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 28 Aug 2024 09:24:35 +0200 Subject: [PATCH 116/264] Repurpose coord expansion (#6027) * `default_expansion()` handles longer `expand` arg * Parser for expand argument * insert parser at relevant places * Use Coord$setup_params() to setup expand * fix plot helper not including params * Redocument parameter * fix `coord_flip()` case * add test * add news bullet --- NEWS.md | 2 ++ R/coord-.R | 25 +++++++++++++++++++-- R/coord-cartesian-.R | 8 +++++-- R/coord-flip.R | 1 + R/coord-radial.R | 37 +++++++++++++++---------------- R/coord-sf.R | 12 +++++----- R/coord-transform.R | 4 ++-- R/scale-expansion.R | 19 +++++++++++++--- man/coord_cartesian.Rd | 6 ++++- man/coord_fixed.Rd | 6 ++++- man/coord_flip.Rd | 6 ++++- man/coord_map.Rd | 6 ++++- man/coord_trans.Rd | 6 ++++- man/ggsf.Rd | 6 ++++- tests/testthat/helper-plot-data.R | 2 +- tests/testthat/test-coord-.R | 16 +++++++++++++ 16 files changed, 120 insertions(+), 42 deletions(-) diff --git a/NEWS.md b/NEWS.md index c527454cdd..02cbf5465f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `coord_*(expand)` can now take a logical vector to control expansion at any + side of the panel (top, right, bottom, left) (@teunbrand, #6020) * (Breaking) The defaults for all geoms can be set at one in the theme. (@teunbrand based on pioneering work by @dpseidel, #2239) * A new `theme(geom)` argument is used to track these defaults. diff --git a/R/coord-.R b/R/coord-.R index 57cf351f92..0d0bb5ecb9 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -184,10 +184,11 @@ Coord <- ggproto("Coord", # Will generally have to return FALSE for coordinate systems that enforce a fixed aspect ratio. is_free = function() FALSE, - setup_params = function(data) { + setup_params = function(self, data) { list( guide_default = guide_axis(), - guide_missing = guide_none() + guide_missing = guide_none(), + expand = parse_coord_expand(self$expand %||% TRUE) ) }, @@ -243,6 +244,26 @@ render_axis <- function(panel_params, axis, scale, position, theme) { } } +# Elaborates an 'expand' argument for every side (top, right, bottom or left) +parse_coord_expand <- function(expand) { + check_logical(expand) + if (anyNA(expand)) { + cli::cli_abort("{.arg expand} cannot contain missing values.") + } + + if (!is_named(expand)) { + return(rep_len(expand, 4)) + } + + # Match by top/right/bottom/left + out <- rep(TRUE, 4) + i <- match(names(expand), .trbl) + if (sum(!is.na(i)) > 0) { + out[i] <- unname(expand)[!is.na(i)] + } + out +} + # Utility function to check coord limits check_coord_limits <- function( limits, arg = caller_arg(limits), call = caller_env() diff --git a/R/coord-cartesian-.R b/R/coord-cartesian-.R index 74f46433db..885918c3d1 100644 --- a/R/coord-cartesian-.R +++ b/R/coord-cartesian-.R @@ -9,6 +9,10 @@ #' @param expand If `TRUE`, the default, adds a small expansion factor to #' the limits to ensure that data and axes don't overlap. If `FALSE`, #' limits are taken exactly from the data or `xlim`/`ylim`. +#' Giving a logical vector will separately control the expansion for the four +#' directions (top, left, bottom and right). The `expand` argument will be +#' recycled to length 4 if necessary. Alternatively, can be a named logical +#' vector to control a single direction, e.g. `expand = c(bottom = FALSE)`. #' @param default Is this the default coordinate system? If `FALSE` (the default), #' then replacing this coordinate system with another one creates a message alerting #' the user that the coordinate system is being replaced. If `TRUE`, that warning @@ -100,8 +104,8 @@ CoordCartesian <- ggproto("CoordCartesian", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { c( - view_scales_from_scale(scale_x, self$limits$x, self$expand), - view_scales_from_scale(scale_y, self$limits$y, self$expand) + view_scales_from_scale(scale_x, self$limits$x, params$expand[c(4, 2)]), + view_scales_from_scale(scale_y, self$limits$y, params$expand[c(3, 1)]) ) }, diff --git a/R/coord-flip.R b/R/coord-flip.R index eb46d12669..502ff56f88 100644 --- a/R/coord-flip.R +++ b/R/coord-flip.R @@ -89,6 +89,7 @@ CoordFlip <- ggproto("CoordFlip", CoordCartesian, }, setup_panel_params = function(self, scale_x, scale_y, params = list()) { + params$expand <- params$expand[c(2, 1, 4, 3)] parent <- ggproto_parent(CoordCartesian, self) panel_params <- parent$setup_panel_params(scale_x, scale_y, params) flip_axis_labels(panel_params) diff --git a/R/coord-radial.R b/R/coord-radial.R index 2f44e1ae4b..3a5ccf1ee2 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -66,7 +66,6 @@ coord_radial <- function(theta = "x", check_bool(r.axis.inside, allow_null = TRUE) } - check_bool(expand) check_bool(rotate.angle) check_number_decimal(start, allow_infinite = FALSE) check_number_decimal(end, allow_infinite = FALSE, allow_null = TRUE) @@ -139,8 +138,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { params <- c( - view_scales_polar(scale_x, self$theta, expand = self$expand), - view_scales_polar(scale_y, self$theta, expand = self$expand), + view_scales_polar(scale_x, self$theta, expand = params$expand[c(4, 2)]), + view_scales_polar(scale_y, self$theta, expand = params$expand[c(3, 1)]), list(bbox = polar_bbox(self$arc, inner_radius = self$inner_radius), arc = self$arc, inner_radius = self$inner_radius) ) @@ -469,27 +468,27 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, setup_params = function(self, data) { - if (isFALSE(self$r_axis_inside)) { - place <- in_arc(c(0, 0.5, 1, 1.5) * pi, self$arc) - if (place[1]) { - return(list(r_axis = "left", fake_arc = c(0, 2) * pi)) - } - if (place[3]) { - return(list(r_axis = "left", fake_arc = c(1, 3)* pi)) - } - if (place[2]) { - return(list(r_axis = "bottom", fake_arc = c(0.5, 2.5) * pi)) - } - if (place[4]) { - return(list(r_axis = "bottom", fake_arc = c(1.5, 3.5) * pi)) - } + params <- ggproto_parent(Coord, self)$setup_params(data) + if (!isFALSE(self$r_axis_inside)) { + return(params) + } + + place <- in_arc(c(0, 0.5, 1, 1.5) * pi, self$arc) + if (!any(place)) { cli::cli_warn(c( "No appropriate placement found for {.arg r_axis_inside}.", i = "Axis will be placed at panel edge." )) - self$r_axis_inside <- TRUE + params$r_axis_inside <- TRUE + return(params) } - return(NULL) + + params$r_axis <- if (any(place[c(1, 3)])) "left" else "bottom" + params$fake_arc <- switch( + which(place[c(1, 3, 2, 4)])[1], + c(0, 2), c(1, 3), c(0.5, 2.5), c(1.5, 3.5) + ) * pi + params } ) diff --git a/R/coord-sf.R b/R/coord-sf.R index a14b3c718c..f129947dc0 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -18,12 +18,10 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, }, setup_params = function(self, data) { - crs <- self$determine_crs(data) + params <- ggproto_parent(Coord, self)$setup_params(data) - params <- list( - crs = crs, - default_crs = self$default_crs - ) + params$crs <- self$determine_crs(data) + params$default_crs <- self$default_crs self$params <- params params @@ -170,8 +168,8 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, setup_panel_params = function(self, scale_x, scale_y, params = list()) { # expansion factors for scale limits - expansion_x <- default_expansion(scale_x, expand = self$expand) - expansion_y <- default_expansion(scale_y, expand = self$expand) + expansion_x <- default_expansion(scale_x, expand = params$expand[c(4, 2)]) + expansion_y <- default_expansion(scale_y, expand = params$expand[c(3, 1)]) # get scale limits and coord limits and merge together # coord limits take precedence over scale limits diff --git a/R/coord-transform.R b/R/coord-transform.R index 83ffd7b9ee..1253529fdd 100644 --- a/R/coord-transform.R +++ b/R/coord-transform.R @@ -153,8 +153,8 @@ CoordTrans <- ggproto("CoordTrans", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { c( - view_scales_from_scale_with_coord_trans(scale_x, self$limits$x, self$trans$x, self$expand), - view_scales_from_scale_with_coord_trans(scale_y, self$limits$y, self$trans$y, self$expand) + view_scales_from_scale_with_coord_trans(scale_x, self$limits$x, self$trans$x, params$expand[c(4, 2)]), + view_scales_from_scale_with_coord_trans(scale_y, self$limits$y, self$trans$y, params$expand[c(3, 1)]) ) }, diff --git a/R/scale-expansion.R b/R/scale-expansion.R index e3392fc5bf..0edb01f1b8 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -98,11 +98,24 @@ expand_range4 <- function(limits, expand) { #' default_expansion <- function(scale, discrete = expansion(add = 0.6), continuous = expansion(mult = 0.05), expand = TRUE) { - if (!expand) { - return(expansion(0, 0)) + out <- expansion() + if (!any(expand)) { + return(out) } + scale_expand <- scale$expand %|W|% + if (scale$is_discrete()) discrete else continuous - scale$expand %|W|% if (scale$is_discrete()) discrete else continuous + # for backward compatibility, we ensure expansions have expected length + expand <- rep_len(expand, 2L) + scale_expand <- rep_len(scale_expand, 4) + + if (expand[1]) { + out[1:2] <- scale_expand[1:2] + } + if (expand[2]) { + out[3:4] <- scale_expand[3:4] + } + out } #' Expand limits in (possibly) transformed space diff --git a/man/coord_cartesian.Rd b/man/coord_cartesian.Rd index 5c39f4d288..20987083a5 100644 --- a/man/coord_cartesian.Rd +++ b/man/coord_cartesian.Rd @@ -17,7 +17,11 @@ coord_cartesian( \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{default}{Is this the default coordinate system? If \code{FALSE} (the default), then replacing this coordinate system with another one creates a message alerting diff --git a/man/coord_fixed.Rd b/man/coord_fixed.Rd index fc8c052506..8877019a91 100644 --- a/man/coord_fixed.Rd +++ b/man/coord_fixed.Rd @@ -14,7 +14,11 @@ coord_fixed(ratio = 1, xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{clip}{Should drawing be clipped to the extent of the plot panel? A setting of \code{"on"} (the default) means yes, and a setting of \code{"off"} diff --git a/man/coord_flip.Rd b/man/coord_flip.Rd index be69644cf0..48ea2e1dba 100644 --- a/man/coord_flip.Rd +++ b/man/coord_flip.Rd @@ -11,7 +11,11 @@ coord_flip(xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{clip}{Should drawing be clipped to the extent of the plot panel? A setting of \code{"on"} (the default) means yes, and a setting of \code{"off"} diff --git a/man/coord_map.Rd b/man/coord_map.Rd index 3aacd167d7..913768f29e 100644 --- a/man/coord_map.Rd +++ b/man/coord_map.Rd @@ -40,7 +40,11 @@ means no. For details, please see \code{\link[=coord_cartesian]{coord_cartesian( \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} diff --git a/man/coord_trans.Rd b/man/coord_trans.Rd index bea5b54716..d1f46dc1ee 100644 --- a/man/coord_trans.Rd +++ b/man/coord_trans.Rd @@ -33,7 +33,11 @@ legend, the plot title, or the plot margins.} \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} } \description{ \code{coord_trans()} is different to scale transformations in that it occurs after diff --git a/man/ggsf.Rd b/man/ggsf.Rd index c4ec76bed1..7424d4107f 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -99,7 +99,11 @@ though they would be visible in the final plot region.} \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{crs}{The coordinate reference system (CRS) into which all data should be projected before plotting. If not specified, will use the CRS defined diff --git a/tests/testthat/helper-plot-data.R b/tests/testthat/helper-plot-data.R index bc1f81f2c9..13e36d861a 100644 --- a/tests/testthat/helper-plot-data.R +++ b/tests/testthat/helper-plot-data.R @@ -5,7 +5,7 @@ cdata <- function(plot) { lapply(pieces$data, function(d) { dapply(d, "PANEL", function(panel_data) { scales <- pieces$layout$get_scales(panel_data$PANEL[1]) - panel_params <- plot$coordinates$setup_panel_params(scales$x, scales$y) + panel_params <- plot$coordinates$setup_panel_params(scales$x, scales$y, params = pieces$layout$coord_params) plot$coordinates$transform(panel_data, panel_params) }) }) diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index 76a174454c..6a50369bbc 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -75,3 +75,19 @@ test_that("coords append a column to the layout correctly", { expect_equal(test$COORD, c(1, 2, 1)) }) +test_that("coord expand takes a vector", { + + base <- ggplot() + lims(x = c(0, 10), y = c(0, 10)) + + p <- ggplot_build(base + coord_cartesian(expand = c(TRUE, FALSE, FALSE, TRUE))) + pp <- p$layout$panel_params[[1]] + expect_equal(pp$x.range, c(-0.5, 10)) + expect_equal(pp$y.range, c(0, 10.5)) + + p <- ggplot_build(base + coord_cartesian(expand = c(top = FALSE, left = FALSE))) + pp <- p$layout$panel_params[[1]] + expect_equal(pp$x.range, c(0, 10.5)) + expect_equal(pp$y.range, c(-0.5, 10)) + +}) + From 3109d1160b3e8b56c21e1b8f4fc557085fea6f38 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 28 Aug 2024 09:55:36 +0200 Subject: [PATCH 117/264] Copy angle heuristic for more guides. (#5957) * generalise angle heuristic * apply heuristic * parameter plumbing * document * add news bullet * digusting simplification * add comments for future generations * accept phase-shift in angles --- NEWS.md | 5 +- R/guide-axis.R | 78 +++++++----------- R/guide-bins.R | 7 ++ R/guide-colorbar.R | 7 ++ R/guide-colorsteps.R | 2 + R/guide-legend.R | 3 + man/guide_bins.Rd | 6 ++ man/guide_colourbar.Rd | 7 ++ man/guide_coloursteps.Rd | 7 ++ .../coord_sf/coord-sf-with-custom-guides.svg | 42 +++++----- .../guides/axis-guides-negative-rotation.svg | 80 +++++++++---------- ...axis-guides-vertical-negative-rotation.svg | 80 +++++++++---------- 12 files changed, 172 insertions(+), 152 deletions(-) diff --git a/NEWS.md b/NEWS.md index 02cbf5465f..713d2198f8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* `guide_bins()`, `guide_colourbar()` and `guide_coloursteps()` gain an `angle` + argument to overrule theme settings, similar to `guide_axis(angle)` + (@teunbrand, #4594). * `coord_*(expand)` can now take a logical vector to control expansion at any side of the panel (top, right, bottom, left) (@teunbrand, #6020) * (Breaking) The defaults for all geoms can be set at one in the theme. @@ -24,7 +27,7 @@ class through new `Coord$draw_panel()` method. * `theme(strip.clip)` now defaults to `"on"` and is independent of Coord clipping (@teunbrand, 5952). -* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). +* (internal) rearranged the code of `Facet$draw_panels()` method (@teunbrand). * Axis labels are now justified across facet panels (@teunbrand, #5820) * Fixed bug in `stat_function()` so x-axis title now produced automatically when no data added. (@phispu, #5647). diff --git a/R/guide-axis.R b/R/guide-axis.R index 8280219f3d..bc2a2e1596 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -254,21 +254,8 @@ GuideAxis <- ggproto( }, override_elements = function(params, elements, theme) { - label <- elements$text - if (!inherits(label, "element_text")) { - return(elements) - } - label_overrides <- axis_label_element_overrides( - params$position, params$angle - ) - # label_overrides is an element_text, but label_element may not be; - # to merge the two elements, we just copy angle, hjust, and vjust - # unless their values are NULL - label$angle <- label_overrides$angle %||% label$angle - label$hjust <- label_overrides$hjust %||% label$hjust - label$vjust <- label_overrides$vjust %||% label$vjust - - elements$text <- label + elements$text <- + label_angle_heuristic(elements$text, params$position, params$angle) return(elements) }, @@ -584,49 +571,40 @@ axis_label_priority_between <- function(x, y) { ) } -#' Override axis text angle and alignment +#' Override text angle and alignment #' +#' @param element An `element_text()` #' @param axis_position One of bottom, left, top, or right #' @param angle The text angle, or NULL to override nothing #' #' @return An [element_text()] that contains parameters that should be #' overridden from the user- or theme-supplied element. #' @noRd -#' -axis_label_element_overrides <- function(axis_position, angle = NULL) { - - if (is.null(angle) || is.waive(angle)) { - return(element_text(angle = NULL, hjust = NULL, vjust = NULL)) +label_angle_heuristic <- function(element, position, angle) { + if (!inherits(element, "element_text") + || is.null(position) + || is.null(angle %|W|% NULL)) { + return(element) } + arg_match0(position, .trbl) check_number_decimal(angle) - angle <- angle %% 360 - arg_match0( - axis_position, - c("bottom", "left", "top", "right") - ) - - if (axis_position == "bottom") { - - hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - - } else if (axis_position == "left") { - - hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - - } else if (axis_position == "top") { - - hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - - } else if (axis_position == "right") { - - hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - - } - - element_text(angle = angle, hjust = hjust, vjust = vjust) + radian <- deg2rad(angle) + digits <- 3 + + # Taking the sign of the (co)sine snaps the value to c(-1, 0, 1) + # Doing `x / 2 + 0.5` rescales it to c(0, 0.5, 1), which are good values for justification + # The rounding step ensures we can get (co)sine to exact 0 so it can become 0.5 + # which we need for center-justifications + cosine <- sign(round(cos(radian), digits)) / 2 + 0.5 + sine <- sign(round(sin(radian), digits)) / 2 + 0.5 + + # Depending on position, we might need to swap or flip justification values + hjust <- switch(position, left = cosine, right = 1 - cosine, top = 1 - sine, sine) + vjust <- switch(position, left = 1 - sine, right = sine, top = 1 - cosine, cosine) + + element$angle <- angle %||% element$angle + element$hjust <- hjust %||% element$hjust + element$vjust <- vjust %||% element$vjust + element } diff --git a/R/guide-bins.R b/R/guide-bins.R index 518655cbba..0124ea6052 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -11,6 +11,10 @@ NULL #' guide if they are mapped in the same way. #' #' @inheritParams guide_legend +#' @param angle Overrules the theme settings to automatically apply appropriate +#' `hjust` and `vjust` for angled legend text. Can be a single number +#' representing the text angle in degrees, or `NULL` to not overrule the +#' settings (default). #' @param show.limits Logical. Should the limits of the scale be shown with #' labels and ticks. Default is `NULL` meaning it will take the value from the #' scale. This argument is ignored if `labels` is given as a vector of @@ -65,6 +69,7 @@ guide_bins <- function( theme = NULL, # general + angle = NULL, position = NULL, direction = NULL, override.aes = list(), @@ -85,6 +90,7 @@ guide_bins <- function( theme = theme, # general + angle = angle, position = position, direction = direction, override.aes = rename_aes(override.aes), @@ -115,6 +121,7 @@ GuideBins <- ggproto( default_axis = element_line("black", linewidth = (0.5 / .pt)), default_ticks = element_line(inherit.blank = TRUE), + angle = NULL, direction = NULL, override.aes = list(), reverse = FALSE, diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index d03484edae..586caee124 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -32,6 +32,10 @@ NULL #' @param alpha A numeric between 0 and 1 setting the colour transparency of #' the bar. Use `NA` to preserve the alpha encoded in the colour itself #' (default). +#' @param angle Overrules the theme settings to automatically apply appropriate +#' `hjust` and `vjust` for angled legend text. Can be a single number +#' representing the text angle in degrees, or `NULL` to not overrule the +#' settings (default). #' @param draw.ulim A logical specifying if the upper limit tick marks should #' be visible. #' @param draw.llim A logical specifying if the lower limit tick marks should @@ -124,6 +128,7 @@ guide_colourbar <- function( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -151,6 +156,7 @@ guide_colourbar <- function( nbin = nbin, display = display, alpha = alpha, + angle = angle, draw_lim = c(isTRUE(draw.llim), isTRUE(draw.ulim)), position = position, direction = direction, @@ -193,6 +199,7 @@ GuideColourbar <- ggproto( direction = NULL, reverse = FALSE, order = 0, + angle = NULL, # parameter name = "colourbar", diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index 52b6e1809d..54cd89a948 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -49,6 +49,7 @@ guide_coloursteps <- function( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -66,6 +67,7 @@ guide_coloursteps <- function( title = title, theme = theme, alpha = alpha, + angle = angle, even.steps = even.steps, show.limits = show.limits, position = position, diff --git a/R/guide-legend.R b/R/guide-legend.R index 4dd088f358..671acf1a1c 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -374,6 +374,9 @@ GuideLegend <- ggproto( ggname("legend.key", element_grob(elements$key)) } + elements$text <- + label_angle_heuristic(elements$text, elements$text_position, params$angle) + elements }, diff --git a/man/guide_bins.Rd b/man/guide_bins.Rd index ead7b8a099..8ee5311445 100644 --- a/man/guide_bins.Rd +++ b/man/guide_bins.Rd @@ -7,6 +7,7 @@ guide_bins( title = waiver(), theme = NULL, + angle = NULL, position = NULL, direction = NULL, override.aes = list(), @@ -26,6 +27,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} differently from the plot's theme settings. The \code{theme} argument in the guide overrides, and is combined with, the plot's theme.} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} diff --git a/man/guide_colourbar.Rd b/man/guide_colourbar.Rd index 8e29943a44..9a441f39cc 100644 --- a/man/guide_colourbar.Rd +++ b/man/guide_colourbar.Rd @@ -14,6 +14,7 @@ guide_colourbar( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -31,6 +32,7 @@ guide_colorbar( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -77,6 +79,11 @@ be visible.} \item{draw.llim}{A logical specifying if the lower limit tick marks should be visible.} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} diff --git a/man/guide_coloursteps.Rd b/man/guide_coloursteps.Rd index a2938df745..5bec4a8d73 100644 --- a/man/guide_coloursteps.Rd +++ b/man/guide_coloursteps.Rd @@ -9,6 +9,7 @@ guide_coloursteps( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -23,6 +24,7 @@ guide_colorsteps( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -47,6 +49,11 @@ guide overrides, and is combined with, the plot's theme.} the bar. Use \code{NA} to preserve the alpha encoded in the colour itself (default).} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{even.steps}{Should the rendered size of the bins be equal, or should they be proportional to their length in the data space? Defaults to \code{TRUE}} diff --git a/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg b/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg index b38125acd3..78e321d395 100644 --- a/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg +++ b/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg @@ -47,27 +47,27 @@ -80 -° -W -79 -° -W -78 -° -W -77 -° -W -76 -° -W -75 -° -W -40 -° -N +80 +° +W +79 +° +W +78 +° +W +77 +° +W +76 +° +W +75 +° +W +40 +° +N 35 ° N diff --git a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg b/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg index f5ad2b2273..8902fa04cd 100644 --- a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg +++ b/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg @@ -70,16 +70,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -91,16 +91,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -112,27 +112,27 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 diff --git a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg b/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg index fb7d39a9d3..1d83ebc1e2 100644 --- a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg +++ b/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg @@ -70,16 +70,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -91,16 +91,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -112,27 +112,27 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 From c32fea1a33d822b6830a13e1f93daf18edcfacde Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 28 Aug 2024 09:55:50 +0200 Subject: [PATCH 118/264] `stat_summary_bin(width)` of preferred over default `width` (#5970) * `stat_summary_bin()` prefers provided `width` over a computed one * add test * add news bullet --- NEWS.md | 1 + R/stat-summary-bin.R | 4 ++-- tests/testthat/test-stat-summary.R | 10 +++++++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 713d2198f8..40bdb3d156 100644 --- a/NEWS.md +++ b/NEWS.md @@ -175,6 +175,7 @@ * {tibble} is now suggested instead of imported (@teunbrand, #5986) * The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, `labs()` and several guides (@teunbrand, #3196). +* `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). # ggplot2 3.5.1 diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index 3a4fea585e..d94b6ddab9 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -79,7 +79,7 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, compute_group = function(data, scales, fun = NULL, bins = 30, binwidth = NULL, breaks = NULL, origin = NULL, right = FALSE, na.rm = FALSE, - flipped_aes = FALSE) { + flipped_aes = FALSE, width = NULL) { data <- flip_data(data, flipped_aes) x <- flipped_names(flipped_aes)$x breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, right = right) @@ -89,7 +89,7 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, locs <- bin_loc(breaks, out$bin) out$x <- locs$mid - out$width <- if (scales[[x]]$is_discrete()) 0.9 else locs$length + out$width <- width %||% if (scales[[x]]$is_discrete()) 0.9 else locs$length out$flipped_aes <- flipped_aes flip_data(out, flipped_aes) } diff --git a/tests/testthat/test-stat-summary.R b/tests/testthat/test-stat-summary.R index 825efd981c..abc2ffe5dd 100644 --- a/tests/testthat/test-stat-summary.R +++ b/tests/testthat/test-stat-summary.R @@ -40,8 +40,16 @@ test_that("stat_summary(_bin) work with lambda expressions", { }) +test_that("stat_summary_bin takes user's `width` argument (#4647)", { + p <- ggplot(mtcars, aes(mpg, disp)) + + stat_summary_bin( + fun.data = mean_se, na.rm = TRUE, + binwidth = 1, width = 2 + ) - + ld <- layer_data(p) + expect_equal(unique(ld$width), 2) +}) test_that("stat_summary_(2d|hex) work with lambda expressions", { From 57ba97fa04dadc6fd73db1904e39a09d57a4fcbe Mon Sep 17 00:00:00 2001 From: Jan Simson Date: Wed, 28 Aug 2024 10:21:17 +0200 Subject: [PATCH 119/264] Include `stat_binhex` aesthetics in documentation for `geom_hex` and `stat_binhex` (#6062) --- R/geom-hex.R | 1 + man/geom_hex.Rd | 11 +++++++++++ 2 files changed, 12 insertions(+) diff --git a/R/geom-hex.R b/R/geom-hex.R index 0eb777b808..6badb8f87a 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -6,6 +6,7 @@ #' the very regular alignment of [geom_bin_2d()]. #' #' @eval rd_aesthetics("geom", "hex") +#' @eval rd_aesthetics("stat", "binhex") #' @seealso [stat_bin_2d()] for rectangular binning #' @param geom,stat Override the default connection between `geom_hex()` and #' `stat_bin_hex()`. For more information about overriding these connections, diff --git a/man/geom_hex.Rd b/man/geom_hex.Rd index 11dbdb1f87..553787761b 100644 --- a/man/geom_hex.Rd +++ b/man/geom_hex.Rd @@ -138,6 +138,17 @@ the very regular alignment of \code{\link[=geom_bin_2d]{geom_bin_2d()}}. \item \code{\link[=aes_linetype_size_shape]{linewidth}} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. + + +\code{stat_binhex()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \strong{\code{\link[=aes_position]{x}}} +\item \strong{\code{\link[=aes_position]{y}}} +\item \code{\link[=aes_colour_fill_alpha]{fill}} +\item \code{\link[=aes_group_order]{group}} +\item \code{weight} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } \section{Computed variables}{ From ce4bce28e54a1571fe4defa7c5838e0acdd488d1 Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Fri, 6 Sep 2024 14:45:43 +0900 Subject: [PATCH 120/264] Change `fill` of `GeomRibbon` to match with the previous default colour (#6079) --- R/geom-ribbon.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 470c013eee..a8f6b1be42 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -98,7 +98,7 @@ geom_ribbon <- function(mapping = NULL, data = NULL, GeomRibbon <- ggproto("GeomRibbon", Geom, default_aes = aes( colour = NA, - fill = from_theme(col_mix(ink, paper, 0.799)), + fill = from_theme(col_mix(ink, paper, 0.2)), linewidth = from_theme(borderwidth), linetype = from_theme(bordertype), alpha = NA), From 0d3757d6ccd994e4cf9ea75c3a48db7fbc1bac8f Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Fri, 6 Sep 2024 16:43:08 +0900 Subject: [PATCH 121/264] Fix the YAML syntax of fig.alt chunk option (#6083) --- README.Rmd | 2 +- vignettes/articles/faq-annotation.Rmd | 24 +++++----- vignettes/articles/faq-axes.Rmd | 64 +++++++++++++------------- vignettes/articles/faq-bars.Rmd | 60 ++++++++++++------------ vignettes/articles/faq-customising.Rmd | 58 +++++++++++------------ vignettes/articles/faq-faceting.Rmd | 37 ++++++++------- vignettes/articles/faq-reordering.Rmd | 31 ++++++------- vignettes/extending-ggplot2.Rmd | 58 +++++++++++------------ vignettes/ggplot2-specs.Rmd | 42 ++++++++--------- vignettes/ggplot2.Rmd | 16 +++---- 10 files changed, 191 insertions(+), 201 deletions(-) diff --git a/README.Rmd b/README.Rmd index 693181ebae..337aa50b45 100644 --- a/README.Rmd +++ b/README.Rmd @@ -47,7 +47,7 @@ pak::pak("tidyverse/ggplot2") It's hard to succinctly describe how ggplot2 works because it embodies a deep philosophy of visualisation. However, in most cases you start with `ggplot()`, supply a dataset and aesthetic mapping (with `aes()`). You then add on layers (like `geom_point()` or `geom_histogram()`), scales (like `scale_colour_brewer()`), faceting specifications (like `facet_wrap()`) and coordinate systems (like `coord_flip()`). ```{r example} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars coloured by 7 'types' of car. The displacement and miles #| per gallon are inversely correlated." library(ggplot2) diff --git a/vignettes/articles/faq-annotation.Rmd b/vignettes/articles/faq-annotation.Rmd index a36ddfb670..b92e93e9e1 100644 --- a/vignettes/articles/faq-annotation.Rmd +++ b/vignettes/articles/faq-annotation.Rmd @@ -39,7 +39,7 @@ You should use `annotate(geom = "text")` instead of `geom_text()` for annotation In the following visualisation we have annotated a histogram with a red line and red text to mark the mean. Note that both the line and the text appears pixellated/fuzzy. ```{r} -#| fig.alt = "Histogram of highway miles per gallon for 234 cars. A red line is +#| fig.alt: "Histogram of highway miles per gallon for 234 cars. A red line is #| placed at the position 23.44 and is adorned with the label 'mean 23.44'. #| Both the line and the text appear pixellated due to overplotting." mean_hwy <- round(mean(mpg$hwy), 2) @@ -62,7 +62,7 @@ This is because `geom_text()` draws the geom once per each row of the data frame ```{r} -#| fig.alt = "Histogram of highway miles per gallon for 234 cars. A red line is +#| fig.alt: "Histogram of highway miles per gallon for 234 cars. A red line is #| placed at the position 23.44 and is adorned with the label 'mean = 23.44'. #| Both the line and the text appear crisp." ggplot(mpg, aes(x = hwy)) + @@ -91,7 +91,7 @@ Set `vjust = "inward"` and `hjust = "inward"` in `geom_text()`. Suppose you have the following data frame and visualization. The labels at the edges of the plot are cut off slightly. ```{r} -#| fig.alt = "A plot showing the words 'two', 'three' and 'four' arranged +#| fig.alt: "A plot showing the words 'two', 'three' and 'four' arranged #| diagonally. The 'two' and 'four' labels have been clipped to the panel's #| edge and are not displayed completely." df <- tibble::tribble( @@ -108,7 +108,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + You could manually extend axis limits to avoid this, but a more straightforward approach is to set `vjust = "inward"` and `hjust = "inward"` in `geom_text()`. ```{r} -#| fig.alt = "A plot showing the words 'two', 'three' and 'four' arranged +#| fig.alt: "A plot showing the words 'two', 'three' and 'four' arranged #| diagonally. The 'two' and 'four' labels are aligned to the top-right and #| bottom-left relative to their anchor points, and are displayed in their #| entirety." @@ -129,7 +129,7 @@ Either calculate the counts ahead of time and place them on bars using `geom_tex Suppose you have the following bar plot and you want to add the number of cars that fall into each `drv` level on their respective bars. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -139,7 +139,7 @@ One option is to calculate the counts with `dplyr::count()` and then pass them t Note that we expanded the y axis limit to get the numbers to fit on the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The count values are displayed on top of the bars as text." mpg %>% dplyr::count(drv) %>% @@ -152,7 +152,7 @@ mpg %>% Another option is to let `ggplot()` do the counting for you, and access these counts with `after_stat(count)` that is mapped to the labels to be placed on the plot with `stat_count()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The count values are displayed on top of the bars as text." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -173,7 +173,7 @@ First calculate the counts for each segment (e.g. with `dplyr::count()`) and the Suppose you have the following stacked bar plot. ```{r} -#| fig.alt = "A stacked bar chart showing the number of cars for each of seven +#| fig.alt: "A stacked bar chart showing the number of cars for each of seven #| types of cars. The fill colour of the bars indicate the type of drive #| train." ggplot(mpg, aes(x = class, fill = drv)) + @@ -190,7 +190,7 @@ mpg %>% You can then pass this result directly to `ggplot()`, draw the segments with appropriate heights with `y = n` in the `aes`thetic mapping and `geom_col()` to draw the bars, and finally place the counts on the plot with `geom_text()`. ```{r} -#| fig.alt = "A stacked bar chart showing the number of cars for each of seven +#| fig.alt: "A stacked bar chart showing the number of cars for each of seven #| types of cars. The fill colour of the bars indicate the type of drive #| train. In the middle of each filled part, the count value is displayed as #| text." @@ -214,7 +214,7 @@ Either calculate the proportions ahead of time and place them on bars using `geo Suppose you have the following bar plot but you want to display the proportion of cars that fall into each `drv` level, instead of the count. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -223,7 +223,7 @@ ggplot(mpg, aes(x = drv)) + One option is to calculate the proportions with `dplyr::count()` and then use `geom_col()` to draw the bars ```{r} -#| fig.alt = "A bar chart showing the proportion of cars for each of three types +#| fig.alt: "A bar chart showing the proportion of cars for each of three types #| of drive train." mpg %>% dplyr::count(drv) %>% @@ -236,7 +236,7 @@ Another option is to let `ggplot()` do the calculation of proportions for you, a Note that we also need to the `group = 1` mapping for this option. ```{r} -#| fig.alt = "A bar chart showing the proportion of cars for each of three types +#| fig.alt: "A bar chart showing the proportion of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv, y = ..prop.., group = 1)) + geom_bar() diff --git a/vignettes/articles/faq-axes.Rmd b/vignettes/articles/faq-axes.Rmd index f9868cdf8e..a6996dbe36 100644 --- a/vignettes/articles/faq-axes.Rmd +++ b/vignettes/articles/faq-axes.Rmd @@ -37,7 +37,7 @@ Set the angle of the text in the `axis.text.x` or `axis.text.y` components of th In the following plot the labels on the x-axis are overlapping. ```{r msleep-order-sleep-total} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -47,7 +47,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Rotate axis labels: We can do this by components of the `theme()`, specifically the `axis.text.x` component. Applying some vertical and horizontal justification to the labels centers them at the axis ticks. The `angle` can be set as desired within the 0 to 360 degree range, here we set it to 90 degrees. ```{r msleep-order-sleep-total-rotate} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The x-axis labels are oriented #| vertically and are readable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -58,7 +58,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Flip the axes: Use the y-axis for long labels. ```{r msleep-order-sleep-total-flip} -#| fig.alt = "A boxplot showing the total amount of sleep on the x-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the x-axis for 19 #| taxonomical orders of mammals on the y-axis. The y-axis labels are oriented #| horizontally and are readable." ggplot(msleep, aes(y = order, x = sleep_total)) + @@ -68,7 +68,7 @@ ggplot(msleep, aes(y = order, x = sleep_total)) + - Dodge axis labels: Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc., and customise the `guide` argument with the `guide_axis()` function. In this case we want to customise the x-axis, and the variable on the x-axis is discrete, so we'll use `scale_x_continuous()`. In the `guide` argument we use the `guide_axis()` and specify how many rows to dodge the labels into with `n.dodge`. This is likely a trial-and-error exercise, depending on the lengths of your labels and the width of your plot. In this case we've settled on 3 rows to render the labels. ```{r msleep-order-sleep-total-dodge} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis are dodged to three levels so that they remain readable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -79,7 +79,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Omit overlapping labels: Alternatively, you can set `guide_axis(check.overlap = TRUE)` to omit axis labels that overlap. ggplot2 will prioritize the first, last, and middle labels. Note that this option might be more preferable for axes representing variables that have an inherent ordering that is obvious to the audience of the plot, so that it's trivial to guess what the missing labels are. (This is not the case for the following plot.) ```{r msleep-order-sleep-total-check-overlap} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. Several of the x-axis labels #| have been omitted, but the one that remain are readable and don't overlap." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -100,7 +100,7 @@ Add a `theme()` layer and set relevant arguments, e.g. `axis.title.x`, `axis.tex Suppose we want to remove the axis labels entirely. ```{r ref.label="msleep-order-sleep-total"} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." ``` @@ -108,7 +108,7 @@ Suppose we want to remove the axis labels entirely. - Remove x or y axis labels: If you want to modify just one of the axes, you can do so by modifying the components of the `theme()`, setting the elements you want to remove to `element_blank()`. You would replace `x` with `y` for applying the same update to the y-axis. Note the distinction between `axis.title` and `axis.ticks` -- `axis.title` is the name of the variable and `axis.text` is the text accompanying each of the ticks. ```{r} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The annotation on the x-axis #| is abent." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -123,7 +123,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Remove all axis labels: You can use `theme_void()` to remove all theming elements. Note that this might remove more features than you like. For finer control over the theme, see below. ```{r} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The plot has no axes, #| gridlines or background panel." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -162,7 +162,7 @@ sales <- tribble( You can create a line plot of these data and facet by `year` to group the quarters for each year together. ```{r} -#| fig.alt = "A line plot with two panels showing value on the y-axis and four +#| fig.alt: "A line plot with two panels showing value on the y-axis and four #| quarters on the x-axis. The left panel is labelled '2020' and the right #| panel is labelled '2021'." ggplot(sales, aes(x = quarter, y = value, group = 1)) + @@ -175,7 +175,7 @@ However it might be preferable to plot all points in a single plot and indicate To achieve this, map the `interaction()` of `quarter` and `year` to the `x` aesthetic. ```{r} -#| fig.alt = "A line plot with one panel showing value on the y-axis and eight +#| fig.alt: "A line plot with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are appended after each quarter label." ggplot(sales, aes(x = interaction(quarter, year), y = value, group = 1)) + geom_line() @@ -186,7 +186,7 @@ To clean this up (1) clip the plotting area with `coord_cartesian()`, (2) remove Note that the x-coordinates of the year labels are manually assigned here, but if you had many more years, you might write some logic to calculate their placement. ```{r} -#| fig.alt = "A line plot with one panel showing value on the y-axis and eight +#| fig.alt: "A line plot with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are shown in the middle of the first four #| and last four quarters. The line touches the panel on the left and right." ggplot(sales, aes(x = interaction(quarter, year), y = value, group = 1)) + @@ -205,7 +205,7 @@ This approach works with other geoms as well. For example, you might can create a bar plot representing the same data using the following. ```{r} -#| fig.alt = "A bar chart with one panel showing value on the y-axis and eight +#| fig.alt: "A bar chart with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are shown in the middle of the first four #| and last four quarters. The outer bars touch the panel on the left and #| right." @@ -225,7 +225,7 @@ If it's undesirable to have the bars flush against the edges of the plot, a simi However note that the space between the bars for 2020 Q4 and 2021 Q1 is greater than the space between the other bars. ```{r} -#| fig.alt = "A bar chart showing value on the y-axis and eight +#| fig.alt: "A bar chart showing value on the y-axis and eight #| quarters on the x-axis. The chart appears as a single panel. The years are #| shown in the middle of the first four and last four quarters. The outer bars #| do not touch the panel on the left and right." @@ -255,7 +255,7 @@ Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc. Suppose you want to give more informative labels for the type of drive train. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'r', 'f' and '4'." ggplot(mpg, aes(y = drv)) + @@ -265,7 +265,7 @@ ggplot(mpg, aes(y = drv)) + - Use the `labels` argument in the appropriate `scale_*()` function. You can find a list of these functions [here](https://ggplot2.tidyverse.org/reference/index.html#section-scales). Type of drive train (`drv`) is a discrete variable on the y-axis, so we'll adjust the labels in `scale_y_discrete()`. One option is to list the labels in the same order as the levels. Note that we start from the bottom and go up, just like we would if the variable was numeric/continuous. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'Rear wheel drive', 'Front wheel drive' #| and 'Four wheel drive'." @@ -279,7 +279,7 @@ ggplot(mpg, aes(y = drv)) + - Another approach is to use a named list. This approach not only makes the relabelling more explicit, but it also means you don't need to worry about the order of the levels. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'Rear wheel drive', 'Front wheel drive' #| and 'Four wheel drive'." @@ -308,7 +308,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc By default, large numbers on the axis labels in the following plot are shown in scientific notation. ```{r} -#| fig.alt = "A scatter plot showing the median sale price of housing in Texas +#| fig.alt: "A scatter plot showing the median sale price of housing in Texas #| on the x-axis and the total volume of sales on the y-axis. The labels of #| both axes are in scientific notation, for example: '1e+09'." ggplot(txhousing, aes(x = median, y = volume)) + @@ -319,7 +319,7 @@ The [**scales**](https://scales.r-lib.org/) package offers a large number of fun Use `scales::label_number()` to force decimal display of numbers rather than using scientific notation or use `scales::label_comma()` to insert a comma every three digits. ```{r} -#| fig.alt = "A scatter plot showing the median sale price of housing in Texas +#| fig.alt: "A scatter plot showing the median sale price of housing in Texas #| on the x-axis and the total volume of sales on the y-axis. The labels of #| the y-axis are written out in full, with commas marking groups of three #| zeroes. The x-axis labels are written out in full, with spaces marking @@ -345,7 +345,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc Suppose you want to increase/decrease the number of decimal spaces shown in the axis text in the following plot. ```{r} -#| fig.alt = "A scatter plot showing the difference in longitude on the x-axis +#| fig.alt: "A scatter plot showing the difference in longitude on the x-axis #| and difference in latitude on the y-axis for seal movements. The x-axis #| labels have one digit after the decimal place. The y-axis labels have two #| digits after the decimal place." @@ -357,7 +357,7 @@ The [**scales**](https://scales.r-lib.org/) package offers a large number of fun Use `scales::label_number()` where the `accuracy` argument indicates the number to round to, e.g. 0.1 to show 1 decimal place, 0.0001 to show 4 decimal places, etc. ```{r} -#| fig.alt = "A scatter plot showing the difference in longitude on the x-axis +#| fig.alt: "A scatter plot showing the difference in longitude on the x-axis #| and difference in latitude on the y-axis for seal movements. The x-axis #| labels have one digit after the decimal place. The y-axis labels have four #| digits after the decimal place." @@ -383,7 +383,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc The variable on the y-axis of the following line plot (`psavert`) indicates the personal savings rate, which is in percentages. ```{r} -#| fig.alt = "A lineplot showing the personal savings rate over time from 1967 +#| fig.alt: "A lineplot showing the personal savings rate over time from 1967 #| to 2015." ggplot(economics, aes(x = date, y = psavert, group = 1)) + geom_line() @@ -392,7 +392,7 @@ ggplot(economics, aes(x = date, y = psavert, group = 1)) + With `scales::label_percent()` you can add `%`s after the numbers shown on the axis to make the units more clear. ```{r} -#| fig.alt = "A lineplot showing the personal savings rate over time from 1967 +#| fig.alt: "A lineplot showing the personal savings rate over time from 1967 #| to 2015. The y-axis labels are appended by percentage signs." ggplot(economics, aes(x = date, y = psavert, group = 1)) + geom_line() + @@ -414,7 +414,7 @@ You can either use `bquote()` to parse mathematical expressions or use the [**gg In the following plot `cty` is squared and `hwy` is log transformed. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the logarithm of highway miles per gallon on the y-axis for #| 234 cars." ggplot(mpg, aes(x = cty^2, y = log(hwy))) + @@ -424,7 +424,7 @@ ggplot(mpg, aes(x = cty^2, y = log(hwy))) + - Use `bquote()` function to parse mathematical expressions. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the base 10 logarithm of highway miles per gallon on the #| y-axis for 234 cars. In the axis titles, the base 10 is indicated in #| subscript on the y-axis and the power 2 is indicated in superscript on @@ -440,7 +440,7 @@ ggplot(mpg, aes(x = cty^2, y = log(hwy, base = 10))) + - If you're already familiar with Markdown and HTML, you might prefer using the [ggtext](https://wilkelab.org/ggtext/) package instead. In Markdown we can write the axis labels as `cty2` and `log10(hwy)` for x and y axes, respectively. Then, we tell ggplot2 to interpret the axis labels as Markdown and not as plain text by setting `axis.title.x` and `axis.title.y` to `ggtext::element_markdown()`. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the base 10 logarithm of highway miles per gallon on the #| y-axis for 234 cars. In the axis titles, the base 10 is indicated in #| subscript on the y-axis and the power 2 is indicated in superscript on @@ -472,7 +472,7 @@ Customise the `breaks` and `minor_breaks` in `scale_x_continuous()`, `scale_y_co Suppose you want to customise the major and minor grid lines on both the x and the y axes of the following plot. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis versus +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis versus #| the highway miles per gallon on the y-axis for 234 cars. The distance #| between axis ticks is constant within each axis." ggplot(mpg, aes(x = cty, y = hwy)) + @@ -483,7 +483,7 @@ You can set `breaks` and `minor_breaks` in `scale_x_continuous()` and `scale_y_c For example, on the x-axis we have major and minor grid breaks defined as a sequence and on the y-axis we have explicitly stated where major breaks should appear as a vector (the value stated are randomly selected for illustrative purposes only, they don't follow a best practice) and we have completely turned off minor grid lines by setting `minor_breaks` to `NULL`. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis versus +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis versus #| the highway miles per gallon on the y-axis for 234 cars. The distance #| between axis ticks varies within the y-axis. There are no minor horizontal #| grid lines, and there are three minor vertical gridlines between major @@ -528,7 +528,7 @@ Remove the padding around the data entirely using by setting `expand = c(0, 0)` - Remove all padding: Suppose you want to remove the padding around the heat map so it's flush against the axes. ```{r} -#| fig.alt = "A heatmap showing a 2D density estimate of the waiting and +#| fig.alt: "A heatmap showing a 2D density estimate of the waiting and #| eruption times of the Old Faithful geyser. The heatmap does not touch the #| panel edges." ggplot(faithfuld, aes(waiting, eruptions)) + @@ -538,7 +538,7 @@ ggplot(faithfuld, aes(waiting, eruptions)) + Since both x and y variables are continuous, we set `expand = c(0, 0)` in both `scale_x_continuous()` and `scale_y_continuous()`. ```{r} -#| fig.alt = "A heatmap showing a 2D density estimate of the waiting and +#| fig.alt: "A heatmap showing a 2D density estimate of the waiting and #| eruption times of the Old Faithful geyser. The heatmap touches the panel #| edges." ggplot(faithfuld, aes(waiting, eruptions)) + @@ -550,7 +550,7 @@ ggplot(faithfuld, aes(waiting, eruptions)) + - Remove some of the padding: Suppose you want to remove the padding below the bars and the x-axis only. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(drv)) + geom_bar() @@ -559,7 +559,7 @@ ggplot(mpg, aes(drv)) + You would make this adjustment on `scale_y_continuous()` since that padding is in the vertical direction. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars touch the bottom of the panel, and the highest bar #| touches the top of the panel." ggplot(mpg, aes(drv)) + @@ -574,7 +574,7 @@ The `mult` argument in `expansion()` takes a multiplicative range expansion fact Given a vector of length 2, the lower limit is expanded by `mult[1]` (in this case 0) and the upper limit is expanded by `mult[2]` (in this case 0.05). ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars touch the bottom of the panel, and no bar touches #| the top of the panel." ggplot(mpg, aes(drv)) + diff --git a/vignettes/articles/faq-bars.Rmd b/vignettes/articles/faq-bars.Rmd index 345ff68c1b..3cbacf4d79 100644 --- a/vignettes/articles/faq-bars.Rmd +++ b/vignettes/articles/faq-bars.Rmd @@ -42,7 +42,7 @@ If assigning color based on another variable, map the variable to the `fill` `ae You can set all bars to be a given color with the `fill` argument of `geom_bar()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars are blue." ggplot(mpg, aes(x = drv)) + geom_bar(fill = "blue") @@ -51,7 +51,7 @@ ggplot(mpg, aes(x = drv)) + Alternatively, if the colors should be based on a variable, this should be should happen in the `aes()` mapping. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. From left-to-right, the bars appear red, green and blue." ggplot(mpg, aes(x = drv, fill = drv)) + geom_bar() @@ -61,7 +61,7 @@ And if you want to then customize the colors, one option is `scale_fill_manual() See other `scale_fill_*()` functions for more options for color choices. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. From left-to-right, the bars are purple, orange and dark #| blue." ggplot(mpg, aes(x = drv, fill = drv)) + @@ -85,12 +85,11 @@ By default, the `width` of bars is `0.9` (90% of the resolution of the data). You can set this argument to a lower value to get bars that are narrower with more space between them. ```{r} -#| fig.alt = c( -#| "A bar chart showing the number of cars for each of three types -#| of drive train. The bars are somewhat narrower than the default.", -#| "A bar chart showing the number of cars for each of three types +#| fig.alt: +#| - "A bar chart showing the number of cars for each of three types +#| of drive train. The bars are somewhat narrower than the default." +#| - "A bar chart showing the number of cars for each of three types #| of drive train. The bars are very narrow." -#| ) ggplot(mpg, aes(x = drv)) + geom_bar(width = 0.5) @@ -111,7 +110,7 @@ Adjust the `expand` argument in `scale_y_continuous()`, e.g. add `scale_y_contin By default ggplot2 expands the axes so the geoms aren't flush against the edges of the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -120,7 +119,7 @@ ggplot(mpg, aes(x = drv)) + To remove the spacing between the bars and the x-axis, but keep the spacing between the bars and the top of the plot, use the following. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The bottom of the bars touch the x-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -131,7 +130,7 @@ To achieve the opposite, switch the values in `mult`. Note that the tallest bar is now flush against top of the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The top of the highest bar touches the top of the panel." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -142,7 +141,7 @@ To adjust spacing around the x-axis, adjust the `expand` argument in `scale_x_di Note that this places the bars flush against the left side and leaves some space on the right side. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The left of the leftmost bar touches the y-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -152,7 +151,7 @@ ggplot(mpg, aes(x = drv)) + The default look of a bar plot can be achieved with the following. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -173,7 +172,7 @@ Set `position = position_dodge2(preserve = "single")` in `geom_bar()`. In the following plot the bars have differing widths within each level of `drv` as there are differing levels of `class` represented. ```{r} -#| fig.alt = "A grouped bar chart showing car counts dodged and filled by 7 +#| fig.alt: "A grouped bar chart showing car counts dodged and filled by 7 #| types of cars for each of three types of drive train. The left group has #| 5 narrower bars, the middle group has 4 bars and the right group has 3 wider #| bars." @@ -184,7 +183,7 @@ ggplot(mpg, aes(x = drv, fill = class)) + You can use `position_dodge2()` with `preserve = "single"` to address this. ```{r} -#| fig.alt = "A grouped bar chart showing car counts dodged and filled by 7 +#| fig.alt: "A grouped bar chart showing car counts dodged and filled by 7 #| types of cars for each of three types of drive train. From left-to-right, #| each groups has respectively 5, 4 and 3 equally wide bars." ggplot(mpg, aes(x = drv, fill = class)) + @@ -207,7 +206,7 @@ If you also want to show percentages on the axis, use `scales::label_percent()`. The following plot is useful for comparing counts but not as useful for comparing proportions, which is what you need if you want to be able to make statements like "in this sample, it's more likely to have a two-seater car that has rear-wheel drive than an SUV that has rear-wheel drive". ```{r} -#| fig.alt = "A horizontal stacked bar chart showing car counts for 7 types of +#| fig.alt: "A horizontal stacked bar chart showing car counts for 7 types of #| cars, stacked and filled by 3 types of drive train." ggplot(mpg, aes(y = class, fill = drv)) + geom_bar() @@ -216,7 +215,7 @@ ggplot(mpg, aes(y = class, fill = drv)) + `position = "fill"` will generate a bar plot with bars of equal length and the stacks in each bar will show the proportion of `drv` for that particular `class`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing proportions of cars for 7 +#| fig.alt: "A horizontal filled bar chart showing proportions of cars for 7 #| types of cars. The fill colour represents 3 types of drive train. Every #| stacked bar spans the width of the panel." ggplot(mpg, aes(y = class, fill = drv)) + @@ -226,7 +225,7 @@ ggplot(mpg, aes(y = class, fill = drv)) + If you want to show percentages instead of proportions on the x-axis, you can define this in `scale_x_continuous()` with `scales::label_percent()`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing percentages of cars for 7 +#| fig.alt: "A horizontal filled bar chart showing percentages of cars for 7 #| types of cars. The fill colour represents 3 types of drive train. Every #| stacked bar spans the width of the panel." ggplot(mpg, aes(y = class, fill = drv)) + @@ -271,7 +270,7 @@ poll_longer Then, you can pass this result to `ggplot()` and create a bar for each `party` on the `y` (or `x`, if you prefer vertical bars) axis and fill the bars in with number of responses for each `opinion`. ```{r} -#| fig.alt = "A horizontal stacked bar chart showing opinion counts for 3 +#| fig.alt: "A horizontal stacked bar chart showing opinion counts for 3 #| parties, stacked and filled by 3 types of opinions." ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + geom_col() @@ -280,7 +279,7 @@ ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + To plot proportions (relative frequencies) instead of counts, use `position = "fill"` in `geom_col()`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing proportions of opinions for +#| fig.alt: "A horizontal filled bar chart showing proportions of opinions for #| 3 parties. The fill colour represents 3 types of opinion. Every #| stacked bar spans the width of the panel." ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + @@ -315,7 +314,7 @@ You can do this with `tidyr::pivot_longer()`. Then, pass the resulting longer data frame to `ggplot()` group responses for each question together. ```{r} -#| fig.alt = "A grouped bar chart showing the number of responses to three +#| fig.alt: "A grouped bar chart showing the number of responses to three #| questions. Within each question, two bars denote an 'Agree' or 'Disagree' #| response." survey %>% @@ -342,7 +341,7 @@ One option for calculating group means is using `dplyr::group_by()` followed by Then, you can pass the resulting data frame to `ggplot()` and plot bars using `geom_col()`. ```{r} -#| fig.alt = "A bar chart showing the average highway miles per gallon for +#| fig.alt: "A bar chart showing the average highway miles per gallon for #| three types of drive train." mpg %>% group_by(drv) %>% @@ -354,7 +353,7 @@ mpg %>% Alternatively, you can use `stat_summary()` to let ggplot2 calculate and plot the means. ```{r} -#| fig.alt = "A bar chart showing the average highway miles per gallon for +#| fig.alt: "A bar chart showing the average highway miles per gallon for #| three types of drive train." ggplot(mpg, aes(x = drv, y = hwy)) + stat_summary(fun = "mean", geom = "bar") @@ -379,7 +378,7 @@ Also note that this will result in a deceiving bar plot, which should be avoided In the following plot the y-axis is limited to 20 to 120, and hence the bars are not showing up. ```{r} -#| fig.alt = "A plot with axes and a panel, but no other geometry." +#| fig.alt: "A plot with axes and a panel, but no other geometry." ggplot(mpg, aes(x = drv)) + geom_bar() + ylim(c(20, 120)) @@ -388,7 +387,7 @@ ggplot(mpg, aes(x = drv)) + In order to obtain a bar plot with limited y-axis, you need to instead set the limits in `coord_cartesian()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The y-axis starts at 20, and all bars touch the x-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -400,7 +399,7 @@ If you're using a bar plot to display values that could not take the value of 0, For example, if you have the following data and plot. ```{r} -#| fig.alt = "A bar chart showing numbers for 3 arbitrary categories. The +#| fig.alt: "A bar chart showing numbers for 3 arbitrary categories. The #| numbers are far away from the x-axis and visually appear broadly similar #| in height." df <- tibble::tribble( @@ -417,14 +416,13 @@ ggplot(df, aes(x = x, y = y)) + Also suppose that you want to cut off the bars at `y = 1000` since you know that the variable you're plotting cannot take a value less than 1000, you might use `geom_point()` instead. ```{r} -#| fig.alt = c( -#| "A bar chart showing numbers for 3 arbitrary categories. The y-axis starts +#| fig.alt: +#| - "A bar chart showing numbers for 3 arbitrary categories. The y-axis starts #| at 1000 and the bars all look different in height. This is not a recommended -#| way of plotting this data.", -#| "A scatter plot with 3 points showing numbers for 3 arbitrary categories. +#| way of plotting this data." +#| - "A scatter plot with 3 points showing numbers for 3 arbitrary categories. #| The y-axis starts at 1000 and the points have visually different values. #| This is a better way of plotting this data." -#| ) # don't do this ggplot(df, aes(x = x, y = y)) + geom_col() + diff --git a/vignettes/articles/faq-customising.Rmd b/vignettes/articles/faq-customising.Rmd index 5c8ed1b44f..b61df09336 100644 --- a/vignettes/articles/faq-customising.Rmd +++ b/vignettes/articles/faq-customising.Rmd @@ -40,7 +40,7 @@ By default your legend label will be the name of the variable that is mapped to You can change the title of your legend using `labs()`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend with the title 'Drive #| train'." @@ -52,16 +52,16 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + If a legend is drawn for multiple aesthetics, you'll want to update the title for all of them. ```{r} -#| fig.alt = c( -#| "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: +#| - "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The point shapes and colours #| indicate three types of drive train. The shapes and colours are displayed in -#| separate legends titled 'drv' and 'Drive train' respectively.", -#| "A scatter plot showing the highway miles per gallon on the x-axis +#| separate legends titled 'drv' and 'Drive train' respectively." +#| - "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The point shapes and colours #| indicate three types of drive train. The shapes and colours are displayed in #| a single legend titled 'Drive train'." -#| ) +#| # not this ggplot(mpg, aes(x = hwy, y = cty, color = drv, shape = drv)) + geom_point() + @@ -89,7 +89,7 @@ You can supply a unit object to this argument, e.g. `unit(1.0, "cm")` for 1 cm s See the documentation for `grid::unit()` for more options for units. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the bottom of the #| plot in a horizontal orientation. Legend elements are spaced widely apart." @@ -104,7 +104,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + For vertical legends changing `legend.spacing.y` changes the space between the legend title and the keys, but not between the keys, e.g. see the large space between the legend title and keys. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, there is a large space between the title and keys." @@ -116,7 +116,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + In order to change the space between the legend keys, you can first make the key size bigger with `legend.key.size` and then remove the grey background color with `legend.key`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, elements are placed widely apart and the title is @@ -133,7 +133,7 @@ Note that the legend title is no longer aligned with the keys with this approach You can also shift it over with the `hjust` setting of `legend.title`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, elements are placed widely apart and the title is @@ -161,7 +161,7 @@ The `labels` argument of `scale_*` functions takes named vectors, which what we Using named lists allows you to declare explicitly which label is assigned to which level, without having to keep track of level order. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. The legend items are name '4-wheel drive', 'Front-wheel drive' and @@ -191,7 +191,7 @@ You can use the following for 14 pts text for legend key labels and 10 pts text (Note that this doesn't result in a visually pleasing legend, by default ggplot2 uses a larger font size for the legend title than the legend text.) ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of cars, which is displayed in the legend on the right of the plot. #| The labels in the legend have a larger font size than the title." @@ -206,7 +206,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = class)) + For further customization of legend text, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of cars, which is displayed in the legend on the right of the plot. #| The labels in the legends have a large, red font. The title has a smaller, @@ -235,7 +235,7 @@ You can set the background colour of the plot with `panel.background` in `theme( In the following example the border is made thicker with `linewidth = 3` to ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The panel background of the plot #| is light blue and is outlined in red with a thick stroke." ggplot(mpg, aes(x = hwy, y = cty)) + @@ -246,7 +246,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + If you want to change the colour of the plotting area but not the panel where the panel, you can so the same thing with `plot.background`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot background is light blue #| and is outlined in red with a thick stroke. The panel background remains #| grey." @@ -259,7 +259,7 @@ Note that ggplot2 has a variety of [complete themes](https://ggplot2.tidyverse.o For example, if you prefer a more minimal look to your plots, without the grey background, you might try `theme_minimal()`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. There is no visible panel #| background and grid lines are in light grey." ggplot(mpg, aes(x = hwy, y = cty)) + @@ -270,7 +270,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + And you can continue customization based on one of these themes. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. There is no visible panel #| background and grid lines are in light grey. The plot as a whole is outlined #| by a thick red line." @@ -309,7 +309,7 @@ df <- tibble::tribble( By default, ggplot2 uses grey to represent `NA`s. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour." ggplot(df, aes(x = group, fill = outcome)) + @@ -319,7 +319,7 @@ ggplot(df, aes(x = group, fill = outcome)) + You can change the color of `NA` with `scale_fill_discrete()` in this case, e.g. make it purple. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour. The 'NA' fill colour is purple." ggplot(df, aes(x = group, fill = outcome)) + @@ -332,7 +332,7 @@ In the plot below this is shown with `theme_minimal()` to demonstrate how that l Note that while this is possible, setting the colour to transparent as such wouldn't be recommended in this particular case as it gives the appearance of a floating bar. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour. The 'NA' fill colour is transparent, giving #| the appearance that one of the stacked bars is floating." @@ -359,7 +359,7 @@ You can change it with the `base_size` argument in the theme you're using. See the [complete theme documentation](https://ggplot2.tidyverse.org/reference/ggtheme.html) for more high level options you can set. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of car. All text sizes in the axes and legend are large." ggplot(mpg, aes(x = hwy, y = cty, color = class)) + @@ -389,7 +389,7 @@ Font characteristics of plot titles and subtitles can be controlled with the `pl You can use the following for 20 pts text for the plot title and 15 pts text for the plot subtitle. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot has a large title #| displaying 'This is the plot title' and a less large subtitle displaying #| 'And this is the subtitle' at the top of the plot." @@ -408,7 +408,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + For further customization of plot title and subtitle, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot has a large red title #| displaying 'This is the plot title' and a less large subtitle in bold and #| italic displaying 'And this is the subtitle' at the top of the plot." @@ -439,7 +439,7 @@ In both cases, set font size in the `size` argument of `element_text()`, e.g. `a Font characteristics of axis labels can be controlled with `axis.title.x` or `axis.title.y` (or `axis.title` if you the same settings for both axes). ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The x-axis title displays #| 'This is HUGE' in a large font size, and the y-axis title displays #| 'This is small' in a smaller font size." @@ -458,7 +458,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + For further customization of plot title and subtitle, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The x-axis title displays #| 'This is HUGE' in a large, red font, and the y-axis title displays #| 'This is tiny' in a smaller, bold and italic font." @@ -477,7 +477,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + You can also change the size of the axis text (e.g. numbers at the axis ticks) using `axis.text` (or `axis.text.x` and `axis.text.y` if you want to set different sizes). ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. Both the x and the y axis titles #| display 'The axis labels are the same size' in a large font. Both axis #| labels are displayed in a larger, blue font." @@ -518,7 +518,7 @@ Please refer to ["Font size" section of the aesthetic specifications](https://gg Suppose you have the following data frame and visualization. ```{r} -#| fig.alt = "A plot showing text at diagonal positions with the labels 'two', +#| fig.alt: "A plot showing text at diagonal positions with the labels 'two', #| 'three' and 'four'." df <- tibble::tribble( ~x, ~y, ~name, @@ -534,7 +534,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + You can set the size of the text with the following. ```{r} -#| fig.alt = "A plot showing larger text at diagonal positions with the labels +#| fig.alt: "A plot showing larger text at diagonal positions with the labels #| 'two', 'three' and 'four'." ggplot(df, aes(x = x, y = y, label = name)) + geom_text(size = 6) @@ -543,7 +543,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + Or you can map it to the `size` `aes`thetic. In the following size is determined by the `x` value with `scale_size_identity()`. ```{r} -#| fig.alt = "A plot showing text at diagonal positions with the labels 'two', +#| fig.alt: "A plot showing text at diagonal positions with the labels 'two', #| 'three' and 'four' that increase in size from left to right." ggplot(df, aes(x = x, y = y, label = name)) + geom_text(aes(size = x)) + diff --git a/vignettes/articles/faq-faceting.Rmd b/vignettes/articles/faq-faceting.Rmd index 93ec538a9e..bb7112edbb 100644 --- a/vignettes/articles/faq-faceting.Rmd +++ b/vignettes/articles/faq-faceting.Rmd @@ -37,7 +37,7 @@ The simplest answer is that you should use `facet_wrap()` when faceting by a sin `facet_wrap()` is most commonly used to facet by a plot by a single categorical variable. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution for +#| fig.alt: "A histogram showing the city miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout." ggplot(mpg, aes(x = cty)) + @@ -48,7 +48,7 @@ ggplot(mpg, aes(x = cty)) + And `facet_grid()` is commonly used to facet by a plot by two categorical variables. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution. The +#| fig.alt: "A histogram showing the city miles per gallon distribution. The #| plot has twelve panels in a 4-row, 3-column layout, showing three types of #| drive train in the horizontal direction, and four numbers of cylinders #| in the vertical direction. Several panels have no data." @@ -63,7 +63,7 @@ You can also use `facet_wrap()` with to facet by two categorical variables. This will only create facets for combinations of the levels of variables for which data exists. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution. The +#| fig.alt: "A histogram showing the city miles per gallon distribution. The #| plot has nine panels in a 3-row, 3-column layout, showing all existing #| combinations of three types of drive train, and four numbers of cylinders." ggplot(mpg, aes(x = cty)) + @@ -78,12 +78,11 @@ Similarly, you can also use `facet_grid()` to facet by a single categorical vari In the formula notation, you use a `.` to indicate that no faceting should be done along that axis, i.e. `cyl ~ .` facets across the y-axis (within a column) while `. ~ cyl` facets across the x-axis (within a row). ```{r out.width = "50%"} -#| fig.alt = c( -#| "A histogram showing the city miles per gallon distribution. The plot has -#| four panels in a 4-row, 1-column layout, showing four numbers of cylinders.", -#| "A histogram showing the city miles per gallon distribution. The plot has +#| fig.alt: +#| - "A histogram showing the city miles per gallon distribution. The plot has +#| four panels in a 4-row, 1-column layout, showing four numbers of cylinders." +#| - "A histogram showing the city miles per gallon distribution. The plot has #| four panels in a 1-row, 4-column layout, showing four numbers of cylinders." -#| ) ggplot(mpg, aes(x = cty)) + geom_histogram() + facet_grid(cyl ~ .) @@ -107,7 +106,7 @@ Then, add a `geom_vline()` layer to your plot that uses the summarized data. Suppose you have the following plot, and you want to add a vertical line at the mean value of `hwy` (highway mileage) for each pane. ```{r} -#| fig.alt = "A histogram showing the highway miles per gallon distribution for +#| fig.alt: "A histogram showing the highway miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout." ggplot(mpg, aes(x = hwy)) + @@ -130,7 +129,7 @@ mpg_summary Then, add a `geom_vline()` layer to your plot that uses the summary data. ```{r} -#| fig.alt = "A histogram showing the highway miles per gallon distribution for +#| fig.alt: "A histogram showing the highway miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout. Each panel has a vertical black line indicating the mean of the #| distribution." @@ -156,7 +155,7 @@ Suppose you have the following faceted plot. By default, both x and y scales are shared across the facets. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -170,7 +169,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + You can control this behaviour with the `scales` argument of faceting functions: varying scales across rows (`"free_x"`), columns (`"free_y"`), or both rows and columns (`"free"`), e.g. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -185,7 +184,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + If you also want to make sure that a particular value or range is included in each of the facets, you can set this with `expand_limits()`, e.g. ensure that 10 is included in the x-axis and values between 20 to 25 are included in the y-axis: ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -213,7 +212,7 @@ Set the `strip.text` element in `theme()` to `element_blank()`. Setting `strip.text` to `element_blank()` will remove all facet labels. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout. The strips, or panel layout titles and #| their backgrounds, are missing." @@ -226,7 +225,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + You can also remove the labels across rows only with `strip.x.text` or across columns only with `strip.y.text`. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout. In the vertical direction, the panels indicate four #| numbers of cylinders. The strips of the horizontal direction are missing." @@ -250,7 +249,7 @@ In the data frame below we have 100 observations, 50 of them come from one group These groups have very long names, and so when you facet the ploy by group, the facet labels (strips) get cut off. ```{r} -#| fig.alt = "A histogram with two panels in a 1-row, 2-column layout of random +#| fig.alt: "A histogram with two panels in a 1-row, 2-column layout of random #| data. The first panel has as title 'A long group name for the first group'. #| The second panel has a title 'A muuuuuuuuuuuuuch longer group name for the #| second group'. However, the second title is clipped to the panel width and @@ -269,7 +268,7 @@ ggplot(df, aes(x = x)) + You can control the maximum width of the facet label by setting the `width` in the `label_wrap_gen()` function, which is then passed to the `labeller` argument of your faceting function. ```{r} -#| fig.alt = "A histogram with two panels in a 1-row, 2-column layout of random +#| fig.alt: "A histogram with two panels in a 1-row, 2-column layout of random #| data. The first panel has as title 'A long group name for the first group' #| in two lines of text. The second panel has a title 'A muuuuuuuuuuuuuch #| longer group name for the second group' in three lines of text. The width @@ -305,7 +304,7 @@ df You can plot `price` versus `time` and facet by `country`, but the resulting plot can be a bit difficult to read due to the shared y-axis label. ```{r warning = FALSE} -#| fig.alt = "A timeseries plot showing price over time for two countries, Japan +#| fig.alt: "A timeseries plot showing price over time for two countries, Japan #| and the US, in two panels in a 2-row, 1-column layout. The countries are #| indicated at the top of each panel. The two y-axes have different ranges." ggplot(df, aes(x = year, y = price)) + @@ -317,7 +316,7 @@ ggplot(df, aes(x = year, y = price)) + With the following you can customize the facet labels first with `as_labeller()`, turn off the default y-axis label, and then place the facet labels where the y-axis label goes (`"outside"` and on the `"left"`). ```{r} -#| fig.alt = "A timeseries plot showing price over time for two countries and +#| fig.alt: "A timeseries plot showing price over time for two countries and #| their currencies, the Japanese Yen and the US Dollar, in two panels in a #| 2-row, 1-column layout. The countries and currency units are indicated at #| the left of each panel. The two y-axes have different ranges." diff --git a/vignettes/articles/faq-reordering.Rmd b/vignettes/articles/faq-reordering.Rmd index 39584e225d..d820c7a50e 100644 --- a/vignettes/articles/faq-reordering.Rmd +++ b/vignettes/articles/faq-reordering.Rmd @@ -44,7 +44,7 @@ Classes are ordered alphabetically. You might prefer them to be ordered by the number of cars in each class. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From bottom to top, the car types are in #| alphabetical order." ggplot(mpg, aes(y = class)) + @@ -54,7 +54,7 @@ ggplot(mpg, aes(y = class)) + To do this, you can use `forcats::fct_infreq()`. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From top to bottom, the car types are ordered #| by increasing number of cars." ggplot(mpg, aes(y = forcats::fct_infreq(class))) + @@ -64,7 +64,7 @@ ggplot(mpg, aes(y = forcats::fct_infreq(class))) + If you'd like to plot the highest value first, you can also reverse the order with `forcats::fct_rev()`. You might also want to simplify the axis label. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From top to bottom, the car types are ordered #| in decreasing number of cars." ggplot(mpg, aes(y = forcats::fct_rev(forcats::fct_infreq(class)))) + @@ -86,7 +86,7 @@ The forcats package offers a variety of options for doing this, such as `forcats Suppose you have the following stacked bar plot of `clarity` of `diamonds` by their `cut`. ```{r} -#| fig.alt = "A stacked bar plot showing counts on the y-axis and five cut +#| fig.alt: "A stacked bar plot showing counts on the y-axis and five cut #| qualities of diamonds on the x-axis. Within every stacked bar, the fill #| colour indicates an ordinal clarity of the diamond. The worst clarity has #| the darkest colour and the best quality has the lightest colour. The best @@ -99,7 +99,7 @@ You can reverse the order `clarity` levels are displayed in the bars with `forca This will also change the order they're presented in the legend so the two orders match. ```{r} -#| fig.alt = "A stacked bar plot showing counts on the y-axis and five cut +#| fig.alt: "A stacked bar plot showing counts on the y-axis and five cut #| qualities of diamonds on the x-axis. Within every stacked bar, the fill #| colour indicates an ordinal clarity of the diamond. The worst clarity has #| the lightest colour and the best quality has the darkest colour. The worst @@ -126,7 +126,7 @@ The order of the boxes is determined by the order of the levels of the variable If the faceting variable is character, this order is alphabetical by default. ```{r} -#| fig.alt = "A boxplot showing the highway miles per gallon on the y-axis for +#| fig.alt: "A boxplot showing the highway miles per gallon on the y-axis for #| seven types of car on the x-axis. The car types on the x-axis are in #| alphabetical order." ggplot(mpg, aes(x = class, y = hwy)) + @@ -138,7 +138,7 @@ You can do this in a data transformation step prior to plotting (e.g. with `dply You might then want to customize the x-axis label as well. ```{r} -#| fig.alt = "A boxplot showing the highway miles per gallon on the y-axis for +#| fig.alt: "A boxplot showing the highway miles per gallon on the y-axis for #| seven types of car on the x-axis. The car types on the x-axis sorted from #| left to right by increasing medians." ggplot(mpg, aes(x = forcats::fct_reorder(class, hwy, .fun = median), y = hwy)) + @@ -163,7 +163,7 @@ The order of the panes is determined by the order of the levels of the variable If the faceting variable is character, this order is alphabetical by default. ```{r} -#| fig.alt = "A scatter plot showing the engine displacement on the x-axis and +#| fig.alt: "A scatter plot showing the engine displacement on the x-axis and #| highway miles per gallon on the y-axis of 234 cars. The plot has three #| panels in a 1-row, 3-column layout for three types of drive train. The drive #| trains are ordered alphabetically in the horizontal direction." @@ -177,7 +177,7 @@ You can use `forcats::fct_relevel()` to reorder the levels of `drv`. You can do this in a data transformation step prior to plotting (e.g. with `dplyr::mutate()`) or you can do it directly in the plotting code as shown below. ```{r} -#| fig.alt = "A scatter plot showing the engine displacement on the x-axis and +#| fig.alt: "A scatter plot showing the engine displacement on the x-axis and #| highway miles per gallon on the y-axis of 234 cars. The plot has three #| panels in a 1-row, 3-column layout for three types of drive train. The drive #| trains are in the order 'r', 'f' and '4' from left to right." @@ -215,7 +215,7 @@ Note that the blue circle is partially covered by the yellow triangle since that Similarly the black asterisk appears on top of the red square. ```{r} -#| fig.alt = "A scatter plot showing four points at the same y-positions but at +#| fig.alt: "A scatter plot showing four points at the same y-positions but at #| four x-positions, of which two are very distinct. Every point has a distinct #| shape and colour. A yellow triangle is plotted on top of a blue circle. #| A black asterisk is plotted on top of a red square." @@ -229,7 +229,7 @@ Suppose you arranged your data in ascending order of the x-coordinates and plott Now the blue circle is over the yellow triangle since 0.01 comes after 0 and similarly the red square is over the black asterisk since 1 comes after 0.99. ```{r} -#| fig.alt = "A scatter plot showing four points at the same y-positions but at +#| fig.alt: "A scatter plot showing four points at the same y-positions but at #| four x-positions, of which two are very distinct. Every point has a distinct #| shape and colour. A blue circle is plotted on top of a yellow triangle. A #| red square is plotted on top of a black asterisk." @@ -245,16 +245,15 @@ df_arranged %>% If you wanted to make sure that the observation identified with an asterisk is always plotted on top, regardless of how the data are arranged in the data frame, you can create an additional layer for that observation. ```{r} -#| fig.alt = c( -#| "A scatter plot showing four points at the same y-positions but at four +#| fig.alt: +#| - "A scatter plot showing four points at the same y-positions but at four #| x-positions, of which two are very distinct. Every point has a distinct shape #| and colour. A yellow triangle is plotted on top of a blue circle. A black -#| asterisk is plotted on top of a red square.", -#| "A scatter plot showing four points at the same y-positions but at four +#| asterisk is plotted on top of a red square." +#| - "A scatter plot showing four points at the same y-positions but at four #| x-positions, of which two are very distinct. Every point has a distinct shape #| and colour. A blue circle is plotted on top of a yellow triangle. A black #| asterisk is plotted on top of a red square." -#| ) ggplot(mapping = aes(x = x, y = y, fill = fill, shape = shape)) + geom_point(data = df %>% filter(shape != "asterisk"), size = 8) + diff --git a/vignettes/extending-ggplot2.Rmd b/vignettes/extending-ggplot2.Rmd index 6ee65ae718..adac6896ea 100644 --- a/vignettes/extending-ggplot2.Rmd +++ b/vignettes/extending-ggplot2.Rmd @@ -86,7 +86,7 @@ stat_chull <- function(mapping = NULL, data = NULL, geom = "polygon", Once we have a layer function we can try our new stat: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hull of all the points is marked by a #| polygon with no fill." ggplot(mpg, aes(displ, hwy)) + @@ -99,7 +99,7 @@ ggplot(mpg, aes(displ, hwy)) + Once we've written this basic object, ggplot2 gives a lot for free. For example, ggplot2 automatically preserves aesthetics that are constant within each group: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hulls of points, grouped and coloured by #| three types of drive train, are marked by polygons with no fill but the #| outline matches the colours of the points." @@ -111,7 +111,7 @@ ggplot(mpg, aes(displ, hwy, colour = drv)) + We can also override the default geom to display the convex hull in a different way: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The points that are part of the convex hull of all #| points are marked with a red outline." ggplot(mpg, aes(displ, hwy)) + @@ -124,7 +124,7 @@ ggplot(mpg, aes(displ, hwy)) + A more complex stat will do some computation. Let's implement a simple version of `geom_smooth()` that adds a line of best fit to a plot. We create a `StatLm` that inherits from `Stat` and a layer function, `stat_lm()`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. A straight line with a negative slope passes through #| the cloud of points." StatLm <- ggproto("StatLm", Stat, @@ -159,7 +159,7 @@ ggplot(mpg, aes(displ, hwy)) + `StatLm` is inflexible because it has no parameters. We might want to allow the user to control the model formula and the number of points used to generate the grid. To do so, we add arguments to the `compute_group()` method and our wrapper function: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. A wobbly line follows the point cloud over the #| horizontal direction. 20 points are placed on top of the line with constant #| horizontal intervals." @@ -224,13 +224,12 @@ Sometimes you have calculations that should be performed once for the complete d To do this we override the `setup_params()` method. It's passed the data and a list of params, and returns an updated list. ```{r} -#| fig.alt = c( -#| "A line plot showing three kernel density estimates of engine displacement, +#| fig.alt: +#| - "A line plot showing three kernel density estimates of engine displacement, #| coloured for three types of drive trains. The lines are a little bit -#| wobbly.", -#| "A line plot showing three kernel density estimates of engine displacement, +#| wobbly." +#| - "A line plot showing three kernel density estimates of engine displacement, #| coloured for three types of drive trains. The lines are fairly smooth." -#| ) StatDensityCommon <- ggproto("StatDensityCommon", Stat, required_aes = "x", @@ -278,7 +277,7 @@ I recommend using `NULL` as a default value. If you pick important parameters au This stat illustrates another important point. If we want to make this stat usable with other geoms, we should return a variable called `density` instead of `y`. Then we can set up the `default_aes` to automatically map `density` to `y`, which allows the user to override it to use with different geoms: ```{r} -#| fig.alt = "A plot showing the engine displacement versus three types of drive +#| fig.alt: "A plot showing the engine displacement versus three types of drive #| trains. Every drive train is represented by a series of densely packed #| points that imitate a horizontal line, and their colour intensity indicates #| the kernel density estimate of the displacement." @@ -299,7 +298,7 @@ ggplot(mpg, aes(displ, drv, colour = after_stat(density))) + However, using this stat with the area geom doesn't work quite right. The areas don't stack on top of each other: ```{r} -#| fig.alt = "An area plot showing the kernel density estimates of +#| fig.alt: "An area plot showing the kernel density estimates of #| engine displacement. Three areas are shown that indicate the estimates for #| three types of drive trains separately. All areas are floored to the x-axis #| and overlap one another." @@ -310,16 +309,15 @@ ggplot(mpg, aes(displ, fill = drv)) + This is because each density is computed independently, and the estimated `x`s don't line up. We can resolve that issue by computing the range of the data once in `setup_params()`. ```{r} -#| fig.alt = c( -#| "A stacked area plot showing kernel density estimates of engine displacement. +#| fig.alt: +#| - "A stacked area plot showing kernel density estimates of engine displacement. #| Three areas are shown that indicate the estimates for three types of drive #| trains separately. The areas are stacked on top of one another and show -#| no overlap.", -#| "A heatmap showing the density of engine displacement for three types of +#| no overlap." +#| - "A heatmap showing the density of engine displacement for three types of #| drive trains. The heatmap has three rows for the drive trains, but are #| continuous in the horizontal direction. The fill intensity of the heatmap #| shows the kernel density estimates." -#| ) StatDensityCommon <- ggproto("StatDensityCommon", Stat, required_aes = "x", default_aes = aes(y = after_stat(density)), @@ -377,7 +375,7 @@ It's harder to create a new geom than a new stat because you also need to know s It's easiest to start with a simple example. The code below is a simplified version of `geom_point()`: ```{r GeomSimplePoint} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The points are larger than the default." GeomSimplePoint <- ggproto("GeomSimplePoint", Geom, required_aes = c("x", "y"), @@ -441,7 +439,7 @@ Overriding `draw_panel()` is most appropriate if there is one graphic element pe The following code makes a simplified version of `GeomPolygon`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hulls of points, grouped by 7 types of #| cars, are displayed as multiple polygons with no fill, but the outer line is #| coloured by the type." @@ -512,7 +510,7 @@ You might want to compare this to the real `GeomPolygon`. You'll see it override Sometimes you just want to make a small modification to an existing geom. In this case, rather than inheriting from `Geom` you can inherit from an existing subclass. For example, we might want to change the defaults for `GeomPolygon` to work better with `StatChull`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hull of all the points is marked by a #| polygon with no fill." GeomPolygonHollow <- ggproto("GeomPolygonHollow", GeomPolygon, @@ -628,12 +626,11 @@ title | `element_text()` | all text in title elements (plot, axes & lege These set default properties that are inherited by more specific settings. These are most useful for setting an overall "background" colour and overall font settings (e.g. family and size). ```{r axis-line-ex} -#| fig.alt = c( -#| "Scatterplot of three observations arranged diagonally. The axis titles 'x' -#| and 'y' are coloured in black", -#| "Scatterplot of three observations arranged diagonally. The axis titles 'x' +#| fig.alt: +#| - "Scatterplot of three observations arranged diagonally. The axis titles 'x' +#| and 'y' are coloured in black" +#| - "Scatterplot of three observations arranged diagonally. The axis titles 'x' #| and 'y' are coloured in red" -#| ) df <- data.frame(x = 1:3, y = 1:3) base <- ggplot(df, aes(x, y)) + geom_point() + @@ -809,11 +806,10 @@ FacetDuplicate <- ggproto("FacetDuplicate", Facet, Now with everything assembled, lets test it out: ```{r} -#| fig.alt = c( -#| "Scatterplot showing horsepower against miles per gallon for 32 cars.", -#| "Scatterplot with two panels showing horsepower against miles per gallon for +#| fig.alt: +#| - "Scatterplot showing horsepower against miles per gallon for 32 cars." +#| - "Scatterplot with two panels showing horsepower against miles per gallon for #| 32 cars. The left and right panels are identical." -#| ) p <- ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point() p p + facet_duplicate() @@ -1005,7 +1001,7 @@ As is very apparent, the `draw_panel` method can become very unwieldy once it be Enough talk - lets see if our new and powerful faceting extension works: ```{r} -#| fig.alt = "Scatterplot with two panels showing horsepower against miles per +#| fig.alt: "Scatterplot with two panels showing horsepower against miles per #| gallon for 32 cars. Both panels show the same datapoints. The left panel is #| titled 'original' and the right panel is titled 'transformed (sqrt)'. On the #| right panel, the miles per gallon are displayed on a square root @@ -1018,7 +1014,7 @@ ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point() + facet_trans('sqrt') As the rendering part of a facet class is often the difficult development step, it is possible to piggyback on the existing faceting classes to achieve a range of new facetings. Below we will subclass `facet_wrap()` to make a `facet_bootstrap()` class that splits the input data into a number of panels at random. ```{r} -#| fig.alt = "Scatterplot with three-by-three panels showing the weight versus +#| fig.alt: "Scatterplot with three-by-three panels showing the weight versus #| the price of about 10.000 diamonds in every panel. The panels are titled 1 #| to 9 and show different points, but are visually similar." diff --git a/vignettes/ggplot2-specs.Rmd b/vignettes/ggplot2-specs.Rmd index d66cb5951b..7829f05f6a 100644 --- a/vignettes/ggplot2-specs.Rmd +++ b/vignettes/ggplot2-specs.Rmd @@ -53,7 +53,7 @@ Line types can be specified with: 4 = dotdash, 5 = longdash, 6 = twodash, as shown below: ```{r} - #| fig.alt = "A series of 6 horizontal lines with different line types. + #| fig.alt: "A series of 6 horizontal lines with different line types. #| From top-to-bottom they are titled 'solid', 'dashed', 'dotted', #| 'dotdash', 'longdash', 'twodash'." lty <- c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash") @@ -76,7 +76,7 @@ Line types can be specified with: three off followed by one on and finally three off. ```{r} - #| fig.alt = "A series of 9 horizontal lines with different line types. + #| fig.alt: "A series of 9 horizontal lines with different line types. #| Each line is titled by two hexadecimal digits that determined the #| lengths of dashes and gaps." lty <- c("11", "18", "1f", "81", "88", "8f", "f1", "f8", "ff") @@ -107,16 +107,15 @@ with this mistake. and can be one of "round", "butt" (the default), or "square". ```{r, out.width = "30%", fig.show = "hold"} - #| fig.alt = c( - #| "A plot showing a line with an angle. A thinner red line is placed over - #| a thicker black line. The black line ends where the red line ends.", - #| "A plot showing a line with an angle. A thinner red line is placed over + #| fig.alt: + #| - "A plot showing a line with an angle. A thinner red line is placed over + #| a thicker black line. The black line ends where the red line ends." + #| - "A plot showing a line with an angle. A thinner red line is placed over #| a thicker black line. The black line ends past where the red line ends, - #| and ends in a semicircle.", - #| "A plot showing a line with an angle. A thinner red line is placed over + #| and ends in a semicircle." + #| - "A plot showing a line with an angle. A thinner red line is placed over #| a thicker black line. The black line ends past where the red line ends, #| and ends in a square shape." - #| ) df <- data.frame(x = 1:3, y = c(4, 1, 9)) base <- ggplot(df, aes(x, y)) + xlim(0.5, 3.5) + ylim(0, 10) base + @@ -136,15 +135,14 @@ with this mistake. "round" (the default), "mitre", or "bevel". ```{r, out.width = "30%", fig.show = "hold"} - #| fig.alt = c( - #| "A plot showing a thin red line on top of a thick black line shaped like - #| the letter 'V'. The corner in the black V-shape is rounded.", - #| "A plot showing a thin red line on top of a thick black line shaped like - #| the letter 'V'. The corner in the black V-shape is sharp.", - #| "A plot showing a thin red line on top of a thick black line shaped like + #| fig.alt: + #| - "A plot showing a thin red line on top of a thick black line shaped like + #| the letter 'V'. The corner in the black V-shape is rounded." + #| - "A plot showing a thin red line on top of a thick black line shaped like + #| the letter 'V'. The corner in the black V-shape is sharp." + #| - "A plot showing a thin red line on top of a thick black line shaped like #| the letter 'V'. A piece of the corner is cut off so that the two #| straight parts are connected by a horizontal part." - #| ) df <- data.frame(x = 1:3, y = c(9, 1, 9)) base <- ggplot(df, aes(x, y)) + ylim(0, 10) base + @@ -175,7 +173,7 @@ Shapes take five types of values: * An __integer__ in $[0, 25]$: ```{r} - #| fig.alt = "A 5-by-5 grid of point symbols annotated by the numbers + #| fig.alt: "A 5-by-5 grid of point symbols annotated by the numbers #| that can be used to represent the symbols. From left to right, the #| first 15 symbols are lines or open shapes, the next 5 symbols are solid #| shapes and the last 5 symbols are filled shaped." @@ -195,7 +193,7 @@ Shapes take five types of values: * The __name__ of the shape: ```{r out.width = "90%", fig.asp = 0.4, fig.width = 8} - #| fig.alt = "An irregular 6-by-7 grid of point symbols annotated by the + #| fig.alt: "An irregular 6-by-7 grid of point symbols annotated by the #| names that can be used to represent the symbols. Broadly, from top to #| bottom, the symbols are circles, squares, diamonds, triangles and #| others. Broadly from left to right, the symbols are solid shapes, @@ -233,7 +231,7 @@ Shapes take five types of values: While `colour` applies to all shapes, `fill` only applies to shapes 21-25, as can be seen above. The size of the filled part is controlled by `size`, the size of the stroke is controlled by `stroke`. Each is measured in mm, and the total size of the point is the sum of the two. Note that the size is constant along the diagonal in the following figure. ```{r} -#| fig.alt = "A plot showing a 4-by-4 grid of red points, the top 12 points with +#| fig.alt: "A plot showing a 4-by-4 grid of red points, the top 12 points with #| black outlines. The size of the points increases horizontally. The stroke of #| the outlines of the points increases vertically. A white diagonal line with #| a negative slope marks that the 'stroke' versus 'size' trade-off has @@ -252,7 +250,7 @@ ggplot(sizes, aes(size, stroke, size = size, stroke = stroke)) + There are only three fonts that are guaranteed to work everywhere: "sans" (the default), "serif", or "mono": ```{r} -#| fig.alt = "A plot showing three text labels arranged vertically. The top +#| fig.alt: "A plot showing three text labels arranged vertically. The top #| label is 'sans' and is displayed in a sans-serif font. The middle label is #| 'serif' and is displayed in a serif font. The bottom label is 'mono' and #| is displayed in a monospaced font." @@ -272,7 +270,7 @@ Both approaches have pros and cons, so you will to need to try both of them and ### Font face ```{r} -#| fig.alt = "A plot showing four text labels arranged vertically. The top +#| fig.alt: "A plot showing four text labels arranged vertically. The top #| label is 'bold.italic' and is displayed in bold and italic. The next three #| labels are 'italic', 'bold' and 'plain' and are displayed in their #| respective styles." @@ -294,7 +292,7 @@ Horizontal and vertical justification have the same parameterisation, either a s * left = 0, center = 0.5, right = 1 ```{r} -#| fig.alt = "A 3-by-3 grid of text on top of points, with horizontal text +#| fig.alt: "A 3-by-3 grid of text on top of points, with horizontal text #| justification increasing from 0 to 1 on the x-axis and vertical #| justification increasing from 0 to 1 on the y-axis. The points make it #| easier to see the relative placement of text." diff --git a/vignettes/ggplot2.Rmd b/vignettes/ggplot2.Rmd index f82f092df8..36193b65a4 100644 --- a/vignettes/ggplot2.Rmd +++ b/vignettes/ggplot2.Rmd @@ -23,7 +23,7 @@ This allows you to 'speak' a graph from composable elements, instead of being li More complete information about how to use ggplot2 can be found in the [book](https://ggplot2-book.org/), but here you'll find a brief overview of the plot components and some terse examples to build a plot like this: ```{r cake, echo = FALSE} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and #| year of manifacture. Every panel has an individual trendline." @@ -41,7 +41,7 @@ ggplot(mpg, aes(cty, hwy)) + For structure, we go over the 7 composable parts that come together as a set of instructions on how to draw a chart. ```{r overview_graphic, echo=FALSE} -#| fig.alt = "A schematic displaying seven overlaying rhombuses indicating the +#| fig.alt: "A schematic displaying seven overlaying rhombuses indicating the #| different composable parts. From bottom to top, the labels read 'Data', #| 'Mapping', 'Layers', 'Scales', 'Facets', 'Coordinates' and 'Theme'." n <- 7 @@ -108,7 +108,7 @@ Every layer consists of three important parts: A layer can be constructed using the `geom_*()` and `stat_*()` functions. These functions often determine one of the three parts of a layer, while the other two can still be specified. Here is how we can use two layers to display the `cty` and `hwy` columns of the `mpg` dataset as points and stack a trend line on top. ```{r example_layer, fig.show='hold'} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The plot has a blue trendline with a positive slope." ggplot(mpg, aes(cty, hwy)) + # to create a scatterplot @@ -125,7 +125,7 @@ Scales are responsible for updating the limits of a plot, setting the breaks, fo To use scales, one can use one of the scale functions that are patterned as `scale_{aesthetic}_{type}()` functions, where `{aesthetic}` is one of the pairings made in the mapping part of a plot. To map the `class` column in the `mpg` dataset to the viridis colour palette, we can write the following: ```{r example_scales} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars." ggplot(mpg, aes(cty, hwy, colour = class)) + geom_point() + @@ -141,7 +141,7 @@ The facets have their own mapping that can be given as a formula. To plot subsets of the `mpg` dataset based on levels of the `drv` and `year` variables, we can use `facet_grid()` as follows: ```{r example_facets} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars. +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars. #| The plot has six panels in a 2-row, 3-column layout, showing the #| combinations of three types of drive train and year of manifacture." ggplot(mpg, aes(cty, hwy)) + @@ -157,7 +157,7 @@ While typically Cartesian coordinates are used, the coordinate system powers the We can also use coordinates to display a plot with a fixed aspect ratio so that one unit has the same length in both the x and y directions. The `coord_fixed()` function sets this ratio automatically. ```{r example_coords} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The aspect ratio of the plot is such that units on the x-axis #| have the same length as units on the y-axis." ggplot(mpg, aes(cty, hwy)) + @@ -172,7 +172,7 @@ The [theme](https://ggplot2-book.org/themes) system controls almost any visuals To tweak the look of the plot, one can use many of the built-in `theme_*()` functions and/or detail specific aspects with the `theme()` function. The `element_*()` functions control the graphical attributes of theme components. ```{r example_theme} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars. The #| legend of the colour is displayed on top of the plot. The plot has thick #| axis lines and the bottom axis line is blue." @@ -191,7 +191,7 @@ ggplot(mpg, aes(cty, hwy, colour = class)) + As mentioned at the start, you can layer all of the pieces to build a customized plot of your data, like the one shown at the beginning of this vignette: ```{r outro} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and #| year of manifacture. Every panel has an individual trendline." From eec7490297d9b5d463f96dc8395285542923b94f Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Fri, 6 Sep 2024 17:31:10 +0900 Subject: [PATCH 122/264] Update code of showing the default size of `geom_text()` (#6084) --- vignettes/articles/faq-customising.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/faq-customising.Rmd b/vignettes/articles/faq-customising.Rmd index b61df09336..0112d64627 100644 --- a/vignettes/articles/faq-customising.Rmd +++ b/vignettes/articles/faq-customising.Rmd @@ -497,10 +497,10 @@ ggplot(mpg, aes(x = hwy, y = cty)) + ### What is the default size of `geom_text()` and how can I change the font size of `geom_text()`? -The default font size of `geom_text()` is 3.88. +The default font size of `geom_text()` is about 3.87. ```{r} -GeomLabel$default_aes$size +get_geom_defaults(geom_text)$size ``` You can change the size using the `size` argument in `geom_text()` for a single plot. If you want to use the same updated size, you can set this with `update_geom_defaults()`, e.g. `update_geom_defaults("text", list(size = 6))`. From 8c724a4576580fa21ede15d82ca713be0ad508b9 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 9 Sep 2024 13:12:33 +0200 Subject: [PATCH 123/264] Make facet section of `summary()` more terse (#6074) * print facets vars instead of whole object * add test * add news bullet --- NEWS.md | 2 ++ R/summary.R | 5 +++-- tests/testthat/_snaps/utilities.md | 16 ++++++++++++++++ tests/testthat/test-utilities.R | 13 +++++++++++++ 4 files changed, 34 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 40bdb3d156..a4bce3f6be 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* The `summary()` method for ggplots is now more terse about facets + (@teunbrand, #5989). * `guide_bins()`, `guide_colourbar()` and `guide_coloursteps()` gain an `angle` argument to overrule theme settings, similar to `guide_axis(angle)` (@teunbrand, #4594). diff --git a/R/summary.R b/R/summary.R index e5422f8ad4..4a227a3599 100644 --- a/R/summary.R +++ b/R/summary.R @@ -29,8 +29,9 @@ summary.ggplot <- function(object, ...) { cat("scales: ", paste(object$scales$input(), collapse = ", "), "\n") } - cat("faceting: ") - print(object$facet) + vars <- object$facet$vars() + vars <- if (length(vars) > 0) paste0("~", vars) else "" + cat("faceting: ", paste0(vars, collapse = ", "), "\n") if (length(object$layers) > 0) cat("-----------------------------------\n") diff --git a/tests/testthat/_snaps/utilities.md b/tests/testthat/_snaps/utilities.md index 0101c1edd1..4560379f1e 100644 --- a/tests/testthat/_snaps/utilities.md +++ b/tests/testthat/_snaps/utilities.md @@ -54,3 +54,19 @@ Can't recycle `..1` (size 4) to match `..2` (size 0). +# summary method gives a nice summary + + Code + summary(p) + Output + data: manufacturer, model, displ, year, cyl, trans, drv, cty, hwy, fl, + class [234x11] + mapping: x = ~displ, y = ~hwy, colour = ~drv + scales: x, xmin, xmax, xend, xintercept, xmin_final, xmax_final, xlower, xmiddle, xupper, x0, colour + faceting: ~year, ~cyl + ----------------------------------- + geom_point: na.rm = FALSE + stat_identity: na.rm = FALSE + position_identity + + diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index 08e948ca82..315ca88ebc 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -196,3 +196,16 @@ test_that("expose/ignore_data() can round-trip a data.frame", { expect_equal(test, df[, c("a", "c", "b", "d")]) }) + +test_that("summary method gives a nice summary", { + # This test isn't important enough to break anything on CRAN + skip_on_cran() + + p <- ggplot(mpg, aes(displ, hwy, colour = drv)) + + geom_point() + + scale_x_continuous() + + scale_colour_brewer() + + facet_grid(year ~ cyl) + + expect_snapshot(summary(p)) +}) From 2bd8cd53fd94891a764d28ca5c31a3fea151f55a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 9 Sep 2024 16:00:02 +0200 Subject: [PATCH 124/264] Fix mistake in alignment docs for `geom_text()` (#6073) * fix docs for `geom_text()` * swap top/right --- R/geom-text.R | 4 ++-- man/geom_text.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/geom-text.R b/R/geom-text.R index b7f0d3f320..ed378734ba 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -31,8 +31,8 @@ #' #' @section Alignment: #' You can modify text alignment with the `vjust` and `hjust` -#' aesthetics. These can either be a number between 0 (right/bottom) and -#' 1 (top/left) or a character (`"left"`, `"middle"`, `"right"`, `"bottom"`, +#' aesthetics. These can either be a number between 0 (left/bottom) and +#' 1 (right/top) or a character (`"left"`, `"middle"`, `"right"`, `"bottom"`, #' `"center"`, `"top"`). There are two special alignments: `"inward"` and #' `"outward"`. Inward always aligns text towards the center, and outward #' aligns it away from the center. diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 91c241ab4b..1b06e73ae1 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -209,8 +209,8 @@ the background colour of the label. \section{Alignment}{ You can modify text alignment with the \code{vjust} and \code{hjust} -aesthetics. These can either be a number between 0 (right/bottom) and -1 (top/left) or a character (\code{"left"}, \code{"middle"}, \code{"right"}, \code{"bottom"}, +aesthetics. These can either be a number between 0 (left/bottom) and +1 (right/top) or a character (\code{"left"}, \code{"middle"}, \code{"right"}, \code{"bottom"}, \code{"center"}, \code{"top"}). There are two special alignments: \code{"inward"} and \code{"outward"}. Inward always aligns text towards the center, and outward aligns it away from the center. From d31c051bb87cd5d5f02e8d19b5c002ad2a129d6c Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Tue, 10 Sep 2024 15:00:02 +0200 Subject: [PATCH 125/264] update revdepcheck results --- revdep/README.md | 1020 +- revdep/cran.md | 1301 +- revdep/failures.md | 6141 ++++++--- revdep/problems.md | 29883 +++++++++++++++++++++++++++++++++++++++++-- 4 files changed, 34562 insertions(+), 3783 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 8976e81c90..498c024ad2 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,386 +1,646 @@ # Revdeps -## Failed to check (132) +## Failed to check (165) -|package |version |error |warning |note | -|:----------------------|:----------|:------|:-------|:----| -|abctools |1.1.7 |1 | | | -|animalEKF |1.2 |1 | | | -|ANOM |0.5 |1 | | | -|atRisk |0.1.0 |1 | | | -|AutoScore |1.0.0 |1 | | | -|bayesdfa |1.3.3 |1 | | | -|bayesDP |1.3.6 |1 | | | -|BayesianFactorZoo |0.0.0.2 |1 | | | -|BayesSurvive |0.0.2 |1 | | | -|BCClong |1.0.3 |1 | | | -|BGGM |2.1.3 |1 | | | -|binsreg |1.0 |1 | | | -|bmstdr |0.7.9 |1 | | | -|bspcov |1.0.0 |1 | | | -|BuyseTest |3.0.4 |1 | | | -|CalibrationCurves |2.0.3 |1 | | | -|CARBayesST |4.0 |1 | | | -|CaseBasedReasoning |0.3 |1 | | | -|CGPfunctions |0.6.3 |1 | | | -|cmprskcoxmsm |0.2.1 |1 | | | -|contrast |0.24.2 |1 | | | -|coxed |0.3.3 |1 | | | -|CRMetrics |0.3.0 |1 | | | -|csmpv |1.0.3 |1 | | | -|ctsem |3.10.0 |1 | | | -|DepthProc |2.1.5 |1 | | | -|DR.SC |3.4 |1 | | | -|DynNom |5.1 |1 | | | -|easybgm |0.1.2 |1 | | | -|ecolottery |1.0.0 |1 | | | -|EpiEstim |2.2-4 |1 | | | -|evolqg |0.3-4 |1 | | | -|ForecastComb |1.3.1 |1 | | | -|gapfill |0.9.6-1 |1 | |1 | -|GeomComb |1.0 |1 | | | -|ggrcs |0.4.0 |1 | | | -|ggrisk |1.3 |1 | | | -|gJLS2 |0.2.0 |1 | | | -|Greg |2.0.2 |1 | | | -|greport |0.7-4 |1 | | | -|hettx |0.1.3 |1 | | | -|hIRT |0.3.0 |1 | | | -|Hmsc |3.0-13 |1 | | | -|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | -|iNZightPlots |2.15.3 |1 | | | -|iNZightRegression |1.3.4 |1 | | | -|IRexamples |0.0.4 |1 | | | -|jmBIG |0.1.2 |1 | | | -|joineRML |0.4.6 |1 | | | -|JWileymisc |1.4.1 |1 | | | -|kmc |0.4-2 |1 | | | -|L2E |2.0 |1 | | | -|llbayesireg |1.0.0 |1 | | | -|LorenzRegression |1.0.0 |1 | | | -|lsirm12pl |1.3.1 |1 | | | -|mbsts |3.0 |1 | | | -|MendelianRandomization |0.10.0 |1 | | | -|MetabolicSurv |1.1.2 |1 | | | -|miWQS |0.4.4 |1 | | | -|MRZero |0.2.0 |1 | | | -|Multiaovbay |0.1.0 |1 | | | -|multilevelTools |0.1.1 |1 | | | -|multinma |0.7.1 |1 | | | -|NCA |4.0.1 |1 | | | -|netcmc |1.0.2 |1 | | | -|NetworkChange |0.8 |1 | | | -|nlmeVPC |2.6 |1 | | | -|NMADiagT |0.1.2 |1 | | | -|optweight |0.2.5 |1 | | | -|OVtool |1.0.3 |1 | | | -|paths |0.1.1 |1 | | | -|PLMIX |2.1.1 |1 | | | -|popstudy |1.0.1 |1 | | | -|pould |1.0.1 |1 | | | -|powerly |1.8.6 |1 | | | -|pre |1.0.7 |1 | | | -|ProFAST |? | | | | -|psbcSpeedUp |2.0.7 |1 | | | -|pscore |0.4.0 |1 | | | -|psfmi |1.4.0 |1 | | | -|qPCRtools |1.0.1 |1 | | | -|qreport |1.0-1 |1 | | | -|qris |1.1.1 |1 | | | -|qte |1.3.1 |1 | | | -|quid |0.0.1 |1 | | | -|RATest |0.1.10 |1 | | | -|RcmdrPlugin.RiskDemo |3.2 |1 | | | -|rddtools |1.6.0 |1 | | | -|riskRegression |2023.12.21 |1 | | | -|rms |6.8-1 |1 | |1 | -|rmsb |1.1-1 |1 | | | -|robmed |1.0.2 |1 | | | -|robmedExtra |0.1.0 |1 | | | -|RPPanalyzer |1.4.9 |1 | | | -|RQdeltaCT |1.3.0 |1 | | | -|scCustomize |2.1.2 |1 | |1 | -|SCdeconR |1.0.0 |1 | | | -|scGate |1.6.2 |1 | | | -|SCIntRuler |0.99.6 |1 | | | -|scMappR |1.0.11 |1 | | | -|scpi |2.2.5 |1 | | | -|scRNAstat |0.1.1 |1 | | | -|sectorgap |0.1.0 |1 | | | -|SEERaBomb |2019.2 |1 | | | -|semicmprskcoxmsm |0.2.0 |1 | | | -|SensMap |0.7 |1 | | | -|Seurat |5.1.0 |1 | | | -|shinyTempSignal |0.0.8 |1 | | | -|sievePH |1.1 |1 | | | -|Signac |1.13.0 |1 | | | -|SimplyAgree |0.2.0 |1 | | | -|sMSROC |0.1.2 |1 | | | -|SNPassoc |2.1-0 |1 | | | -|snplinkage |? | | | | -|SoupX |1.6.2 |1 | | | -|sparsereg |1.2 |1 | | | -|spikeSlabGAM |1.1-19 |1 | | | -|statsr |0.3.0 |1 | | | -|streamDAG |? | | | | -|survHE |2.0.1 |1 | |1 | -|survidm |1.3.2 |1 | | | -|tempted |0.1.1 |1 | | | -|[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | -|tidyEdSurvey |0.1.3 |1 | | | -|tidyseurat |0.8.0 |1 | | | -|tidyvpc |1.5.1 |1 | | | -|TriDimRegression |1.0.2 |1 | | | -|TSrepr |1.1.0 |1 | | | -|twang |2.6 |1 | | | -|vdg |1.2.3 |1 | | | -|visa |0.1.0 |1 | | | -|WRTDStidal |1.1.4 |1 | | | +|package |version |error |warning |note | +|:-----------------------|:-------|:------|:-------|:----| +|abctools |1.1.7 |1 | | | +|adjclust |? | | | | +|animalEKF |1.2 |1 | | | +|ANOM |0.5 |1 | | | +|atRisk |0.1.0 |1 | | | +|AutoScore |? | | | | +|baRulho |? | | | | +|bayesDP |1.3.6 |1 | | | +|BayesianFactorZoo |0.0.0.2 |1 | | | +|BayesSurvive |0.0.2 |1 | | | +|BCClong |1.0.3 |1 | | | +|BGGM |2.1.3 |1 | | | +|binsreg |1.1 |1 | | | +|bspcov |1.0.0 |1 | | | +|bsub |1.1.0 |1 | | | +|BuyseTest |3.0.4 |1 | | | +|CARBayesST |4.0 |1 | | | +|CGPfunctions |0.6.3 |1 | | | +|chemodiv |? | | | | +|cinaR |? | | | | +|cmprskcoxmsm |0.2.1 |1 | | | +|CNVScope |? | | | | +|COMMA |1.0.0 |1 | | | +|conos |? | | | | +|counterfactuals |? | | | | +|CRMetrics |? | | | | +|crosstalkr |? | | | | +|ctsem |3.10.1 |1 | | | +|DepthProc |2.1.5 |1 | | | +|DR.SC |3.4 |1 | | | +|easybgm |0.1.2 |1 | | | +|EcoEnsemble |1.1.0 |1 | | | +|ecolottery |1.0.0 |1 | | | +|EMAS |? | | | | +|EpiEstim |2.2-4 |1 | | | +|evolqg |0.3-4 |1 | | | +|EWSmethods |? | | | | +|fmx |? | | | | +|ForecastComb |1.3.1 |1 | | | +|GALLO |? | | | | +|gap |? | | | | +|gapfill |0.9.6-1 |1 | |1 | +|geneHapR |? | | | | +|GeneSelectR |? | | | | +|GeomComb |1.0 |1 | | | +|geomorph |? | | | | +|gJLS2 |0.2.0 |1 | | | +|hettx |0.1.3 |1 | | | +|Hmisc |? | | | | +|Hmsc |3.0-13 |1 | | | +|iClusterVB |0.1.2 |1 | | | +|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | +|iNZightPlots |2.15.3 |1 | | | +|iNZightRegression |1.3.4 |1 | | | +|IRexamples |0.0.4 |1 | | | +|jmBIG |0.1.2 |1 | | | +|joineRML |0.4.6 |1 | | | +|kibior |? | | | | +|kmc |0.4-2 |1 | | | +|L2E |2.0 |1 | | | +|llbayesireg |1.0.0 |1 | | | +|locuszoomr |? | | | | +|LorenzRegression |2.0.0 |1 | | | +|lsirm12pl |1.3.3 |1 | | | +|MantaID |? | | | | +|MARVEL |? | | | | +|mbsts |3.0 |1 | | | +|MitoHEAR |? | | | | +|miWQS |0.4.4 |1 | | | +|mlmts |1.1.2 |1 | | | +|mlr |? | | | | +|MOCHA |? | | | | +|MRZero |0.2.0 |1 | | | +|multilevelTools |0.1.1 |1 | | | +|multinma |0.7.1 |1 | | | +|NCA |4.0.1 |1 | | | +|netcmc |1.0.2 |1 | | | +|NetworkChange |0.8 |1 | | | +|nlmeVPC |2.6 |1 | | | +|NMADiagT |0.1.2 |1 | | | +|ohun |? | | | | +|optweight |0.2.5 |1 | | | +|OVtool |1.0.3 |1 | | | +|pagoda2 |? | | | | +|PAMpal |1.2.1 |1 | | | +|PAMscapes |0.6.0 |1 | | | +|paths |0.1.1 |1 | | | +|PathwaySpace |? | | | | +|pcvr |1.0.0 |1 | | | +|PlasmaMutationDetector |? | | | | +|PlasmaMutationDetector2 |? | | | | +|PLMIX |2.1.1 |1 | | | +|polyRAD |? | | | | +|popstudy |1.0.1 |1 | | | +|pould |1.0.1 |1 | | | +|PoweREST |0.1.0 |1 | | | +|powerly |1.8.6 |1 | | | +|pre |1.0.7 |1 | | | +|ProFAST |? | | | | +|psbcSpeedUp |2.0.7 |1 | | | +|pscore |0.4.0 |1 | | | +|qPCRtools |1.0.1 |1 | | | +|qris |1.1.1 |1 | | | +|qte |1.3.1 |1 | | | +|quantilogram |3.1.1 |1 | | | +|quid |0.0.1 |1 | | | +|RcmdrPlugin.RiskDemo |3.2 |1 | | | +|rddtools |1.6.0 |1 | | | +|RGraphSpace |? | | | | +|rms |? | | | | +|RNAseqQC |? | | | | +|robmed |1.0.2 |1 | | | +|robmedExtra |0.1.0 |1 | | | +|RPPanalyzer |1.4.9 |1 | | | +|RQdeltaCT |1.3.0 |1 | | | +|RRPP |? | | | | +|rstanarm |2.32.1 |1 | | | +|RTIGER |? | | | | +|rTwig |1.1.0 |1 | | | +|RVA |? | | | | +|scCustomize |? | | | | +|SCdeconR |1.0.0 |1 | | | +|scGate |1.6.2 |1 | | | +|SCIntRuler |0.99.6 |1 | | | +|scITD |? | | | | +|scMappR |1.0.11 |1 | | | +|scpi |2.2.5 |1 | | | +|scRNAstat |0.1.1 |1 | | | +|sectorgap |0.1.0 |1 | | | +|SeedMatchR |? | | | | +|SEERaBomb |2019.2 |1 | | | +|semicmprskcoxmsm |0.2.0 |1 | | | +|SensMap |0.7 |1 | | | +|sephora |? | | | | +|Seurat |? | | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|sigminer |? | | | | +|Signac |? | | | | +|SimplyAgree |0.2.0 |1 | | | +|SNPassoc |? | | | | +|snplinkage |? | | | | +|SoupX |1.6.2 |1 | | | +|sparsereg |1.2 |1 | | | +|SpatialDDLS |? | | | | +|spikeSlabGAM |1.1-19 |1 | | | +|statsr |0.3.0 |1 | | | +|streamDAG |? | | | | +|survidm |1.3.2 |1 | | | +|tempted |0.1.1 |1 | | | +|TestAnaAPP |1.1.1 |1 | | | +|[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | +|tidyEdSurvey |0.1.3 |1 | | | +|tidyseurat |0.8.0 |1 | | | +|tidyvpc |1.5.1 |1 | | | +|TriDimRegression |1.0.2 |1 | | | +|TSrepr |1.1.0 |1 | | | +|twang |2.6.1 |1 | | | +|updog |? | | | | +|valr |? | | | | +|vdg |1.2.3 |1 | | | +|visa |0.1.0 |1 | | | +|VisualizeSimon2Stage |? | | | | +|WRTDStidal |1.1.4 |1 | | | +|xxdi |? | | | | -## New problems (242) +## New problems (469) -|package |version |error |warning |note | -|:------------------|:-------|:--------|:-------|:--------| -|[activAnalyzer](problems.md#activanalyzer)|2.1.1 |__+1__ | |1 __+1__ | -|[actxps](problems.md#actxps)|1.5.0 |__+1__ | |__+1__ | -|[AeRobiology](problems.md#aerobiology)|2.0.1 |1 | |__+1__ | -|[agricolaeplotr](problems.md#agricolaeplotr)|0.5.0 |__+1__ | | | -|[AnalysisLin](problems.md#analysislin)|0.1.2 |__+1__ | | | -|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | | -|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 | -|[aplot](problems.md#aplot)|0.2.3 |__+1__ | | | -|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | -|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+1__ | |1 | -|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | -|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | |__+1__ | -|[bartMan](problems.md#bartman)|0.1.0 |__+1__ | | | -|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | -|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | -|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+2__ | |__+1__ | -|[BayesMallows](problems.md#bayesmallows)|2.2.1 |__+1__ | |1 | -|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+1__ | |1 | -|[bayestestR](problems.md#bayestestr)|0.13.2 |1 __+1__ | | | -|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | -|[besthr](problems.md#besthr)|0.3.2 |__+2__ | |__+1__ | -|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | -|[biodosetools](problems.md#biodosetools)|3.6.1 |__+1__ | | | -|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | | -|[braidReports](problems.md#braidreports)|0.5.4 |__+1__ | | | -|[breathtestcore](problems.md#breathtestcore)|0.8.7 |__+1__ | | | -|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | -|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | -|[cartographr](problems.md#cartographr)|0.2.2 |__+1__ | |1 | -|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | -|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | -|[chillR](problems.md#chillr)|0.75 |__+1__ | | | -|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | -|[circhelp](problems.md#circhelp)|1.1 |__+2__ | |__+1__ | -|[clifro](problems.md#clifro)|3.2-5 |__+1__ | | | -|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | -|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | -|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | -|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | | -|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 | -|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | -|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | -|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | -|[cubble](problems.md#cubble)|0.3.1 |__+1__ | |1 __+1__ | -|[deeptime](problems.md#deeptime)|1.1.1 |__+1__ | | | -|[distributional](problems.md#distributional)|0.4.0 |__+1__ | | | -|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | -|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | -|[entropart](problems.md#entropart)|1.6-13 |__+2__ | |__+1__ | -|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 | -|[esci](problems.md#esci)|1.0.3 |__+2__ | | | -|[evalITR](problems.md#evalitr)|1.0.0 |1 | |1 __+1__ | -|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | | -|[EvoPhylo](problems.md#evophylo)|0.3.2 |1 __+1__ | |1 __+1__ | -|[expirest](problems.md#expirest)|0.1.6 |__+1__ | | | -|[explainer](problems.md#explainer)|1.0.1 |__+1__ | |1 | -|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | | -|[ezplot](problems.md#ezplot)|0.7.13 |__+2__ | |__+1__ | -|[fable.prophet](problems.md#fableprophet)|0.1.0 |__+1__ | |1 __+1__ | -|[fabletools](problems.md#fabletools)|0.4.2 |__+2__ | | | -|[factoextra](problems.md#factoextra)|1.0.7 |__+1__ | | | -|[fairmodels](problems.md#fairmodels)|1.2.1 |__+1__ | | | -|[fddm](problems.md#fddm)|1.0-2 |__+1__ | |1 | -|[feasts](problems.md#feasts)|0.3.2 |__+1__ | | | -|[ffp](problems.md#ffp)|0.2.2 |__+1__ | | | -|[fido](problems.md#fido)|1.1.1 |1 __+2__ | |2 | -|[flipr](problems.md#flipr)|0.3.3 |1 | |1 __+1__ | -|[foqat](problems.md#foqat)|2.0.8.2 |__+1__ | |__+1__ | -|[forestly](problems.md#forestly)|0.1.1 |__+1__ | |__+1__ | -|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | -|[funcharts](problems.md#funcharts)|1.4.1 |__+1__ | | | -|[geomtextpath](problems.md#geomtextpath)|0.1.4 |__+2__ | | | -|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | -|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | -|[ggbrain](problems.md#ggbrain)|0.8.1 |__+1__ | |1 __+1__ | -|[ggbreak](problems.md#ggbreak)|0.1.2 |__+2__ | |__+1__ | -|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | -|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | -|[ggDoubleHeat](problems.md#ggdoubleheat)|0.1.2 |__+1__ | | | -|[ggeasy](problems.md#ggeasy)|0.1.4 |__+3__ | |__+1__ | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggESDA](problems.md#ggesda)|0.2.0 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | -|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 | -|[ggformula](problems.md#ggformula)|0.12.0 | |__+1__ |1 | -|[ggfortify](problems.md#ggfortify)|0.4.17 |__+1__ | | | -|[gggenomes](problems.md#gggenomes)|1.0.0 |__+2__ | |__+1__ | -|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | -|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ | |__+1__ | -|[ggHoriPlot](problems.md#gghoriplot)|1.0.1 |__+1__ | |__+1__ | -|[ggiraph](problems.md#ggiraph)|0.8.10 |__+2__ | |1 | -|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+2__ | |__+1__ | -|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | |__+1__ | -|[ggmulti](problems.md#ggmulti)|1.0.7 |__+3__ | |__+1__ | -|[ggnewscale](problems.md#ggnewscale)|0.4.10 |__+2__ | | | -|[ggparallel](problems.md#ggparallel)|0.4.0 |__+1__ | | | -|[ggpicrust2](problems.md#ggpicrust2)|1.7.3 |__+1__ | |1 | -|[ggpie](problems.md#ggpie)|0.2.5 |__+2__ | |__+1__ | -|[ggplotlyExtra](problems.md#ggplotlyextra)|0.0.1 |__+1__ | |1 | -|[ggpol](problems.md#ggpol)|0.0.7 |__+1__ | |2 | -|[ggpubr](problems.md#ggpubr)|0.6.0 |__+1__ | | | -|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | 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|__+2__ | |2 | +|[unmconf](problems.md#unmconf)|1.0.0 |__+1__ | |__+1__ | +|[usmap](problems.md#usmap)|0.7.1 |__+3__ | |1 __+1__ | +|[vannstats](problems.md#vannstats)|1.3.4.14 |__+1__ | | | +|[vDiveR](problems.md#vdiver)|1.2.1 |__+1__ | |1 | +|[venn](problems.md#venn)|1.12 |__+1__ | | | +|[vimpclust](problems.md#vimpclust)|0.1.0 |__+1__ | |1 __+1__ | +|[vip](problems.md#vip)|0.4.1 |__+2__ | |2 | +|[VirtualPop](problems.md#virtualpop)|2.0.2 |__+1__ | |__+1__ | +|[viscomp](problems.md#viscomp)|1.0.0 |__+1__ | | | +|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 __+1__ | +|[voiceR](problems.md#voicer)|0.1.0 |__+2__ | |1 | +|[volcano3D](problems.md#volcano3d)|2.0.9 |__+2__ | |__+1__ | +|[voluModel](problems.md#volumodel)|0.2.2 |1 __+1__ | |__+1__ | +|[vsd](problems.md#vsd)|0.1.0 |__+1__ | |1 | +|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | | +|[walker](problems.md#walker)|1.0.10 |__+1__ | |2 __+1__ | +|[WVPlots](problems.md#wvplots)|1.3.8 |__+3__ | |__+1__ | +|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|[yamlet](problems.md#yamlet)|1.0.3 |__+2__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 4a9f813633..4a1365f7a5 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,9 +1,9 @@ ## revdepcheck results -We checked 5166 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 5209 reverse dependencies (5199 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 242 new problems - * We failed to check 132 packages + * We saw 469 new problems + * We failed to check 155 packages Issues with CRAN packages are summarised below. @@ -18,12 +18,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* adaptr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * AeRobiology checking re-building of vignette outputs ... NOTE * agricolaeplotr checking tests ... ERROR +* alien + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AlphaPart + checking examples ... ERROR + * AnalysisLin checking examples ... ERROR @@ -33,6 +46,28 @@ Issues with CRAN packages are summarised below. * ANN2 checking tests ... ERROR +* AnnoProbe + checking examples ... ERROR + +* ANOFA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ANOPA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AntMAN + checking examples ... ERROR + checking tests ... ERROR + +* APCI + checking tests ... ERROR + * aplot checking examples ... ERROR @@ -41,6 +76,10 @@ Issues with CRAN packages are summarised below. * ASRgenomics checking examples ... ERROR + checking tests ... ERROR + +* autocogs + checking tests ... ERROR * autoplotly checking examples ... ERROR @@ -51,9 +90,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* baggr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* banter + checking examples ... ERROR + * bartMan checking examples ... ERROR +* BasketballAnalyzeR + checking examples ... ERROR + +* bayefdr + checking examples ... ERROR + checking tests ... ERROR + * bayesAB checking tests ... ERROR @@ -69,49 +124,105 @@ Issues with CRAN packages are summarised below. * BayesMallows checking tests ... ERROR +* bayesplay + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * bayesplot + checking examples ... ERROR checking tests ... ERROR * bayestestR checking examples ... ERROR +* BCEA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BDgraph + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BEAMR + checking examples ... ERROR + * beastt checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* BeeGUTS + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * besthr checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* betaclust + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * biclustermd checking tests ... ERROR * biodosetools checking tests ... ERROR +* BioPred + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BlandAltmanLeh + checking running R code from vignettes ... ERROR + +* bmggum + checking examples ... ERROR + * boxly checking tests ... ERROR * braidReports checking examples ... ERROR +* BRcal + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * breathtestcore checking tests ... ERROR * brolgar checking examples ... ERROR +* calibrationband + checking examples ... ERROR + * cartograflow checking examples ... ERROR -* cartographr - checking tests ... ERROR +* cases + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * cats checking examples ... ERROR +* ceterisParibus + checking tests ... ERROR + +* cfda + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * cheem checking tests ... ERROR @@ -123,6 +234,11 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* CINNA + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * circhelp checking examples ... ERROR checking running R code from vignettes ... ERROR @@ -140,11 +256,43 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* cloneRate + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* clustEff + checking examples ... ERROR + +* ClustImpute + checking running R code from vignettes ... ERROR + +* cmstatr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* codaredistlm + checking examples ... ERROR + +* coefplot + checking examples ... ERROR + * CohortPlat checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* complmrob + checking examples ... ERROR + +* conjoint + checking examples ... ERROR + +* conquestr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * CoreMicrobiomeR checking examples ... ERROR @@ -156,14 +304,47 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* corx + checking tests ... ERROR + +* cosinor2 + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* CoSMoS + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * countfitteR checking tests ... ERROR +* coursekata + checking examples ... ERROR + checking tests ... ERROR + * covidcast checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* Coxmos + checking examples ... ERROR + +* cpr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* cpsvote + checking running R code from vignettes ... ERROR + +* crimeutils + checking examples ... ERROR + +* crmPack + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * crosshap checking examples ... ERROR @@ -174,8 +355,37 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* curtailment + checking examples ... ERROR + +* dabestr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* DAISIEprep + checking tests ... ERROR + +* dbmss + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * deeptime + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* descriptio + checking examples ... ERROR + +* directlabels + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* disto checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * distributional checking examples ... ERROR @@ -184,17 +394,60 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR +* dotwhisker + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* DRomics + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* dtwclust + checking tests ... ERROR + +* duke + checking tests ... ERROR + +* easysurv + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* EGAnet + checking examples ... ERROR + * EGM checking tests ... ERROR +* emmeans + checking examples ... ERROR + +* EMMIXmfa + checking examples ... ERROR + * entropart checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* EnvStats + checking examples ... ERROR + * epiCleanr checking examples ... ERROR +* epiphy + checking examples ... ERROR + +* EQUALSTATS + checking examples ... ERROR + +* ergm.multi + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * esci checking examples ... ERROR checking tests ... ERROR @@ -215,13 +468,15 @@ Issues with CRAN packages are summarised below. * explainer checking examples ... ERROR +* exuber + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ezEDA checking tests ... ERROR * ezplot checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * fable.prophet checking running R code from vignettes ... ERROR @@ -237,41 +492,95 @@ Issues with CRAN packages are summarised below. * fairmodels checking tests ... ERROR +* fastR2 + checking examples ... ERROR + +* faux + checking re-building of vignette outputs ... NOTE + * fddm checking running R code from vignettes ... ERROR * feasts checking tests ... ERROR +* fergm + checking examples ... ERROR + * ffp checking examples ... ERROR +* fic + checking running R code from vignettes ... ERROR + * fido checking examples ... ERROR checking tests ... ERROR +* fitdistrplus + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fitlandr + checking examples ... ERROR + +* flexsurv + checking running R code from vignettes ... ERROR + * flipr checking re-building of vignette outputs ... NOTE -* foqat +* FLOPART + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fmesher + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* fmf + checking examples ... ERROR + * forestly checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* FossilSim + checking examples ... ERROR + +* FPDclustering + checking examples ... ERROR + * frailtyEM checking examples ... ERROR * funcharts checking examples ... ERROR +* FunnelPlotR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* genekitr + checking examples ... ERROR + +* geoheatmap + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * geomtextpath checking examples ... ERROR checking tests ... ERROR +* geostan + checking examples ... ERROR + * GGally + checking examples ... ERROR checking tests ... ERROR * gganimate @@ -288,6 +597,12 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* ggcharts + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggdark checking examples ... ERROR checking tests ... ERROR @@ -297,9 +612,6 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... NOTE -* ggDoubleHeat - checking examples ... ERROR - * ggeasy checking examples ... ERROR checking tests ... ERROR @@ -311,18 +623,38 @@ Issues with CRAN packages are summarised below. * ggESDA checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggExtra + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggfacto + checking examples ... ERROR * ggfixest checking tests ... ERROR +* ggfocus + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggforce checking examples ... ERROR * ggformula + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR checking for code/documentation mismatches ... WARNING + checking re-building of vignette outputs ... NOTE * ggfortify + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * gggenomes checking examples ... ERROR @@ -330,7 +662,6 @@ Issues with CRAN packages are summarised below. checking re-building of vignette outputs ... NOTE * ggh4x - checking examples ... ERROR checking tests ... ERROR checking re-building of vignette outputs ... NOTE @@ -353,6 +684,12 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* ggmatplot + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggmice checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -363,30 +700,49 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggnewscale +* ggpackets checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggparallel checking tests ... ERROR +* ggparty + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggpicrust2 checking examples ... ERROR -* ggpie +* ggplotlyExtra + checking examples ... ERROR + +* ggPMX checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggplotlyExtra +* ggpol checking examples ... ERROR -* ggpol +* ggprism checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggpubr + checking examples ... ERROR checking tests ... ERROR +* ggrain + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggraph checking examples ... ERROR checking re-building of vignette outputs ... NOTE @@ -409,10 +765,16 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking for code/documentation mismatches ... WARNING +* ggsmc + checking running R code from vignettes ... ERROR + * ggspatial checking examples ... ERROR checking tests ... ERROR +* ggstatsplot + checking examples ... ERROR + * ggtern checking examples ... ERROR @@ -423,6 +785,27 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* GimmeMyPlot + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* giniVarCI + checking examples ... ERROR + +* gMCPLite + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* gMOIP + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* GofCens + checking examples ... ERROR + * greatR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -430,6 +813,12 @@ Issues with CRAN packages are summarised below. * Greymodels checking examples ... ERROR +* gsDesign + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * gtExtras checking tests ... ERROR @@ -455,11 +844,18 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* hesim - checking tests ... ERROR +* heumilkr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* hidecan - checking tests ... ERROR +* hilldiv + checking examples ... ERROR + +* hmclearn + checking examples ... ERROR + +* HTLR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * HVT @@ -468,7 +864,17 @@ Issues with CRAN packages are summarised below. * hypsoLoop checking whether package ‘hypsoLoop’ can be installed ... WARNING -* ICvectorfields +* ibdsim2 + checking examples ... ERROR + +* ICtest + checking examples ... ERROR + +* idiogramFISH + checking installed package size ... NOTE + +* IDMIR + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -476,7 +882,27 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* inferCSN +* ihclust + checking examples ... ERROR + +* immunarch + checking examples ... ERROR + +* incidental + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* infer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* injurytools + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* inlabru checking examples ... ERROR * insurancerating @@ -487,6 +913,32 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* IPV + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* IRon + checking examples ... ERROR + +* irt + checking examples ... ERROR + +* isoorbi + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ivDiag + checking examples ... ERROR + +* ivreg + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* jarbes + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * karel checking examples ... ERROR checking tests ... ERROR @@ -494,6 +946,10 @@ Issues with CRAN packages are summarised below. * kDGLM checking examples ... ERROR +* KMEANS.KNN + checking examples ... ERROR + checking tests ... ERROR + * latentcor checking examples ... ERROR @@ -512,18 +968,55 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* lgpr + checking tests ... ERROR + +* LightLogR + checking examples ... ERROR + * LMoFit checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* manydata +* lnmixsurv checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* LocalControl + checking running R code from vignettes ... ERROR + +* LocalCop + checking re-building of vignette outputs ... NOTE + +* LongDat + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* MARVEL +* longreadvqs checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* lpdensity + checking examples ... ERROR + +* lspartition + checking examples ... ERROR + +* LSTbook + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* manydata + checking tests ... ERROR + +* manymome + checking examples ... ERROR + +* mapbayr + checking examples ... ERROR + * MBNMAdose checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -531,26 +1024,58 @@ Issues with CRAN packages are summarised below. * MBNMAtime checking re-building of vignette outputs ... NOTE +* mecoturn + checking examples ... ERROR + * MetaNet checking examples ... ERROR * metR checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* metrica + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* miceRanger + checking running R code from vignettes ... ERROR + +* microbial + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MicrobiomeSurv + checking examples ... ERROR + * migraph checking tests ... ERROR +* mikropml + checking tests ... ERROR + * MiMIR checking examples ... ERROR * miRetrieve checking tests ... ERROR +* MiscMetabar + checking examples ... ERROR + checking tests ... ERROR + * misspi checking examples ... ERROR +* mixpoissonreg + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * mizer checking tests ... ERROR @@ -559,47 +1084,146 @@ Issues with CRAN packages are summarised below. * mlr3viz checking examples ... ERROR + checking tests ... ERROR * modeltime.resample checking tests ... ERROR -* move - checking installed package size ... NOTE +* moreparty + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mosaicCalc + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mosaicData + checking examples ... ERROR + +* mosaicModel + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mppR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MSCMT + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mstate + checking examples ... ERROR + checking running R code from vignettes ... ERROR * mtb checking tests ... ERROR +* mulgar + checking examples ... ERROR + +* MultivariateAnalysis + checking examples ... ERROR + +* mxfda + checking installed package size ... NOTE + * neatmaps checking examples ... ERROR +* neatStats + checking examples ... ERROR + +* netcom + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * NetFACS checking examples ... ERROR checking running R code from vignettes ... ERROR -* NeuralSens +* neuroUp checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * NHSRplotthedots checking tests ... ERROR +* nichetools + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * NIMAA checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* nonmem2R + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* nphRCT + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* nprobust + checking examples ... ERROR + +* nzelect + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * OBIC checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* oceanic + checking examples ... ERROR + +* oddsratio + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ofpetrial + checking examples ... ERROR + * OmicNavigator checking tests ... ERROR +* omu + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* OncoBayes2 + checking examples ... ERROR + * oncomsm checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* OneSampleLogRankTest + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* onpoint + checking examples ... ERROR + +* ordbetareg + checking examples ... ERROR + +* packcircles + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * pafr checking tests ... ERROR @@ -609,6 +1233,13 @@ Issues with CRAN packages are summarised below. * pathviewr checking tests ... ERROR +* patientProfilesVis + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* PCADSC + checking examples ... ERROR + * pcutils checking examples ... ERROR @@ -619,16 +1250,29 @@ Issues with CRAN packages are summarised below. * personalized checking tests ... ERROR -* phylepic +* phyloseqGraphTest + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* PieGlyph + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + * Plasmidprofiler checking examples ... ERROR * platetools checking tests ... ERROR +* PLNmodels + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* plotBart + checking tests ... ERROR + * plotDK checking tests ... ERROR @@ -652,16 +1296,20 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* precrec +* PPtreeregViz + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* priorsense +* precintcon checking examples ... ERROR + +* precrec checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ProAE +* priorsense + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -671,58 +1319,143 @@ Issues with CRAN packages are summarised below. * processmapR checking tests ... ERROR +* projpred + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * psborrow checking tests ... ERROR +* pubh + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* PUPMSI + checking examples ... ERROR + +* qacBase + checking examples ... ERROR + +* qPCRhelper + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * r2dii.plot checking tests ... ERROR +* r2spss + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* radiant.basics + checking examples ... ERROR + +* radiant.data + checking examples ... ERROR + +* radiant.model + checking examples ... ERROR + * Radviz checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* randomForestExplainer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * rassta checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR -* REddyProc - checking installed package size ... NOTE +* rater + checking tests ... ERROR + +* RBesT + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rddensity + checking examples ... ERROR + +* RecordTest + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reda + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * redist checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* reReg +* registr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reliabilitydiag + checking examples ... ERROR + +* relliptical checking examples ... ERROR +* reportRmd + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * reservr checking examples ... ERROR checking re-building of vignette outputs ... NOTE -* rKOMICS +* RestoreNet + checking examples ... ERROR + +* rfPermute checking examples ... ERROR * RKorAPClient checking tests ... ERROR -* RNAseqQC - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * roahd checking examples ... ERROR +* robCompositions + checking examples ... ERROR + * romic + checking examples ... ERROR checking tests ... ERROR * roptions checking examples ... ERROR +* rSAFE + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * santaR checking tests ... ERROR +* saros + checking examples ... ERROR + checking tests ... ERROR + +* scatterpie + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * scdtb checking tests ... ERROR @@ -736,10 +1469,30 @@ Issues with CRAN packages are summarised below. * SCVA checking examples ... ERROR +* sdmTMB + checking examples ... ERROR + * SDMtune checking tests ... ERROR -* SeaVal +* sedproxy + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* see + checking examples ... ERROR + +* seedreg + checking examples ... ERROR + +* semfindr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* sensiPhy checking examples ... ERROR * sglg @@ -751,21 +1504,34 @@ Issues with CRAN packages are summarised below. * SHAPforxgboost checking examples ... ERROR -* SHELF +* ShapleyOutlier + checking examples ... ERROR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * shinipsum checking tests ... ERROR -* SimNPH - checking tests ... ERROR +* signatureSurvival + checking examples ... ERROR -* smallsets +* SimCorrMix checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* spbal +* SimMultiCorrData + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* SimNPH + checking tests ... ERROR + +* slendr + checking examples ... ERROR + +* smallsets + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -775,34 +1541,90 @@ Issues with CRAN packages are summarised below. * sport checking tests ... ERROR +* spotoroo + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * SqueakR checking re-building of vignette outputs ... NOTE +* stability + checking examples ... ERROR + * statgenGWAS checking tests ... ERROR +* statgenHTP + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* sugrrants + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* superb + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * surveyexplorer checking examples ... ERROR +* survivalAnalysis + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* survminer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* survParamSim + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* survstan + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* SVMMaj + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * Sysrecon checking examples ... ERROR * tabledown checking examples ... ERROR -* TCIU - checking examples ... ERROR +* tcgaViz checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* tensorEVD +* TCIU + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* tcpl + checking tests ... ERROR + +* tern + checking examples ... ERROR + * thematic checking examples ... ERROR checking tests ... ERROR +* Thermistor + checking examples ... ERROR + * tidybayes checking examples ... ERROR @@ -818,16 +1640,29 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* tidySEM + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * tidytreatment checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* timeplyr + checking examples ... ERROR + * timetk checking tests ... ERROR * tinyarray checking examples ... ERROR +* tipmap + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * tornado checking examples ... ERROR checking tests ... ERROR @@ -843,6 +1678,21 @@ Issues with CRAN packages are summarised below. * TreatmentPatterns checking tests ... ERROR +* TreatmentSelection + checking examples ... ERROR + +* TreeDep + checking examples ... ERROR + +* TreeDist + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* treeheatr + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * trelliscopejs checking tests ... ERROR @@ -857,26 +1707,88 @@ Issues with CRAN packages are summarised below. * tsnet checking tests ... ERROR +* UBayFS + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* Umatrix + checking examples ... ERROR + * umiAnalyzer checking examples ... ERROR -* valr +* UnalR + checking examples ... ERROR checking tests ... ERROR +* unmconf + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* usmap + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vannstats + checking examples ... ERROR + +* vDiveR + checking examples ... ERROR + +* venn + checking examples ... ERROR + +* vimpclust + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vip + checking examples ... ERROR + checking tests ... ERROR + +* VirtualPop + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* viscomp + checking examples ... ERROR + * vivaldi checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* vivid +* voiceR + checking examples ... ERROR + checking tests ... ERROR + +* volcano3D + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* voluModel + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* vsd checking examples ... ERROR * vvshiny checking tests ... ERROR -* wilson +* walker + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* WVPlots + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * xaringanthemer checking tests ... ERROR @@ -887,135 +1799,158 @@ Issues with CRAN packages are summarised below. ### Failed to check -* abctools (NA) -* animalEKF (NA) -* ANOM (NA) -* atRisk (NA) -* AutoScore (NA) -* bayesdfa (NA) -* bayesDP (NA) -* BayesianFactorZoo (NA) -* BayesSurvive (NA) -* BCClong (NA) -* BGGM (NA) -* binsreg (NA) -* bmstdr (NA) -* bspcov (NA) -* BuyseTest (NA) -* CalibrationCurves (NA) -* CARBayesST (NA) -* CaseBasedReasoning (NA) -* CGPfunctions (NA) -* cmprskcoxmsm (NA) -* contrast (NA) -* coxed (NA) -* CRMetrics (NA) -* csmpv (NA) -* ctsem (NA) -* DepthProc (NA) -* DR.SC (NA) -* DynNom (NA) -* easybgm (NA) -* ecolottery (NA) -* EpiEstim (NA) -* evolqg (NA) -* ForecastComb (NA) -* gapfill (NA) -* GeomComb (NA) -* ggrcs (NA) -* ggrisk (NA) -* gJLS2 (NA) -* Greg (NA) -* greport (NA) -* hettx (NA) -* hIRT (NA) -* Hmsc (NA) -* inventorize (NA) -* iNZightPlots (NA) -* iNZightRegression (NA) -* IRexamples (NA) -* jmBIG (NA) -* joineRML (NA) -* JWileymisc (NA) -* kmc (NA) -* L2E (NA) -* llbayesireg (NA) -* LorenzRegression (NA) -* lsirm12pl (NA) -* mbsts (NA) -* MendelianRandomization (NA) -* MetabolicSurv (NA) -* miWQS (NA) -* MRZero (NA) -* Multiaovbay (NA) -* multilevelTools (NA) -* multinma (NA) -* NCA (NA) -* netcmc (NA) -* NetworkChange (NA) -* nlmeVPC (NA) -* NMADiagT (NA) -* optweight (NA) -* OVtool (NA) -* paths (NA) -* PLMIX (NA) -* popstudy (NA) -* pould (NA) -* powerly (NA) -* pre (NA) -* ProFAST (NA) -* psbcSpeedUp (NA) -* pscore (NA) -* psfmi (NA) -* qPCRtools (NA) -* qreport (NA) -* qris (NA) -* qte (NA) -* quid (NA) -* RATest (NA) -* RcmdrPlugin.RiskDemo (NA) -* rddtools (NA) -* riskRegression (NA) -* rms (NA) -* rmsb (NA) -* robmed (NA) -* robmedExtra (NA) -* RPPanalyzer (NA) -* RQdeltaCT (NA) -* scCustomize (NA) -* SCdeconR (NA) -* scGate (NA) -* SCIntRuler (NA) -* scMappR (NA) -* scpi (NA) -* scRNAstat (NA) -* sectorgap (NA) -* SEERaBomb (NA) -* semicmprskcoxmsm (NA) -* SensMap (NA) -* Seurat (NA) -* shinyTempSignal (NA) -* sievePH (NA) -* Signac (NA) -* SimplyAgree (NA) -* sMSROC (NA) -* SNPassoc (NA) -* snplinkage (NA) -* SoupX (NA) -* sparsereg (NA) -* spikeSlabGAM (NA) -* statsr (NA) -* streamDAG (NA) -* survHE (NA) -* survidm (NA) -* tempted (NA) -* tidydr (NA) -* tidyEdSurvey (NA) -* tidyseurat (NA) -* tidyvpc (NA) -* TriDimRegression (NA) -* TSrepr (NA) -* twang (NA) -* vdg (NA) -* visa (NA) -* WRTDStidal (NA) +* abctools (NA) +* adjclust (NA) +* animalEKF (NA) +* ANOM (NA) +* atRisk (NA) +* AutoScore (NA) +* baRulho (NA) +* bayesDP (NA) +* BayesianFactorZoo (NA) +* BayesSurvive (NA) +* BCClong (NA) +* BGGM (NA) +* binsreg (NA) +* bspcov (NA) +* bsub (NA) +* BuyseTest (NA) +* CARBayesST (NA) +* CGPfunctions (NA) +* chemodiv (NA) +* cinaR (NA) +* cmprskcoxmsm (NA) +* CNVScope (NA) +* COMMA (NA) +* conos (NA) +* counterfactuals (NA) +* CRMetrics (NA) +* crosstalkr (NA) +* ctsem (NA) +* DepthProc (NA) +* DR.SC (NA) +* easybgm (NA) +* EcoEnsemble (NA) +* ecolottery (NA) +* EMAS (NA) +* EpiEstim (NA) +* evolqg (NA) +* ForecastComb (NA) +* GALLO (NA) +* gap (NA) +* gapfill (NA) +* geneHapR (NA) +* GeneSelectR (NA) +* GeomComb (NA) +* gJLS2 (NA) +* hettx (NA) +* Hmisc (NA) +* Hmsc (NA) +* iClusterVB (NA) +* inventorize (NA) +* iNZightPlots (NA) +* iNZightRegression (NA) +* IRexamples (NA) +* jmBIG (NA) +* joineRML (NA) +* kibior (NA) +* kmc (NA) +* L2E (NA) +* llbayesireg (NA) +* locuszoomr (NA) +* LorenzRegression (NA) +* lsirm12pl (NA) +* MARVEL (NA) +* mbsts (NA) +* MitoHEAR (NA) +* miWQS (NA) +* mlmts (NA) +* mlr (NA) +* MOCHA (NA) +* MRZero (NA) +* multilevelTools (NA) +* multinma (NA) +* NCA (NA) +* netcmc (NA) +* NetworkChange (NA) +* nlmeVPC (NA) +* NMADiagT (NA) +* ohun (NA) +* optweight (NA) +* OVtool (NA) +* pagoda2 (NA) +* PAMpal (NA) +* PAMscapes (NA) +* paths (NA) +* pcvr (NA) +* PlasmaMutationDetector (NA) +* PlasmaMutationDetector2 (NA) +* PLMIX (NA) +* polyRAD (NA) +* popstudy (NA) +* pould (NA) +* PoweREST (NA) +* powerly (NA) +* pre (NA) +* ProFAST (NA) +* psbcSpeedUp (NA) +* pscore (NA) +* qPCRtools (NA) +* qris (NA) +* qte (NA) +* quantilogram (NA) +* quid (NA) +* RcmdrPlugin.RiskDemo (NA) +* rddtools (NA) +* RNAseqQC (NA) +* robmed (NA) +* robmedExtra (NA) +* RPPanalyzer (NA) +* RQdeltaCT (NA) +* rstanarm (NA) +* RTIGER (NA) +* rTwig (NA) +* RVA (NA) +* scCustomize (NA) +* SCdeconR (NA) +* scGate (NA) +* SCIntRuler (NA) +* scITD (NA) +* scMappR (NA) +* scpi (NA) +* scRNAstat (NA) +* sectorgap (NA) +* SeedMatchR (NA) +* SEERaBomb (NA) +* semicmprskcoxmsm (NA) +* SensMap (NA) +* sephora (NA) +* Seurat (NA) +* shinyTempSignal (NA) +* sievePH (NA) +* sigminer (NA) +* Signac (NA) +* SimplyAgree (NA) +* SNPassoc (NA) +* snplinkage (NA) +* SoupX (NA) +* sparsereg (NA) +* SpatialDDLS (NA) +* spikeSlabGAM (NA) +* statsr (NA) +* streamDAG (NA) +* survidm (NA) +* tempted (NA) +* TestAnaAPP (NA) +* tidydr (NA) +* tidyEdSurvey (NA) +* tidyseurat (NA) +* tidyvpc (NA) +* TriDimRegression (NA) +* TSrepr (NA) +* twang (NA) +* updog (NA) +* valr (NA) +* vdg (NA) +* visa (NA) +* WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 84ae909aa5..444f4e174b 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -69,6 +69,82 @@ ERROR: lazy loading failed for package ‘abctools’ * removing ‘/tmp/workdir/abctools/old/abctools.Rcheck/abctools’ +``` +# adjclust + +
+ +* Version: 0.6.9 +* GitHub: https://github.com/pneuvial/adjclust +* Source code: https://github.com/cran/adjclust +* Date/Publication: 2024-02-08 08:50:05 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "adjclust")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/adjclust/new/adjclust.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘adjclust/DESCRIPTION’ ... OK +... + When sourcing ‘hicClust.R’: +Error: there is no package called ‘HiTC’ +Execution halted + + ‘hicClust.Rmd’ using ‘UTF-8’... failed + ‘notesCHAC.Rmd’ using ‘UTF-8’... OK + ‘snpClust.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/adjclust/old/adjclust.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘adjclust/DESCRIPTION’ ... OK +... + When sourcing ‘hicClust.R’: +Error: there is no package called ‘HiTC’ +Execution halted + + ‘hicClust.Rmd’ using ‘UTF-8’... failed + ‘notesCHAC.Rmd’ using ‘UTF-8’... OK + ‘snpClust.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 2 NOTEs + + + + + ``` # animalEKF @@ -272,131 +348,141 @@ Run `revdepcheck::cloud_details(, "AutoScore")` for more info -## In both - -* checking whether package ‘AutoScore’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘AutoScore’ ... -** package ‘AutoScore’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘AutoScore’ -* removing ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/AutoScore’ +* using log directory ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AutoScore/DESCRIPTION’ ... OK +... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘survAUC’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘AutoScore’ ... -** package ‘AutoScore’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘AutoScore’ -* removing ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck/AutoScore’ +* using log directory ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AutoScore/DESCRIPTION’ ... OK +... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘survAUC’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# bayesdfa +# baRulho
-* Version: 1.3.3 -* GitHub: https://github.com/fate-ewi/bayesdfa -* Source code: https://github.com/cran/bayesdfa -* Date/Publication: 2024-02-26 20:50:06 UTC -* Number of recursive dependencies: 89 +* Version: 2.1.2 +* GitHub: https://github.com/ropensci/baRulho +* Source code: https://github.com/cran/baRulho +* Date/Publication: 2024-08-31 13:10:07 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "bayesdfa")` for more info +Run `revdepcheck::cloud_details(, "baRulho")` for more info
-## In both - -* checking whether package ‘bayesdfa’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/baRulho/new/baRulho.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘baRulho/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'warbleR', 'ohun' + +Package suggested but not available for checking: ‘Rraven’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’ ``` ### CRAN ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/baRulho/old/baRulho.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘baRulho/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'warbleR', 'ohun' + +Package suggested but not available for checking: ‘Rraven’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’ ``` @@ -546,7 +632,7 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’ * GitHub: https://github.com/ocbe-uio/BayesSurvive * Source code: https://github.com/cran/BayesSurvive * Date/Publication: 2024-06-04 13:20:12 UTC -* Number of recursive dependencies: 128 +* Number of recursive dependencies: 129 Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info @@ -581,8 +667,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘BayesSurvive’ * removing ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/BayesSurvive’ @@ -608,8 +694,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘BayesSurvive’ * removing ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck/BayesSurvive’ @@ -702,7 +788,7 @@ ERROR: lazy loading failed for package ‘BCClong’ * GitHub: https://github.com/donaldRwilliams/BGGM * Source code: https://github.com/cran/BGGM * Date/Publication: 2024-07-05 20:30:02 UTC -* Number of recursive dependencies: 208 +* Number of recursive dependencies: 209 Run `revdepcheck::cloud_details(, "BGGM")` for more info @@ -776,10 +862,10 @@ ERROR: lazy loading failed for package ‘BGGM’
-* Version: 1.0 +* Version: 1.1 * GitHub: NA * Source code: https://github.com/cran/binsreg -* Date/Publication: 2023-07-11 12:00:24 UTC +* Date/Publication: 2024-07-23 14:30:01 UTC * Number of recursive dependencies: 35 Run `revdepcheck::cloud_details(, "binsreg")` for more info @@ -830,26 +916,26 @@ ERROR: lazy loading failed for package ‘binsreg’ ``` -# bmstdr +# bspcov
-* Version: 0.7.9 -* GitHub: https://github.com/sujit-sahu/bmstdr -* Source code: https://github.com/cran/bmstdr -* Date/Publication: 2023-12-18 15:00:02 UTC -* Number of recursive dependencies: 215 +* Version: 1.0.0 +* GitHub: https://github.com/statjs/bspcov +* Source code: https://github.com/cran/bspcov +* Date/Publication: 2024-02-06 16:50:08 UTC +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "bmstdr")` for more info +Run `revdepcheck::cloud_details(, "bspcov")` for more info
## In both -* checking whether package ‘bmstdr’ can be installed ... ERROR +* checking whether package ‘bspcov’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/00install.out’ for details. ``` ## Installation @@ -857,77 +943,61 @@ Run `revdepcheck::cloud_details(, "bmstdr")` for more info ### Devel ``` -* installing *source* package ‘bmstdr’ ... -** package ‘bmstdr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... +** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bmstdr’ -* removing ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/bmstdr’ +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/bspcov’ ``` ### CRAN ``` -* installing *source* package ‘bmstdr’ ... -** package ‘bmstdr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... +** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bmstdr’ -* removing ‘/tmp/workdir/bmstdr/old/bmstdr.Rcheck/bmstdr’ +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/old/bspcov.Rcheck/bspcov’ ``` -# bspcov +# bsub
-* Version: 1.0.0 -* GitHub: https://github.com/statjs/bspcov -* Source code: https://github.com/cran/bspcov -* Date/Publication: 2024-02-06 16:50:08 UTC -* Number of recursive dependencies: 121 +* Version: 1.1.0 +* GitHub: https://github.com/jokergoo/bsub +* Source code: https://github.com/cran/bsub +* Date/Publication: 2021-07-01 15:50:10 UTC +* Number of recursive dependencies: 79 -Run `revdepcheck::cloud_details(, "bspcov")` for more info +Run `revdepcheck::cloud_details(, "bsub")` for more info
## In both -* checking whether package ‘bspcov’ can be installed ... ERROR +* checking whether package ‘bsub’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bsub/new/bsub.Rcheck/00install.out’ for details. ``` ## Installation @@ -935,38 +1005,36 @@ Run `revdepcheck::cloud_details(, "bspcov")` for more info ### Devel ``` -* installing *source* package ‘bspcov’ ... -** package ‘bspcov’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bsub’ ... +** package ‘bsub’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘bspcov’ -* removing ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/bspcov’ +ERROR: lazy loading failed for package ‘bsub’ +* removing ‘/tmp/workdir/bsub/new/bsub.Rcheck/bsub’ ``` ### CRAN ``` -* installing *source* package ‘bspcov’ ... -** package ‘bspcov’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bsub’ ... +** package ‘bsub’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘bspcov’ -* removing ‘/tmp/workdir/bspcov/old/bspcov.Rcheck/bspcov’ +ERROR: lazy loading failed for package ‘bsub’ +* removing ‘/tmp/workdir/bsub/old/bsub.Rcheck/bsub’ ``` @@ -1013,7 +1081,7 @@ installing to /tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00LOCK-BuyseTest/00new ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + there is no package called ‘rms’ Error: unable to load R code in package ‘BuyseTest’ Execution halted ERROR: lazy loading failed for package ‘BuyseTest’ @@ -1040,75 +1108,13 @@ installing to /tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/00LOCK-BuyseTest/00new ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + there is no package called ‘rms’ Error: unable to load R code in package ‘BuyseTest’ Execution halted ERROR: lazy loading failed for package ‘BuyseTest’ * removing ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/BuyseTest’ -``` -# CalibrationCurves - -
- -* Version: 2.0.3 -* GitHub: NA -* Source code: https://github.com/cran/CalibrationCurves -* Date/Publication: 2024-07-02 08:50:02 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info - -
- -## In both - -* checking whether package ‘CalibrationCurves’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ - - -``` -### CRAN - -``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ - - ``` # CARBayesST @@ -1118,7 +1124,7 @@ ERROR: lazy loading failed for package ‘CalibrationCurves’ * GitHub: https://github.com/duncanplee/CARBayesST * Source code: https://github.com/cran/CARBayesST * Date/Publication: 2023-10-30 16:40:02 UTC -* Number of recursive dependencies: 117 +* Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "CARBayesST")` for more info @@ -1181,84 +1187,6 @@ ERROR: lazy loading failed for package ‘CARBayesST’ * removing ‘/tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/CARBayesST’ -``` -# CaseBasedReasoning - -
- -* Version: 0.3 -* GitHub: https://github.com/sipemu/case-based-reasoning -* Source code: https://github.com/cran/CaseBasedReasoning -* Date/Publication: 2023-05-02 08:40:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "CaseBasedReasoning")` for more info - -
- -## In both - -* checking whether package ‘CaseBasedReasoning’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o -... -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CaseBasedReasoning’ -* removing ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ - - -``` -### CRAN - -``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o -... -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CaseBasedReasoning’ -* removing ‘/tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ - - ``` # CGPfunctions @@ -1268,7 +1196,7 @@ ERROR: lazy loading failed for package ‘CaseBasedReasoning’ * GitHub: https://github.com/ibecav/CGPfunctions * Source code: https://github.com/cran/CGPfunctions * Date/Publication: 2020-11-12 14:50:09 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "CGPfunctions")` for more info @@ -1323,6 +1251,158 @@ ERROR: lazy loading failed for package ‘CGPfunctions’ * removing ‘/tmp/workdir/CGPfunctions/old/CGPfunctions.Rcheck/CGPfunctions’ +``` +# chemodiv + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/hpetren/chemodiv +* Source code: https://github.com/cran/chemodiv +* Date/Publication: 2023-08-17 17:52:33 UTC +* Number of recursive dependencies: 170 + +Run `revdepcheck::cloud_details(, "chemodiv")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/chemodiv/new/chemodiv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘chemodiv/DESCRIPTION’ ... OK +... +* this is package ‘chemodiv’ version ‘0.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'fmcsR', 'ChemmineR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/chemodiv/old/chemodiv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘chemodiv/DESCRIPTION’ ... OK +... +* this is package ‘chemodiv’ version ‘0.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'fmcsR', 'ChemmineR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# cinaR + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/eonurk/cinaR +* Source code: https://github.com/cran/cinaR +* Date/Publication: 2022-05-18 14:00:09 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "cinaR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/cinaR/new/cinaR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cinaR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Packages required but not available: + 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', + 'TxDb.Mmusculus.UCSC.mm10.knownGene' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/cinaR/old/cinaR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cinaR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Packages required but not available: + 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', + 'TxDb.Mmusculus.UCSC.mm10.knownGene' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # cmprskcoxmsm @@ -1386,152 +1466,102 @@ ERROR: lazy loading failed for package ‘cmprskcoxmsm’ ``` -# contrast +# CNVScope
-* Version: 0.24.2 -* GitHub: https://github.com/Alanocallaghan/contrast -* Source code: https://github.com/cran/contrast -* Date/Publication: 2022-10-05 17:20:09 UTC -* Number of recursive dependencies: 111 +* Version: 3.7.2 +* GitHub: https://github.com/jamesdalg/CNVScope +* Source code: https://github.com/cran/CNVScope +* Date/Publication: 2022-03-30 23:40:08 UTC +* Number of recursive dependencies: 206 -Run `revdepcheck::cloud_details(, "contrast")` for more info +Run `revdepcheck::cloud_details(, "CNVScope")` for more info
-## In both - -* checking whether package ‘contrast’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ - +* using log directory ‘/tmp/workdir/CNVScope/new/CNVScope.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CNVScope/DESCRIPTION’ ... OK +... +Packages required but not available: 'GenomicInteractions', 'rtracklayer' -``` -### CRAN +Packages suggested but not available for checking: + 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', + 'BSgenome.Hsapiens.UCSC.hg19' -``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ - - -``` -# coxed - -
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -* Version: 0.3.3 -* GitHub: https://github.com/jkropko/coxed -* Source code: https://github.com/cran/coxed -* Date/Publication: 2020-08-02 01:20:07 UTC -* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "coxed")` for more info -
-## In both -* checking whether package ‘coxed’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. - ``` +``` +### CRAN -## Installation +``` +* using log directory ‘/tmp/workdir/CNVScope/old/CNVScope.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CNVScope/DESCRIPTION’ ... OK +... +Packages required but not available: 'GenomicInteractions', 'rtracklayer' -### Devel +Packages suggested but not available for checking: + 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', + 'BSgenome.Hsapiens.UCSC.hg19' -``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -``` -### CRAN -``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ ``` -# CRMetrics +# COMMA
-* Version: 0.3.0 -* GitHub: https://github.com/khodosevichlab/CRMetrics -* Source code: https://github.com/cran/CRMetrics -* Date/Publication: 2023-09-01 09:00:06 UTC -* Number of recursive dependencies: 239 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/COMMA +* Date/Publication: 2024-07-21 10:10:05 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "CRMetrics")` for more info +Run `revdepcheck::cloud_details(, "COMMA")` for more info
## In both -* checking whether package ‘CRMetrics’ can be installed ... ERROR +* checking whether package ‘COMMA’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/COMMA/new/COMMA.Rcheck/00install.out’ for details. ``` ## Installation @@ -1539,8 +1569,8 @@ Run `revdepcheck::cloud_details(, "CRMetrics")` for more info ### Devel ``` -* installing *source* package ‘CRMetrics’ ... -** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +* installing *source* package ‘COMMA’ ... +** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -1549,16 +1579,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘CRMetrics’ -* removing ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/CRMetrics’ +ERROR: lazy loading failed for package ‘COMMA’ +* removing ‘/tmp/workdir/COMMA/new/COMMA.Rcheck/COMMA’ ``` ### CRAN ``` -* installing *source* package ‘CRMetrics’ ... -** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +* installing *source* package ‘COMMA’ ... +** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -1567,192 +1597,432 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘CRMetrics’ -* removing ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/CRMetrics’ +ERROR: lazy loading failed for package ‘COMMA’ +* removing ‘/tmp/workdir/COMMA/old/COMMA.Rcheck/COMMA’ ``` -# csmpv +# conos
-* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/csmpv -* Date/Publication: 2024-03-01 18:12:44 UTC -* Number of recursive dependencies: 178 +* Version: 1.5.2 +* GitHub: https://github.com/kharchenkolab/conos +* Source code: https://github.com/cran/conos +* Date/Publication: 2024-02-26 19:30:05 UTC +* Number of recursive dependencies: 240 -Run `revdepcheck::cloud_details(, "csmpv")` for more info +Run `revdepcheck::cloud_details(, "conos")` for more info
-## In both - -* checking whether package ‘csmpv’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ +* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Package suggested but not available for checking: ‘pagoda2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ +* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Package suggested but not available for checking: ‘pagoda2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# ctsem +# counterfactuals
-* Version: 3.10.0 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2024-05-09 14:40:03 UTC -* Number of recursive dependencies: 158 +* Version: 0.1.4 +* GitHub: https://github.com/dandls/counterfactuals +* Source code: https://github.com/cran/counterfactuals +* Date/Publication: 2024-05-14 19:00:02 UTC +* Number of recursive dependencies: 227 -Run `revdepcheck::cloud_details(, "ctsem")` for more info +Run `revdepcheck::cloud_details(, "counterfactuals")` for more info
-## In both - -* checking whether package ‘ctsem’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/counterfactuals/new/counterfactuals.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘counterfactuals/DESCRIPTION’ ... OK +... +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘how-to-add-new-cf-methods.html.asis’ using ‘UTF-8’... OK + ‘introduction.html.asis’ using ‘UTF-8’... OK + ‘other_models.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ ``` ### CRAN ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/counterfactuals/old/counterfactuals.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘counterfactuals/DESCRIPTION’ ... OK +... +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘how-to-add-new-cf-methods.html.asis’ using ‘UTF-8’... OK + ‘introduction.html.asis’ using ‘UTF-8’... OK + ‘other_models.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ ``` -# DepthProc +# CRMetrics
-* Version: 2.1.5 -* GitHub: https://github.com/zzawadz/DepthProc -* Source code: https://github.com/cran/DepthProc -* Date/Publication: 2022-02-03 20:30:02 UTC -* Number of recursive dependencies: 134 +* Version: 0.3.0 +* GitHub: https://github.com/khodosevichlab/CRMetrics +* Source code: https://github.com/cran/CRMetrics +* Date/Publication: 2023-09-01 09:00:06 UTC +* Number of recursive dependencies: 239 -Run `revdepcheck::cloud_details(, "DepthProc")` for more info +Run `revdepcheck::cloud_details(, "CRMetrics")` for more info
-## In both - -* checking whether package ‘DepthProc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs +* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘CRMetrics’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘CRMetrics’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +# crosstalkr + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/crosstalkr +* Date/Publication: 2024-05-17 11:40:09 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "crosstalkr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/crosstalkr/new/crosstalkr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘crosstalkr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ensembldb’ + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/crosstalkr/old/crosstalkr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘crosstalkr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ensembldb’ + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# ctsem + +
+ +* Version: 3.10.1 +* GitHub: https://github.com/cdriveraus/ctsem +* Source code: https://github.com/cran/ctsem +* Date/Publication: 2024-08-19 14:40:06 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "ctsem")` for more info + +
+ +## In both + +* checking whether package ‘ctsem’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ + + +``` +### CRAN + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ + + +``` +# DepthProc + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "DepthProc")` for more info + +
+ +## In both + +* checking whether package ‘DepthProc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst @@ -1870,26 +2140,26 @@ ERROR: lazy loading failed for package ‘DR.SC’ ``` -# DynNom +# easybgm
-* Version: 5.1 -* GitHub: NA -* Source code: https://github.com/cran/DynNom -* Date/Publication: 2024-06-07 12:20:21 UTC -* Number of recursive dependencies: 104 +* Version: 0.1.2 +* GitHub: https://github.com/KarolineHuth/easybgm +* Source code: https://github.com/cran/easybgm +* Date/Publication: 2024-03-13 13:40:02 UTC +* Number of recursive dependencies: 175 -Run `revdepcheck::cloud_details(, "DynNom")` for more info +Run `revdepcheck::cloud_details(, "easybgm")` for more info
## In both -* checking whether package ‘DynNom’ can be installed ... ERROR +* checking whether package ‘easybgm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. ``` ## Installation @@ -1897,8 +2167,8 @@ Run `revdepcheck::cloud_details(, "DynNom")` for more info ### Devel ``` -* installing *source* package ‘DynNom’ ... -** package ‘DynNom’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading @@ -1906,16 +2176,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DynNom’ -* removing ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/DynNom’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ ``` ### CRAN ``` -* installing *source* package ‘DynNom’ ... -** package ‘DynNom’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading @@ -1923,31 +2193,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DynNom’ -* removing ‘/tmp/workdir/DynNom/old/DynNom.Rcheck/DynNom’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ ``` -# easybgm +# EcoEnsemble
-* Version: 0.1.2 -* GitHub: https://github.com/KarolineHuth/easybgm -* Source code: https://github.com/cran/easybgm -* Date/Publication: 2024-03-13 13:40:02 UTC -* Number of recursive dependencies: 174 +* Version: 1.1.0 +* GitHub: https://github.com/CefasRepRes/EcoEnsemble +* Source code: https://github.com/cran/EcoEnsemble +* Date/Publication: 2024-08-19 17:20:06 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "easybgm")` for more info +Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info
## In both -* checking whether package ‘easybgm’ can be installed ... ERROR +* checking whether package ‘EcoEnsemble’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. ``` ## Installation @@ -1955,34 +2225,54 @@ Run `revdepcheck::cloud_details(, "easybgm")` for more info ### Devel ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 -``` -### CRAN +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ + ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked +### CRAN + +``` +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ ``` @@ -2045,6 +2335,82 @@ ERROR: lazy loading failed for package ‘ecolottery’ * removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ +``` +# EMAS + +
+ +* Version: 0.2.2 +* GitHub: NA +* Source code: https://github.com/cran/EMAS +* Date/Publication: 2022-08-11 13:50:07 UTC +* Number of recursive dependencies: 186 + +Run `revdepcheck::cloud_details(, "EMAS")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/EMAS/new/EMAS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘EMAS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: + 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', + 'IlluminaHumanMethylation450kanno.ilmn12.hg19' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/EMAS/old/EMAS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘EMAS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: + 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', + 'IlluminaHumanMethylation450kanno.ilmn12.hg19' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # EpiEstim @@ -2181,6 +2547,76 @@ ERROR: lazy loading failed for package ‘evolqg’ * removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ +``` +# EWSmethods + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/EWSmethods +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "EWSmethods")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# fmx + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/fmx +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fmx")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # ForecastComb @@ -2243,6 +2679,158 @@ ERROR: lazy loading failed for package ‘ForecastComb’ * removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ +``` +# GALLO + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/GALLO +* Date/Publication: 2024-06-04 15:30:20 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "GALLO")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GALLO/new/GALLO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GALLO/DESCRIPTION’ ... OK +... +* this is package ‘GALLO’ version ‘1.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GALLO/old/GALLO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GALLO/DESCRIPTION’ ... OK +... +* this is package ‘GALLO’ version ‘1.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# gap + +
+ +* Version: 1.6 +* GitHub: https://github.com/jinghuazhao/R +* Source code: https://github.com/cran/gap +* Date/Publication: 2024-08-27 04:40:06 UTC +* Number of recursive dependencies: 199 + +Run `revdepcheck::cloud_details(, "gap")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/gap/new/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/gap/old/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + ``` # gapfill @@ -2300,31 +2888,183 @@ ERROR: lazy loading failed for package ‘gapfill’ * removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ -``` -### CRAN +``` +### CRAN + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ + + +``` +# geneHapR + +
+ +* Version: 1.2.4 +* GitHub: NA +* Source code: https://github.com/cran/geneHapR +* Date/Publication: 2024-03-01 14:32:40 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "geneHapR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/geneHapR/new/geneHapR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘geneHapR/DESCRIPTION’ ... OK +... +* this is package ‘geneHapR’ version ‘1.2.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/geneHapR/old/geneHapR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘geneHapR/DESCRIPTION’ ... OK +... +* this is package ‘geneHapR’ version ‘1.2.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# GeneSelectR + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/dzhakparov/GeneSelectR +* Source code: https://github.com/cran/GeneSelectR +* Date/Publication: 2024-02-03 14:00:05 UTC +* Number of recursive dependencies: 191 + +Run `revdepcheck::cloud_details(, "GeneSelectR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/new/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/old/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + -``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ ``` @@ -2386,129 +3126,38 @@ ERROR: lazy loading failed for package ‘GeomComb’ ``` -# ggrcs +# geomorph
-* Version: 0.4.0 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/ggrcs -* Date/Publication: 2024-06-29 02:40:02 UTC -* Number of recursive dependencies: 78 +* Source code: https://github.com/cran/geomorph +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "ggrcs")` for more info +Run `revdepcheck::cloud_details(, "geomorph")` for more info
-## In both - -* checking whether package ‘ggrcs’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ - - -``` -### CRAN - -``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ - - -``` -# ggrisk - -
- -* Version: 1.3 -* GitHub: https://github.com/yikeshu0611/ggrisk -* Source code: https://github.com/cran/ggrisk -* Date/Publication: 2021-08-09 07:40:06 UTC -* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "ggrisk")` for more info -
-## In both -* checking whether package ‘ggrisk’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. - ``` -## Installation -### Devel +``` +### CRAN ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ -``` -### CRAN -``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ + ``` @@ -2576,26 +3225,26 @@ ERROR: lazy loading failed for package ‘gJLS2’ ``` -# Greg +# hettx
-* Version: 2.0.2 -* GitHub: https://github.com/gforge/Greg -* Source code: https://github.com/cran/Greg -* Date/Publication: 2024-01-29 13:30:21 UTC -* Number of recursive dependencies: 151 +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 85 -Run `revdepcheck::cloud_details(, "Greg")` for more info +Run `revdepcheck::cloud_details(, "hettx")` for more info
## In both -* checking whether package ‘Greg’ can be installed ... ERROR +* checking whether package ‘hettx’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. ``` ## Installation @@ -2603,183 +3252,139 @@ Run `revdepcheck::cloud_details(, "Greg")` for more info ### Devel ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ ``` ### CRAN ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# greport +# Hmisc
-* Version: 0.7-4 -* GitHub: https://github.com/harrelfe/greport -* Source code: https://github.com/cran/greport -* Date/Publication: 2023-09-02 22:20:02 UTC -* Number of recursive dependencies: 84 +* Version: 5.1-3 +* GitHub: NA +* Source code: https://github.com/cran/Hmisc +* Date/Publication: 2024-05-28 07:10:02 UTC +* Number of recursive dependencies: 170 -Run `revdepcheck::cloud_details(, "greport")` for more info +Run `revdepcheck::cloud_details(, "Hmisc")` for more info
-## In both - -* checking whether package ‘greport’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ +* using log directory ‘/tmp/workdir/Hmisc/new/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs -``` -### CRAN -``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ ``` -# hettx - -
- -* Version: 0.1.3 -* GitHub: https://github.com/bfifield/hettx -* Source code: https://github.com/cran/hettx -* Date/Publication: 2023-08-19 22:22:34 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "hettx")` for more info - -
- -## In both - -* checking whether package ‘hettx’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel +### CRAN ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ +* using log directory ‘/tmp/workdir/Hmisc/old/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs -``` -### CRAN -``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# hIRT +# Hmsc
-* Version: 0.3.0 -* GitHub: https://github.com/xiangzhou09/hIRT -* Source code: https://github.com/cran/hIRT -* Date/Publication: 2020-03-26 17:10:02 UTC -* Number of recursive dependencies: 88 +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "hIRT")` for more info +Run `revdepcheck::cloud_details(, "Hmsc")` for more info
## In both -* checking whether package ‘hIRT’ can be installed ... ERROR +* checking whether package ‘Hmsc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. ``` ## Installation @@ -2787,61 +3392,63 @@ Run `revdepcheck::cloud_details(, "hIRT")` for more info ### Devel ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ ``` ### CRAN ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ ``` -# Hmsc - -
- -* Version: 3.0-13 -* GitHub: https://github.com/hmsc-r/HMSC -* Source code: https://github.com/cran/Hmsc -* Date/Publication: 2022-08-11 14:10:14 UTC -* Number of recursive dependencies: 76 +# iClusterVB -Run `revdepcheck::cloud_details(, "Hmsc")` for more info +
+ +* Version: 0.1.2 +* GitHub: https://github.com/AbdalkarimA/iClusterVB +* Source code: https://github.com/cran/iClusterVB +* Date/Publication: 2024-08-20 19:10:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "iClusterVB")` for more info
## In both -* checking whether package ‘Hmsc’ can be installed ... ERROR +* checking whether package ‘iClusterVB’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00install.out’ for details. ``` ## Installation @@ -2849,10 +3456,17 @@ Run `revdepcheck::cloud_details(, "Hmsc")` for more info ### Devel ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R +... ** data *** moving datasets to lazyload DB ** inst @@ -2861,18 +3475,25 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/iClusterVB’ ``` ### CRAN ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R +... ** data *** moving datasets to lazyload DB ** inst @@ -2881,8 +3502,8 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/iClusterVB’ ``` @@ -2935,7 +3556,6 @@ ERROR: lazy loading failed for package ‘inventorize’ ** R ** byte-compile and prepare package for lazy loading Warning in qgamma(service_level, alpha, beta) : NaNs produced -Warning in qgamma(service_level, alpha, beta) : NaNs produced ** help *** installing help indices ** building package indices @@ -3014,7 +3634,7 @@ ERROR: lazy loading failed for package ‘iNZightPlots’ * GitHub: https://github.com/iNZightVIT/iNZightRegression * Source code: https://github.com/cran/iNZightRegression * Date/Publication: 2024-04-05 02:32:59 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 159 Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info @@ -3280,77 +3900,79 @@ ERROR: lazy loading failed for package ‘joineRML’ ``` -# JWileymisc +# kibior
-* Version: 1.4.1 -* GitHub: https://github.com/JWiley/JWileymisc -* Source code: https://github.com/cran/JWileymisc -* Date/Publication: 2023-10-05 04:50:02 UTC -* Number of recursive dependencies: 167 +* Version: 0.1.1 +* GitHub: https://github.com/regisoc/kibior +* Source code: https://github.com/cran/kibior +* Date/Publication: 2021-01-28 15:20:02 UTC +* Number of recursive dependencies: 140 -Run `revdepcheck::cloud_details(, "JWileymisc")` for more info +Run `revdepcheck::cloud_details(, "kibior")` for more info
-## In both - -* checking whether package ‘JWileymisc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ +* using log directory ‘/tmp/workdir/kibior/new/kibior.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘kibior/DESCRIPTION’ ... OK +... +* this is package ‘kibior’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ +* using log directory ‘/tmp/workdir/kibior/old/kibior.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘kibior/DESCRIPTION’ ... OK +... +* this is package ‘kibior’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -3551,16 +4173,92 @@ ERROR: lazy loading failed for package ‘llbayesireg’ * removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ +``` +# locuszoomr + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/myles-lewis/locuszoomr +* Source code: https://github.com/cran/locuszoomr +* Date/Publication: 2024-09-06 10:10:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "locuszoomr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/locuszoomr/new/locuszoomr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'rtracklayer' + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/locuszoomr/old/locuszoomr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'rtracklayer' + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # LorenzRegression
-* Version: 1.0.0 -* GitHub: NA +* Version: 2.0.0 +* GitHub: https://github.com/AlJacq/LorenzRegression * Source code: https://github.com/cran/LorenzRegression -* Date/Publication: 2023-02-28 17:32:34 UTC -* Number of recursive dependencies: 63 +* Date/Publication: 2024-09-09 11:20:33 UTC +* Number of recursive dependencies: 83 Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info @@ -3634,10 +4332,10 @@ ERROR: lazy loading failed for package ‘LorenzRegression’
-* Version: 1.3.1 +* Version: 1.3.3 * GitHub: NA * Source code: https://github.com/cran/lsirm12pl -* Date/Publication: 2023-06-22 14:12:35 UTC +* Date/Publication: 2024-08-28 23:00:02 UTC * Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info @@ -3663,10 +4361,10 @@ Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o ... ** R ** data @@ -3690,21 +4388,132 @@ ERROR: lazy loading failed for package ‘lsirm12pl’ ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o +... +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ + + +``` +# MantaID + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/MantaID +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "MantaID")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# MARVEL + +
+ +* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/MARVEL +* Date/Publication: 2022-10-31 10:22:50 UTC +* Number of recursive dependencies: 231 + +Run `revdepcheck::cloud_details(, "MARVEL")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/MARVEL/new/MARVEL.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MARVEL/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MARVEL.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/MARVEL/old/MARVEL.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MARVEL/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MARVEL.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` @@ -3768,98 +4577,102 @@ ERROR: lazy loading failed for package ‘mbsts’ ``` -# MendelianRandomization +# MitoHEAR
-* Version: 0.10.0 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/MendelianRandomization -* Date/Publication: 2024-04-12 10:10:02 UTC -* Number of recursive dependencies: 88 +* Source code: https://github.com/cran/MitoHEAR +* Date/Publication: 2022-03-01 21:20:02 UTC +* Number of recursive dependencies: 183 -Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info +Run `revdepcheck::cloud_details(, "MitoHEAR")` for more info
-## In both - -* checking whether package ‘MendelianRandomization’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ +* using log directory ‘/tmp/workdir/MitoHEAR/new/MitoHEAR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'karyoploteR', 'regioneR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ +* using log directory ‘/tmp/workdir/MitoHEAR/old/MitoHEAR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'karyoploteR', 'regioneR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# MetabolicSurv +# miWQS
-* Version: 1.1.2 -* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv -* Source code: https://github.com/cran/MetabolicSurv -* Date/Publication: 2021-06-11 08:30:02 UTC -* Number of recursive dependencies: 131 +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info +Run `revdepcheck::cloud_details(, "miWQS")` for more info
## In both -* checking whether package ‘MetabolicSurv’ can be installed ... ERROR +* checking whether package ‘miWQS’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. ``` ## Installation @@ -3867,8 +4680,8 @@ Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info ### Devel ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -3879,16 +4692,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ ``` ### CRAN ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -3899,31 +4712,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ ``` -# miWQS +# mlmts
-* Version: 0.4.4 -* GitHub: https://github.com/phargarten2/miWQS -* Source code: https://github.com/cran/miWQS -* Date/Publication: 2021-04-02 21:50:02 UTC -* Number of recursive dependencies: 151 +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/mlmts +* Date/Publication: 2024-08-18 08:40:06 UTC +* Number of recursive dependencies: 242 -Run `revdepcheck::cloud_details(, "miWQS")` for more info +Run `revdepcheck::cloud_details(, "mlmts")` for more info
## In both -* checking whether package ‘miWQS’ can be installed ... ERROR +* checking whether package ‘mlmts’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details. ``` ## Installation @@ -3931,121 +4744,215 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info ### Devel ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’ ``` ### CRAN ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’ ``` -# MRZero +# mlr
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/MRZero -* Date/Publication: 2024-04-14 09:30:03 UTC -* Number of recursive dependencies: 82 +* Version: 2.19.2 +* GitHub: https://github.com/mlr-org/mlr +* Source code: https://github.com/cran/mlr +* Date/Publication: 2024-06-12 10:50:02 UTC +* Number of recursive dependencies: 362 -Run `revdepcheck::cloud_details(, "MRZero")` for more info +Run `revdepcheck::cloud_details(, "mlr")` for more info
-## In both +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/mlr/new/mlr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mlr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘mlr.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + -* checking whether package ‘MRZero’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. - ``` -## Installation + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/mlr/old/mlr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mlr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘mlr.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# MOCHA + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/MOCHA +* Date/Publication: 2024-01-25 12:20:12 UTC +* Number of recursive dependencies: 249 + +Run `revdepcheck::cloud_details(, "MOCHA")` for more info + +
+ +## Error before installation ### Devel ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ +* using log directory ‘/tmp/workdir/MOCHA/new/MOCHA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MOCHA/DESCRIPTION’ ... OK +... + +Packages suggested but not available for checking: + 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', + 'chromVAR', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ +* using log directory ‘/tmp/workdir/MOCHA/old/MOCHA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MOCHA/DESCRIPTION’ ... OK +... + +Packages suggested but not available for checking: + 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', + 'chromVAR', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# Multiaovbay +# MRZero
-* Version: 0.1.0 +* Version: 0.2.0 * GitHub: NA -* Source code: https://github.com/cran/Multiaovbay -* Date/Publication: 2023-03-17 17:20:02 UTC -* Number of recursive dependencies: 153 +* Source code: https://github.com/cran/MRZero +* Date/Publication: 2024-04-14 09:30:03 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info +Run `revdepcheck::cloud_details(, "MRZero")` for more info
## In both -* checking whether package ‘Multiaovbay’ can be installed ... ERROR +* checking whether package ‘MRZero’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. ``` ## Installation @@ -4053,34 +4960,34 @@ Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info ### Devel ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ ``` ### CRAN ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ ``` @@ -4192,14 +5099,14 @@ using C++17 g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ /opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ @@ -4219,14 +5126,14 @@ using C++17 g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ /opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ @@ -4378,7 +5285,7 @@ ERROR: lazy loading failed for package ‘netcmc’ * GitHub: https://github.com/jongheepark/NetworkChange * Source code: https://github.com/cran/NetworkChange * Date/Publication: 2022-03-04 07:30:02 UTC -* Number of recursive dependencies: 132 +* Number of recursive dependencies: 133 Run `revdepcheck::cloud_details(, "NetworkChange")` for more info @@ -4561,6 +5468,82 @@ ERROR: lazy loading failed for package ‘NMADiagT’ * removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ +``` +# ohun + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/ropensci/ohun +* Source code: https://github.com/cran/ohun +* Date/Publication: 2024-08-19 18:40:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "ohun")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ohun/new/ohun.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ohun/DESCRIPTION’ ... OK +... +* this is package ‘ohun’ version ‘1.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘warbleR’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ohun/old/ohun.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ohun/DESCRIPTION’ ... OK +... +* this is package ‘ohun’ version ‘1.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘warbleR’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # optweight @@ -4572,16 +5555,212 @@ ERROR: lazy loading failed for package ‘NMADiagT’ * Date/Publication: 2019-09-16 15:40:02 UTC * Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "optweight")` for more info +Run `revdepcheck::cloud_details(, "optweight")` for more info + +
+ +## In both + +* checking whether package ‘optweight’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ + + +``` +### CRAN + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ + + +``` +# OVtool + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "OVtool")` for more info + +
+ +## In both + +* checking whether package ‘OVtool’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ + + +``` +### CRAN + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ + + +``` +# pagoda2 + +
+ +* Version: 1.0.12 +* GitHub: https://github.com/kharchenkolab/pagoda2 +* Source code: https://github.com/cran/pagoda2 +* Date/Publication: 2024-02-27 00:50:02 UTC +* Number of recursive dependencies: 162 + +Run `revdepcheck::cloud_details(, "pagoda2")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/pagoda2/new/pagoda2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pagoda2/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rjson’ + +Package suggested but not available for checking: ‘scde’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/pagoda2/old/pagoda2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pagoda2/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rjson’ + +Package suggested but not available for checking: ‘scde’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# PAMpal + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/PAMpal +* Date/Publication: 2024-07-11 22:50:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "PAMpal")` for more info
## In both -* checking whether package ‘optweight’ can be installed ... ERROR +* checking whether package ‘PAMpal’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/00install.out’ for details. ``` ## Installation @@ -4589,57 +5768,63 @@ Run `revdepcheck::cloud_details(, "optweight")` for more info ### Devel ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMpal’ ... +** package ‘PAMpal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘PAMpal’ +* removing ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/PAMpal’ ``` ### CRAN ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMpal’ ... +** package ‘PAMpal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘PAMpal’ +* removing ‘/tmp/workdir/PAMpal/old/PAMpal.Rcheck/PAMpal’ ``` -# OVtool +# PAMscapes
-* Version: 1.0.3 +* Version: 0.6.0 * GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 157 +* Source code: https://github.com/cran/PAMscapes +* Date/Publication: 2024-07-09 22:50:02 UTC +* Number of recursive dependencies: 110 -Run `revdepcheck::cloud_details(, "OVtool")` for more info +Run `revdepcheck::cloud_details(, "PAMscapes")` for more info
## In both -* checking whether package ‘OVtool’ can be installed ... ERROR +* checking whether package ‘PAMscapes’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/00install.out’ for details. ``` ## Installation @@ -4647,38 +5832,36 @@ Run `revdepcheck::cloud_details(, "OVtool")` for more info ### Devel ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMscapes’ ... +** package ‘PAMscapes’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘PAMscapes’ +* removing ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/PAMscapes’ ``` ### CRAN ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMscapes’ ... +** package ‘PAMscapes’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘PAMscapes’ +* removing ‘/tmp/workdir/PAMscapes/old/PAMscapes.Rcheck/PAMscapes’ ``` @@ -4745,6 +5928,263 @@ ERROR: lazy loading failed for package ‘paths’ * removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ +``` +# PathwaySpace + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/PathwaySpace +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# pcvr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/danforthcenter/pcvr +* Source code: https://github.com/cran/pcvr +* Date/Publication: 2024-09-05 17:30:02 UTC +* Number of recursive dependencies: 189 + +Run `revdepcheck::cloud_details(, "pcvr")` for more info + +
+ +## In both + +* checking whether package ‘pcvr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’ + + +``` +### CRAN + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’ + + +``` +# PlasmaMutationDetector + +
+ +* Version: 1.7.2 +* GitHub: NA +* Source code: https://github.com/cran/PlasmaMutationDetector +* Date/Publication: 2018-06-11 07:43:09 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PlasmaMutationDetector")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector/new/PlasmaMutationDetector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector/old/PlasmaMutationDetector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# PlasmaMutationDetector2 + +
+ +* Version: 1.1.11 +* GitHub: NA +* Source code: https://github.com/cran/PlasmaMutationDetector2 +* Date/Publication: 2022-05-03 10:00:08 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PlasmaMutationDetector2")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/new/PlasmaMutationDetector2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/old/PlasmaMutationDetector2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # PLMIX @@ -4754,7 +6194,7 @@ ERROR: lazy loading failed for package ‘paths’ * GitHub: NA * Source code: https://github.com/cran/PLMIX * Date/Publication: 2019-09-04 11:50:02 UTC -* Number of recursive dependencies: 138 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "PLMIX")` for more info @@ -4823,6 +6263,82 @@ ERROR: lazy loading failed for package ‘PLMIX’ * removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ +``` +# polyRAD + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/lvclark/polyRAD +* Source code: https://github.com/cran/polyRAD +* Date/Publication: 2022-11-06 21:50:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "polyRAD")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/polyRAD/new/polyRAD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘polyRAD/DESCRIPTION’ ... OK +... + + When sourcing ‘polyRADtutorial.R’: +Error: Probabilities must be finite and non-negative! +Execution halted + + ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK + ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/polyRAD/old/polyRAD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘polyRAD/DESCRIPTION’ ... OK +... + + When sourcing ‘polyRADtutorial.R’: +Error: Probabilities must be finite and non-negative! +Execution halted + + ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK + ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 3 NOTEs + + + + + ``` # popstudy @@ -4923,9 +6439,9 @@ Run `revdepcheck::cloud_details(, "pould")` for more info *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘pould’ * removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ @@ -4943,14 +6459,78 @@ ERROR: lazy loading failed for package ‘pould’ *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘pould’ * removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ +``` +# PoweREST + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/PoweREST +* Date/Publication: 2024-09-09 09:30:02 UTC +* Number of recursive dependencies: 171 + +Run `revdepcheck::cloud_details(, "PoweREST")` for more info + +
+ +## In both + +* checking whether package ‘PoweREST’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/PoweREST/new/PoweREST.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘PoweREST’ ... +** package ‘PoweREST’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PoweREST’ +* removing ‘/tmp/workdir/PoweREST/new/PoweREST.Rcheck/PoweREST’ + + +``` +### CRAN + +``` +* installing *source* package ‘PoweREST’ ... +** package ‘PoweREST’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PoweREST’ +* removing ‘/tmp/workdir/PoweREST/old/PoweREST.Rcheck/PoweREST’ + + ``` # powerly @@ -5170,7 +6750,7 @@ Status: 1 ERROR * GitHub: https://github.com/ocbe-uio/psbcSpeedUp * Source code: https://github.com/cran/psbcSpeedUp * Date/Publication: 2024-07-01 09:00:02 UTC -* Number of recursive dependencies: 129 +* Number of recursive dependencies: 130 Run `revdepcheck::cloud_details(, "psbcSpeedUp")` for more info @@ -5205,8 +6785,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘psbcSpeedUp’ * removing ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/psbcSpeedUp’ @@ -5232,8 +6812,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘psbcSpeedUp’ * removing ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck/psbcSpeedUp’ @@ -5311,70 +6891,6 @@ ERROR: lazy loading failed for package ‘pscore’ * removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ -``` -# psfmi - -
- -* Version: 1.4.0 -* GitHub: https://github.com/mwheymans/psfmi -* Source code: https://github.com/cran/psfmi -* Date/Publication: 2023-06-17 22:40:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "psfmi")` for more info - -
- -## In both - -* checking whether package ‘psfmi’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ - - -``` -### CRAN - -``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ - - ``` # qPCRtools @@ -5436,26 +6952,26 @@ ERROR: lazy loading failed for package ‘qPCRtools’ ``` -# qreport +# qris
-* Version: 1.0-1 -* GitHub: NA -* Source code: https://github.com/cran/qreport -* Date/Publication: 2024-05-26 21:50:03 UTC -* Number of recursive dependencies: 77 +* Version: 1.1.1 +* GitHub: https://github.com/Kyuhyun07/qris +* Source code: https://github.com/cran/qris +* Date/Publication: 2024-03-05 14:40:03 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "qreport")` for more info +Run `revdepcheck::cloud_details(, "qris")` for more info
## In both -* checking whether package ‘qreport’ can be installed ... ERROR +* checking whether package ‘qris’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. ``` ## Installation @@ -5463,57 +6979,77 @@ Run `revdepcheck::cloud_details(, "qreport")` for more info ### Devel ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ ``` ### CRAN ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ ``` -# qris +# qte
-* Version: 1.1.1 -* GitHub: https://github.com/Kyuhyun07/qris -* Source code: https://github.com/cran/qris -* Date/Publication: 2024-03-05 14:40:03 UTC -* Number of recursive dependencies: 55 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/qte +* Date/Publication: 2022-09-01 14:30:02 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "qris")` for more info +Run `revdepcheck::cloud_details(, "qte")` for more info
## In both -* checking whether package ‘qris’ can be installed ... ERROR +* checking whether package ‘qte’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. ``` ## Installation @@ -5521,77 +7057,63 @@ Run `revdepcheck::cloud_details(, "qris")` for more info ### Devel ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ ``` ### CRAN ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked +** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ ``` -# qte +# quantilogram
-* Version: 1.3.1 +* Version: 3.1.1 * GitHub: NA -* Source code: https://github.com/cran/qte -* Date/Publication: 2022-09-01 14:30:02 UTC -* Number of recursive dependencies: 87 +* Source code: https://github.com/cran/quantilogram +* Date/Publication: 2024-08-27 12:40:02 UTC +* Number of recursive dependencies: 58 -Run `revdepcheck::cloud_details(, "qte")` for more info +Run `revdepcheck::cloud_details(, "quantilogram")` for more info
## In both -* checking whether package ‘qte’ can be installed ... ERROR +* checking whether package ‘quantilogram’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/quantilogram/new/quantilogram.Rcheck/00install.out’ for details. ``` ## Installation @@ -5599,40 +7121,38 @@ Run `revdepcheck::cloud_details(, "qte")` for more info ### Devel ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quantilogram’ ... +** package ‘quantilogram’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘quantilogram’ +* removing ‘/tmp/workdir/quantilogram/new/quantilogram.Rcheck/quantilogram’ ``` ### CRAN ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quantilogram’ ... +** package ‘quantilogram’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘quantilogram’ +* removing ‘/tmp/workdir/quantilogram/old/quantilogram.Rcheck/quantilogram’ ``` @@ -5700,26 +7220,26 @@ ERROR: lazy loading failed for package ‘quid’ ``` -# RATest +# RcmdrPlugin.RiskDemo
-* Version: 0.1.10 -* GitHub: https://github.com/ignaciomsarmiento/RATest -* Source code: https://github.com/cran/RATest -* Date/Publication: 2022-09-29 04:30:02 UTC -* Number of recursive dependencies: 54 +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 200 -Run `revdepcheck::cloud_details(, "RATest")` for more info +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info
## In both -* checking whether package ‘RATest’ can be installed ... ERROR +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. ``` ## Installation @@ -5727,63 +7247,277 @@ Run `revdepcheck::cloud_details(, "RATest")` for more info ### Devel ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` ### CRAN ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` -# RcmdrPlugin.RiskDemo +# rddtools
-* Version: 3.2 +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "rddtools")` for more info + +
+ +## In both + +* checking whether package ‘rddtools’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ + + +``` +### CRAN + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ + + +``` +# RGraphSpace + +
+ +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo -* Date/Publication: 2024-02-06 09:20:02 UTC -* Number of recursive dependencies: 200 +* Source code: https://github.com/cran/RGraphSpace +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info +Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# rms + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/rms +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "rms")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# RNAseqQC + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/frederikziebell/RNAseqQC +* Source code: https://github.com/cran/RNAseqQC +* Date/Publication: 2024-07-15 14:40:02 UTC +* Number of recursive dependencies: 162 + +Run `revdepcheck::cloud_details(, "RNAseqQC")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/RNAseqQC/new/RNAseqQC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'ComplexHeatmap' + +Package suggested but not available for checking: ‘recount3’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/RNAseqQC/old/RNAseqQC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'ComplexHeatmap' + +Package suggested but not available for checking: ‘recount3’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# robmed + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/aalfons/robmed +* Source code: https://github.com/cran/robmed +* Date/Publication: 2023-06-16 23:00:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "robmed")` for more info
## In both -* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR +* checking whether package ‘robmed’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. ``` ## Installation @@ -5791,71 +7525,63 @@ Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info ### Devel ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ ``` ### CRAN ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ ``` -# rddtools +# robmedExtra
-* Version: 1.6.0 -* GitHub: https://github.com/bquast/rddtools -* Source code: https://github.com/cran/rddtools -* Date/Publication: 2022-01-10 12:42:49 UTC -* Number of recursive dependencies: 106 +* Version: 0.1.0 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2023-06-02 14:40:02 UTC +* Number of recursive dependencies: 90 -Run `revdepcheck::cloud_details(, "rddtools")` for more info +Run `revdepcheck::cloud_details(, "robmedExtra")` for more info
## In both -* checking whether package ‘rddtools’ can be installed ... ERROR +* checking whether package ‘robmedExtra’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. ``` ## Installation @@ -5863,59 +7589,57 @@ Run `revdepcheck::cloud_details(, "rddtools")` for more info ### Devel ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ ``` ### CRAN ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ ``` -# riskRegression +# RPPanalyzer
-* Version: 2023.12.21 -* GitHub: https://github.com/tagteam/riskRegression -* Source code: https://github.com/cran/riskRegression -* Date/Publication: 2023-12-19 17:00:02 UTC -* Number of recursive dependencies: 186 +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/RPPanalyzer +* Date/Publication: 2024-01-25 11:00:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "riskRegression")` for more info +Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info
## In both -* checking whether package ‘riskRegression’ can be installed ... ERROR +* checking whether package ‘RPPanalyzer’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. ``` ## Installation @@ -5923,17 +7647,9 @@ Run `revdepcheck::cloud_details(, "riskRegression")` for more info ### Devel ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R ** data ** inst @@ -5942,25 +7658,17 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ ``` ### CRAN ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R ** data ** inst @@ -5969,36 +7677,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ ``` -# rms +# RQdeltaCT
-* Version: 6.8-1 -* GitHub: https://github.com/harrelfe/rms -* Source code: https://github.com/cran/rms -* Date/Publication: 2024-05-27 12:00:02 UTC -* Number of recursive dependencies: 145 +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/RQdeltaCT +* Date/Publication: 2024-04-17 15:50:02 UTC +* Number of recursive dependencies: 166 -Run `revdepcheck::cloud_details(, "rms")` for more info +Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info
## In both -* checking whether package ‘rms’ can be installed ... ERROR +* checking whether package ‘RQdeltaCT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rmsb’ + See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. ``` ## Installation @@ -6006,129 +7709,98 @@ Run `revdepcheck::cloud_details(, "rms")` for more info ### Devel ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ ``` ### CRAN ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ ``` -# rmsb +# RRPP
-* Version: 1.1-1 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/rmsb -* Date/Publication: 2024-07-08 11:10:03 UTC -* Number of recursive dependencies: 135 +* Source code: https://github.com/cran/RRPP +* Number of recursive dependencies: 68 -Run `revdepcheck::cloud_details(, "rmsb")` for more info +Run `revdepcheck::cloud_details(, "RRPP")` for more info
-## In both - -* checking whether package ‘rmsb’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ + + + + ``` ### CRAN ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ + + + + ``` -# robmed +# rstanarm
-* Version: 1.0.2 -* GitHub: https://github.com/aalfons/robmed -* Source code: https://github.com/cran/robmed -* Date/Publication: 2023-06-16 23:00:02 UTC -* Number of recursive dependencies: 60 +* Version: 2.32.1 +* GitHub: https://github.com/stan-dev/rstanarm +* Source code: https://github.com/cran/rstanarm +* Date/Publication: 2024-01-18 23:00:03 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "robmed")` for more info +Run `revdepcheck::cloud_details(, "rstanarm")` for more info
## In both -* checking whether package ‘robmed’ can be installed ... ERROR +* checking whether package ‘rstanarm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. ``` ## Installation @@ -6136,121 +7808,153 @@ Run `revdepcheck::cloud_details(, "robmed")` for more info ### Devel ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ ``` ### CRAN ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ ``` -# robmedExtra +# RTIGER
-* Version: 0.1.0 -* GitHub: https://github.com/aalfons/robmedExtra -* Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2023-06-02 14:40:02 UTC -* Number of recursive dependencies: 96 +* Version: 2.1.0 +* GitHub: NA +* Source code: https://github.com/cran/RTIGER +* Date/Publication: 2023-03-29 09:20:02 UTC +* Number of recursive dependencies: 160 -Run `revdepcheck::cloud_details(, "robmedExtra")` for more info +Run `revdepcheck::cloud_details(, "RTIGER")` for more info
-## In both - -* checking whether package ‘robmedExtra’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ +* using log directory ‘/tmp/workdir/RTIGER/new/RTIGER.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RTIGER/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ +* using log directory ‘/tmp/workdir/RTIGER/old/RTIGER.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RTIGER/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` -# RPPanalyzer +# rTwig
-* Version: 1.4.9 -* GitHub: NA -* Source code: https://github.com/cran/RPPanalyzer -* Date/Publication: 2024-01-25 11:00:02 UTC -* Number of recursive dependencies: 82 +* Version: 1.1.0 +* GitHub: https://github.com/aidanmorales/rTwig +* Source code: https://github.com/cran/rTwig +* Date/Publication: 2024-08-21 00:50:02 UTC +* Number of recursive dependencies: 147 -Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info +Run `revdepcheck::cloud_details(, "rTwig")` for more info
## In both -* checking whether package ‘RPPanalyzer’ can be installed ... ERROR +* checking whether package ‘rTwig’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/00install.out’ for details. ``` ## Installation @@ -6258,102 +7962,130 @@ Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info ### Devel ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rTwig’ ... +** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘rTwig’ +* removing ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/rTwig’ ``` ### CRAN ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rTwig’ ... +** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘rTwig’ +* removing ‘/tmp/workdir/rTwig/old/rTwig.Rcheck/rTwig’ ``` -# RQdeltaCT +# RVA
-* Version: 1.3.0 -* GitHub: NA -* Source code: https://github.com/cran/RQdeltaCT -* Date/Publication: 2024-04-17 15:50:02 UTC -* Number of recursive dependencies: 165 +* Version: 0.0.5 +* GitHub: https://github.com/THERMOSTATS/RVA +* Source code: https://github.com/cran/RVA +* Date/Publication: 2021-11-01 21:40:02 UTC +* Number of recursive dependencies: 207 -Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info +Run `revdepcheck::cloud_details(, "RVA")` for more info
-## In both - -* checking whether package ‘RQdeltaCT’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘RQdeltaCT’ ... -** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RQdeltaCT’ -* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ +* using log directory ‘/tmp/workdir/RVA/new/RVA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RVA/DESCRIPTION’ ... OK +... +* this is package ‘RVA’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘RQdeltaCT’ ... -** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RQdeltaCT’ -* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ +* using log directory ‘/tmp/workdir/RVA/old/RVA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RVA/DESCRIPTION’ ... OK +... +* this is package ‘RVA’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6371,54 +8103,65 @@ Run `revdepcheck::cloud_details(, "scCustomize")` for more info
-## In both +## Error before installation -* checking whether package ‘scCustomize’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. - ``` +### Devel -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘Nebulosa’ - ``` +``` +* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘scCustomize’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE -## Installation -### Devel -``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ ``` ### CRAN ``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ +* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘scCustomize’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -6617,16 +8360,92 @@ g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler installing to /tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SCIntRuler’ -* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ + + +``` +# scITD + +
+ +* Version: 1.0.4 +* GitHub: NA +* Source code: https://github.com/cran/scITD +* Date/Publication: 2023-09-08 16:00:02 UTC +* Number of recursive dependencies: 233 + +Run `revdepcheck::cloud_details(, "scITD")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scITD/new/scITD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scITD/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'simplifyEnrichment', 'conos', 'pagoda2' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scITD/old/scITD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scITD/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'simplifyEnrichment', 'conos', 'pagoda2' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6638,7 +8457,7 @@ ERROR: lazy loading failed for package ‘SCIntRuler’ * GitHub: NA * Source code: https://github.com/cran/scMappR * Date/Publication: 2023-06-30 08:40:08 UTC -* Number of recursive dependencies: 234 +* Number of recursive dependencies: 241 Run `revdepcheck::cloud_details(, "scMappR")` for more info @@ -6913,6 +8732,82 @@ ERROR: lazy loading failed for package ‘sectorgap’ * removing ‘/tmp/workdir/sectorgap/old/sectorgap.Rcheck/sectorgap’ +``` +# SeedMatchR + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/SeedMatchR +* Date/Publication: 2023-10-24 20:30:02 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "SeedMatchR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SeedMatchR/new/SeedMatchR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK +... +* this is package ‘SeedMatchR’ version ‘1.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'msa', 'GenomicFeatures' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SeedMatchR/old/SeedMatchR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK +... +* this is package ‘SeedMatchR’ version ‘1.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'msa', 'GenomicFeatures' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # SEERaBomb @@ -7113,6 +9008,82 @@ ERROR: lazy loading failed for package ‘SensMap’ * removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ +``` +# sephora + +
+ +* Version: 0.1.31 +* GitHub: NA +* Source code: https://github.com/cran/sephora +* Date/Publication: 2024-01-17 18:40:02 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "sephora")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/sephora/new/sephora.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sephora/DESCRIPTION’ ... OK +... +* this is package ‘sephora’ version ‘0.1.31’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘spiralize’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/sephora/old/sephora.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sephora/DESCRIPTION’ ... OK +... +* this is package ‘sephora’ version ‘0.1.31’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘spiralize’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # Seurat @@ -7122,73 +9093,71 @@ ERROR: lazy loading failed for package ‘SensMap’ * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat * Date/Publication: 2024-05-10 17:23:17 UTC -* Number of recursive dependencies: 266 +* Number of recursive dependencies: 267 Run `revdepcheck::cloud_details(, "Seurat")` for more info
-## In both - -* checking whether package ‘Seurat’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘Seurat’ ... -** package ‘Seurat’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘Seurat’ -* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘Seurat’ ... -** package ‘Seurat’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘Seurat’ -* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7321,82 +9290,156 @@ ERROR: lazy loading failed for package ‘sievePH’ * removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ +``` +# sigminer + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/ShixiangWang/sigminer +* Source code: https://github.com/cran/sigminer +* Date/Publication: 2024-05-11 08:50:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "sigminer")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/sigminer/new/sigminer.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sigminer/DESCRIPTION’ ... OK +... + 18. └─rlang::abort(...) +Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘cnsignature.Rmd’ using ‘UTF-8’... OK + ‘sigminer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/sigminer/old/sigminer.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sigminer/DESCRIPTION’ ... OK +... +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘cnsignature.Rmd’ using ‘UTF-8’... OK + ‘sigminer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + ``` # Signac
-* Version: 1.13.0 +* Version: 1.14.0 * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac -* Date/Publication: 2024-04-04 02:42:57 UTC -* Number of recursive dependencies: 250 +* Date/Publication: 2024-08-21 07:40:02 UTC +* Number of recursive dependencies: 247 Run `revdepcheck::cloud_details(, "Signac")` for more info
-## In both - -* checking whether package ‘Signac’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘Signac’ ... -** package ‘Signac’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o +* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Signac’ -* removing ‘/tmp/workdir/Signac/new/Signac.Rcheck/Signac’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Signac’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘Signac’ ... -** package ‘Signac’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o +* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Signac’ -* removing ‘/tmp/workdir/Signac/old/Signac.Rcheck/Signac’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Signac’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Signac/old/Signac.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7473,68 +9516,6 @@ ERROR: lazy loading failed for package ‘SimplyAgree’ * removing ‘/tmp/workdir/SimplyAgree/old/SimplyAgree.Rcheck/SimplyAgree’ -``` -# sMSROC - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/sMSROC -* Date/Publication: 2023-12-07 15:50:02 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "sMSROC")` for more info - -
- -## In both - -* checking whether package ‘sMSROC’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘sMSROC’ ... -** package ‘sMSROC’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sMSROC’ -* removing ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/sMSROC’ - - -``` -### CRAN - -``` -* installing *source* package ‘sMSROC’ ... -** package ‘sMSROC’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sMSROC’ -* removing ‘/tmp/workdir/sMSROC/old/sMSROC.Rcheck/sMSROC’ - - ``` # SNPassoc @@ -7544,57 +9525,71 @@ ERROR: lazy loading failed for package ‘sMSROC’ * GitHub: https://github.com/isglobal-brge/SNPassoc * Source code: https://github.com/cran/SNPassoc * Date/Publication: 2022-12-14 20:20:02 UTC -* Number of recursive dependencies: 166 +* Number of recursive dependencies: 168 Run `revdepcheck::cloud_details(, "SNPassoc")` for more info
-## In both - -* checking whether package ‘SNPassoc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘SNPassoc’ ... -** package ‘SNPassoc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SNPassoc’ -* removing ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/SNPassoc’ +* using log directory ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SNPassoc/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘SNPassoc’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘SNPassoc’ ... -** package ‘SNPassoc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SNPassoc’ -* removing ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/SNPassoc’ +* using log directory ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SNPassoc/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘SNPassoc’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7602,11 +9597,11 @@ ERROR: lazy loading failed for package ‘SNPassoc’
-* Version: 1.0.0 +* Version: 1.2.0 * GitHub: NA * Source code: https://github.com/cran/snplinkage -* Date/Publication: 2023-05-04 08:10:02 UTC -* Number of recursive dependencies: 145 +* Date/Publication: 2024-09-09 19:10:02 UTC +* Number of recursive dependencies: 153 Run `revdepcheck::cloud_details(, "snplinkage")` for more info @@ -7628,7 +9623,7 @@ Run `revdepcheck::cloud_details(, "snplinkage")` for more info * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK ... -* this is package ‘snplinkage’ version ‘1.0.0’ +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -7658,7 +9653,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK ... -* this is package ‘snplinkage’ version ‘1.0.0’ +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -7746,7 +9741,7 @@ ERROR: lazy loading failed for package ‘SoupX’ * GitHub: NA * Source code: https://github.com/cran/sparsereg * Date/Publication: 2016-03-10 23:32:18 -* Number of recursive dependencies: 49 +* Number of recursive dependencies: 50 Run `revdepcheck::cloud_details(, "sparsereg")` for more info @@ -7811,6 +9806,82 @@ ERROR: lazy loading failed for package ‘sparsereg’ * removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ +``` +# SpatialDDLS + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/diegommcc/SpatialDDLS +* Source code: https://github.com/cran/SpatialDDLS +* Date/Publication: 2024-04-26 16:10:02 UTC +* Number of recursive dependencies: 207 + +Run `revdepcheck::cloud_details(, "SpatialDDLS")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SpatialDDLS/new/SpatialDDLS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SpatialExperiment’ + +Package suggested but not available for checking: ‘ComplexHeatmap’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SpatialDDLS/old/SpatialDDLS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SpatialExperiment’ + +Package suggested but not available for checking: ‘ComplexHeatmap’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # spikeSlabGAM @@ -8008,83 +10079,13 @@ Status: 1 ERROR * checking package dependencies ... ERROR Package required but not available: ‘asbio’ -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# survHE - -
- -* Version: 2.0.1 -* GitHub: https://github.com/giabaio/survHE -* Source code: https://github.com/cran/survHE -* Date/Publication: 2023-03-19 22:10:02 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "survHE")` for more info - -
- -## In both - -* checking whether package ‘survHE’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/survHE/new/survHE.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - 'survHEinla', 'survHEhmc' - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘survHE’ ... -** package ‘survHE’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘survHE’ -* removing ‘/tmp/workdir/survHE/new/survHE.Rcheck/survHE’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -``` -### CRAN -``` -* installing *source* package ‘survHE’ ... -** package ‘survHE’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘survHE’ -* removing ‘/tmp/workdir/survHE/old/survHE.Rcheck/survHE’ ``` @@ -8223,6 +10224,76 @@ ERROR: lazy loading failed for package ‘tempted’ * removing ‘/tmp/workdir/tempted/old/tempted.Rcheck/tempted’ +``` +# TestAnaAPP + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/jiangyouxiang/TestAnaAPP +* Source code: https://github.com/cran/TestAnaAPP +* Date/Publication: 2024-09-10 07:30:02 UTC +* Number of recursive dependencies: 250 + +Run `revdepcheck::cloud_details(, "TestAnaAPP")` for more info + +
+ +## In both + +* checking whether package ‘TestAnaAPP’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/TestAnaAPP’ + + +``` +### CRAN + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck/TestAnaAPP’ + + ``` # tidydr @@ -8232,7 +10303,7 @@ ERROR: lazy loading failed for package ‘tempted’ * GitHub: https://github.com/YuLab-SMU/tidydr * Source code: https://github.com/cran/tidydr * Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 74 +* Number of recursive dependencies: 79 Run `revdepcheck::cloud_details(, "tidydr")` for more info @@ -8360,7 +10431,7 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ * GitHub: https://github.com/stemangiola/tidyseurat * Source code: https://github.com/cran/tidyseurat * Date/Publication: 2024-01-10 04:50:02 UTC -* Number of recursive dependencies: 207 +* Number of recursive dependencies: 208 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info @@ -8612,10 +10683,10 @@ ERROR: lazy loading failed for package ‘TSrepr’
-* Version: 2.6 +* Version: 2.6.1 * GitHub: NA * Source code: https://github.com/cran/twang -* Date/Publication: 2023-12-06 00:30:02 UTC +* Date/Publication: 2024-07-22 16:10:01 UTC * Number of recursive dependencies: 53 Run `revdepcheck::cloud_details(, "twang")` for more info @@ -8681,6 +10752,158 @@ ERROR: lazy loading failed for package ‘twang’ * removing ‘/tmp/workdir/twang/old/twang.Rcheck/twang’ +``` +# updog + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/dcgerard/updog +* Source code: https://github.com/cran/updog +* Date/Publication: 2023-11-29 15:50:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "updog")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/updog/new/updog.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘updog/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘multidog.Rmd’ using ‘UTF-8’... OK + ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK + ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK + ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/updog/old/updog.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘updog/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘multidog.Rmd’ using ‘UTF-8’... OK + ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK + ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK + ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# valr + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/rnabioco/valr +* Source code: https://github.com/cran/valr +* Date/Publication: 2024-08-30 22:10:03 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "valr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/valr/new/valr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘valr/DESCRIPTION’ ... OK +... +* this is package ‘valr’ version ‘0.8.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/valr/old/valr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘valr/DESCRIPTION’ ... OK +... +* this is package ‘valr’ version ‘0.8.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # vdg @@ -8817,6 +11040,41 @@ ERROR: lazy loading failed for package ‘visa’ * removing ‘/tmp/workdir/visa/old/visa.Rcheck/visa’ +``` +# VisualizeSimon2Stage + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/VisualizeSimon2Stage +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "VisualizeSimon2Stage")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # WRTDStidal @@ -8881,4 +11139,39 @@ ERROR: lazy loading failed for package ‘WRTDStidal’ * removing ‘/tmp/workdir/WRTDStidal/old/WRTDStidal.Rcheck/WRTDStidal’ +``` +# xxdi + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/xxdi +* Number of recursive dependencies: 37 + +Run `revdepcheck::cloud_details(, "xxdi")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` diff --git a/revdep/problems.md b/revdep/problems.md index 8e2e437056..73ee83725d 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,1317 +1,28608 @@ -# activAnalyzer (patchwork) +# activAnalyzer + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/pydemull/activAnalyzer +* Source code: https://github.com/cran/activAnalyzer +* Date/Publication: 2024-05-05 22:40:03 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "activAnalyzer")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘activAnalyzer.Rmd’ + ... + > p3 <- accum_metrics_sed$p_UBD + + > p4 <- accum_metrics_sed$p_gini + + > (p1 | p2)/(p3 | p4) + plot_layout(guides = "collect") & + + theme(legend.position = "bottom") + + When sourcing ‘activAnalyzer.R’: + Error: object is not a unit + Execution halted + + ‘activAnalyzer.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘activAnalyzer.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.0Mb + extdata 2.0Mb + ``` + +# actxps + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/mattheaphy/actxps +* Source code: https://github.com/cran/actxps +* Date/Publication: 2024-06-25 12:40:02 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "actxps")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘actxps.Rmd’ + ... + # ℹ 2 more variables: ae_expected_1 , ae_expected_2 + + > autoplot(exp_res) + Warning: thematic was unable to resolve `bg='auto'`. Try providing an actual color (or `NA`) to the `bg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `fg='auto'`. Try providing an actual color (or `NA`) to the `fg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `accent='auto'`. Try providing an actual color (or `NA`) to the `accent` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + + ... + + When sourcing ‘transactions.R’: + Error: Internal error: adjust_color() expects an input of length 1 + Execution halted + + ‘actxps.Rmd’ using ‘UTF-8’... failed + ‘exp_summary.Rmd’ using ‘UTF-8’... OK + ‘exposures.Rmd’ using ‘UTF-8’... OK + ‘misc.Rmd’ using ‘UTF-8’... failed + ‘transactions.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘actxps.Rmd’ using rmarkdown + Warning: thematic was unable to resolve `bg='auto'`. Try providing an actual color (or `NA`) to the `bg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `fg='auto'`. Try providing an actual color (or `NA`) to the `fg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `accent='auto'`. Try providing an actual color (or `NA`) to the `accent` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + + Quitting from lines 129-130 [plot] (actxps.Rmd) + Error: processing vignette 'actxps.Rmd' failed with diagnostics: + Internal error: adjust_color() expects an input of length 1 + --- failed re-building ‘actxps.Rmd’ + ... + Quitting from lines 205-211 [trx-plot] (transactions.Rmd) + Error: processing vignette 'transactions.Rmd' failed with diagnostics: + Internal error: adjust_color() expects an input of length 1 + --- failed re-building ‘transactions.Rmd’ + + SUMMARY: processing the following files failed: + ‘actxps.Rmd’ ‘misc.Rmd’ ‘transactions.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# adaptr + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/INCEPTdk/adaptr +* Source code: https://github.com/cran/adaptr +* Date/Publication: 2024-05-03 12:10:02 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "adaptr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘adaptr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_history + > ### Title: Plot trial metric history + > ### Aliases: plot_history plot_history.trial_result + > ### plot_history.trial_results + > + > ### ** Examples + > + ... + + # Run a single simulation with a fixed random seed + + res <- run_trial(binom_trial, seed = 12345) + + + + # Plot total allocations to each arm according to overall total allocations + + plot_history(res, x_value = "total n", y_value = "n") + + + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_history ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(adaptr) + Loading 'adaptr' package v1.4.0. + For instructions, type 'help("adaptr")' + or see https://inceptdk.github.io/adaptr/. + > + > test_check("adaptr") + ... + • plot_history/history-plot-binomial-single-ratio-ys-look.svg + • plot_metrics_ecdf/errors.svg + • plot_metrics_ecdf/selected.svg + • plot_metrics_ecdf/size-only.svg + • plot_metrics_ecdf/superior.svg + • plot_status/status-plot-across-arms-binomial.svg + • plot_status/status-plot-for-all-arms-binomial.svg + • plot_status/status-plot-for-arm-c-binom.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Overview.Rmd’ + ... + + > plot_convergence(calibrated_binom_trial$best_sims, + + metrics = c("size mean", "prob_superior", "prob_equivalence"), + + n_split = 4) + + > plot_status(calibrated_binom_trial$best_sims, x_value = "total n") + + When sourcing ‘Overview.R’: + Error: argument is of length zero + Execution halted + + ‘Advanced-example.Rmd’ using ‘UTF-8’... OK + ‘Basic-examples.Rmd’ using ‘UTF-8’... OK + ‘Overview.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Advanced-example.Rmd’ using rmarkdown + ``` + +# AeRobiology + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/AeRobiology +* Date/Publication: 2019-06-03 06:20:03 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "AeRobiology")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘my-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘my-vignette.Rmd’ + ... + Warning: Ignoring unknown labels: + • `size = "14"` + + > iplot_abundance(munich_pollen, interpolation = FALSE, + + export.plot = FALSE, export.result = FALSE, n.types = 3, + + y.start = 2011, y.end = .... [TRUNCATED] + + When sourcing ‘my-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘my-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# agricolaeplotr + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/jensharbers/agricolaeplotr +* Source code: https://github.com/cran/agricolaeplotr +* Date/Publication: 2024-01-17 16:42:04 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "agricolaeplotr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(agricolaeplotr) + + Type 'citation("agricolaeplotr")' for citing this R package in publications. + + Attaching package: 'agricolaeplotr' + + ... + `expected` is a character vector ('ROW') + ── Failure ('testall.R:847:3'): plot a plot design from FielDHub package shows COLUMN as x axis ── + p$labels$x (`actual`) not identical to "COLUMN" (`expected`). + + `actual` is NULL + `expected` is a character vector ('COLUMN') + + [ FAIL 30 | WARN 92 | SKIP 0 | PASS 107 ] + Error: Test failures + Execution halted + ``` + +# alien + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/alien +* Date/Publication: 2024-06-19 16:20:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "alien")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic_usage.Rmd’ + ... + 2 0.3330822 6.848124e-06 1.620061e+04 + 3 0.3377835 1.902532e-07 5.997150e+05 + 4 0.3425512 5.285577e-09 2.220028e+07 + + > plot_snc(model, cumulative = T) + coord_cartesian(ylim = c(0, + + 150)) + scale_y_continuous(breaks = seq(0, 150, 50)) + ylab("Cumulative discove ..." ... [TRUNCATED] + + When sourcing ‘basic_usage.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘basic_usage.Rmd’ using ‘UTF-8’... failed + ‘native_discoveries.Rmd’ using ‘UTF-8’... OK + ‘simulations.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basic_usage.Rmd’ using rmarkdown + ``` + +# AlphaPart + +
+ +* Version: 0.9.8 +* GitHub: NA +* Source code: https://github.com/cran/AlphaPart +* Date/Publication: 2022-11-15 21:40:05 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "AlphaPart")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AlphaPart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.plotSummaryAlphaPart + > ### Title: Print a plot generate by the function 'plotSummaryAlphaPart' + > ### Aliases: print.plotSummaryAlphaPart + > + > ### ** Examples + > + > ## Partition additive genetic values + ... + 4 4 1 105.00000 66 39.00000 + + > + > ## Plot the partitions + > p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation") + > print(p[[1]]) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘alphapart-variance.Rmd’ + ... + + > data <- readRDS("./../inst/extdata/AlphaPartCattleSim.rds") %>% + + dplyr::mutate(across(generation:mother, as.numeric)) %>% + + dplyr::rename .... [TRUNCATED] + Warning in gzfile(file, "rb") : + cannot open compressed file './../inst/extdata/AlphaPartCattleSim.rds', probable reason 'No such file or directory' + + When sourcing ‘alphapart-variance.R’: + Error: cannot open the connection + Execution halted + + ‘alphapart-variance.Rmd’ using ‘UTF-8’... failed + ‘alphapart-vignette.Rmd’ using ‘UTF-8’... OK + ``` + +# AnalysisLin + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/AnalysisLin +* Date/Publication: 2024-01-30 00:10:10 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "AnalysisLin")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AnalysisLin-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bar_plot + > ### Title: Bar Plots for Categorical Variables + > ### Aliases: bar_plot + > + > ### ** Examples + > + > data(iris) + > bar_plot(iris) + Error in pm[[2]] : subscript out of bounds + Calls: bar_plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# animbook + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/KrisanatA/animbook +* Source code: https://github.com/cran/animbook +* Date/Publication: 2023-12-05 17:50:07 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "animbook")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘animbook-Ex.R’ failed + The error most likely occurred in: + + > ### Name: anim_animate + > ### Title: Modified the ggplot object + > ### Aliases: anim_animate + > + > ### ** Examples + > + > animbook <- anim_prep(data = osiris, id = ID, values = sales, time = year, group = japan) + ... + transform it into an animated object + > + > animate <- anim_animate(plot) + You can now pass it to gganimate::animate(). + The recommended setting is nframes = 89 + > + > plotly::ggplotly(animate) + Error in pm[[2]] : subscript out of bounds + Calls: -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# ANN2 + +
+ +* Version: 2.3.4 +* GitHub: https://github.com/bflammers/ANN2 +* Source code: https://github.com/cran/ANN2 +* Date/Publication: 2020-12-01 10:00:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "ANN2")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ANN2) + > + > # Only test if not on mac + > if (tolower(Sys.info()[["sysname"]]) != "darwin") { + + test_check("ANN2") + + } + ... + ── Failure ('test-plotting.R:59:3'): the reconstruction_plot.ANN() function works correctly ── + p_AE$labels$colour not equal to "col". + target is NULL, current is character + ── Failure ('test-plotting.R:77:3'): the compression_plot.ANN() function works correctly ── + p_AE$labels$colour not equal to "col". + target is NULL, current is character + + [ FAIL 5 | WARN 1 | SKIP 4 | PASS 143 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 58.9Mb + sub-directories of 1Mb or more: + cereal 1.4Mb + libs 57.3Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# AnnoProbe + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/jmzeng1314/AnnoProbe +* Source code: https://github.com/cran/AnnoProbe +* Date/Publication: 2022-11-14 08:30:11 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "AnnoProbe")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AnnoProbe-Ex.R’ failed + The error most likely occurred in: + + > ### Name: check_diff_genes + > ### Title: Check a list of genes how they show difference. + > ### Aliases: check_diff_genes + > + > ### ** Examples + > + > attach(GSE95166) + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# ANOFA + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/dcousin3/ANOFA +* Source code: https://github.com/cran/ANOFA +* Date/Publication: 2023-11-18 14:20:08 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ANOFA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ANOFA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Gillet1993 + > ### Title: Gillet1993 + > ### Aliases: Gillet1993 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + > # run the base analysis + > w <- anofa( Freq ~ species * location * florished, Gillet1993) + > + > # display a plot of the results + > anofaPlot(w) + superb::FYI: The variables will be plotted in that order: species, location, florished (use factorOrder to change). + Error in superb::superbPlot(cdata, BSFactors = bsfact, variables = as.character(w$freqColumn), : + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Calls: anofaPlot -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("ANOFA") + Loading required package: ANOFA + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-ANOFA-2.R:36:5'): TESTS of emFrequencies function (2/3) ──────── + ... + statistic = "count", errorbar = "CI", gamma = confidenceLevel, + plotStyle = plotStyle, errorbarParams = errorbarParams, ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Backtrace: + ▆ + 1. └─ANOFA::anofaPlot(w, Freq ~ B) at test-ANOFA-3.R:46:5 + 2. └─superb::superbPlot(...) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ConfidenceIntervals.Rmd’ + ... + > library(ANOFA) + + > w <- anofa(obsfreq ~ vocation * gender, LightMargolin1971) + + > anofaPlot(w) + superb::FYI: The variables will be plotted in that order: vocation, gender (use factorOrder to change). + + ... + + > anofaPlot(w) + + When sourcing ‘WhatIsANOFA.R’: + Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Execution halted + + ‘ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed + ‘DataFormatsForFrequencies.Rmd’ using ‘UTF-8’... OK + ‘WhatIsANOFA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ConfidenceIntervals.Rmd’ using rmarkdown + + Quitting from lines 70-73 [unnamed-chunk-2] (ConfidenceIntervals.Rmd) + Error: processing vignette 'ConfidenceIntervals.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘ConfidenceIntervals.Rmd’ + + --- re-building ‘DataFormatsForFrequencies.Rmd’ using rmarkdown + ... + Quitting from lines 108-109 [unnamed-chunk-4] (WhatIsANOFA.Rmd) + Error: processing vignette 'WhatIsANOFA.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘WhatIsANOFA.Rmd’ + + SUMMARY: processing the following files failed: + ‘ConfidenceIntervals.Rmd’ ‘WhatIsANOFA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ANOPA + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/dcousin3/ANOPA +* Source code: https://github.com/cran/ANOPA +* Date/Publication: 2024-03-22 19:40:05 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ANOPA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ANOPA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ArringtonEtAl2002 + > ### Title: Arrington et al. (2002) dataset + > ### Aliases: ArringtonEtAl2002 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + Africa Nocturnal Omnivore 0 0 + North America Nocturnal Detritivore 0 0 + Warning: ANOPA::warning(1): Some cells have zero over zero data. Imputing... + > + > # make a plot with all the factors + > anopaPlot(w) + Error in superb::superbPlot(wdata, BSFactors = bsfact, WSFactors = wsfact, : + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Calls: anopaPlot -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("ANOPA") + Loading required package: ANOPA + ------------------------------------------------------------ + Design is: 2 x ( 3 ) with 2 independent groups. + ------------------------------------------------------------ + 1.Between-Subject Factors ( 2 groups ) : + ... + 1) "UA" else "none"), plotStyle = plotStyle, errorbarParams = errorbarParams, + ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Backtrace: + ▆ + 1. └─ANOPA::anopaPlot(w) at test-ANOPA-4.R:106:9 + 2. └─superb::superbPlot(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘A-WhatIsANOPA.Rmd’ + ... + > w <- anopa({ + + nSuccess + + nParticipants + + } ~ DistractingTask, ArticleExample1) + + > anopaPlot(w) + + ... + When sourcing ‘E-ArcsineIsAsinine.R’: + Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Execution halted + + ‘A-WhatIsANOPA.Rmd’ using ‘UTF-8’... failed + ‘B-DataFormatsForProportions.Rmd’ using ‘UTF-8’... OK + ‘C-ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed + ‘D-ArringtonExample.Rmd’ using ‘UTF-8’... failed + ‘E-ArcsineIsAsinine.Rmd’ using ‘UTF-8’... failed + ‘F-TestingTypeIError.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘A-WhatIsANOPA.Rmd’ using rmarkdown + + Quitting from lines 182-183 [unnamed-chunk-5] (A-WhatIsANOPA.Rmd) + Error: processing vignette 'A-WhatIsANOPA.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘A-WhatIsANOPA.Rmd’ + + --- re-building ‘B-DataFormatsForProportions.Rmd’ using rmarkdown + --- finished re-building ‘B-DataFormatsForProportions.Rmd’ + ... + + --- re-building ‘F-TestingTypeIError.Rmd’ using rmarkdown + --- finished re-building ‘F-TestingTypeIError.Rmd’ + + SUMMARY: processing the following files failed: + ‘A-WhatIsANOPA.Rmd’ ‘C-ConfidenceIntervals.Rmd’ + ‘D-ArringtonExample.Rmd’ ‘E-ArcsineIsAsinine.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# AntMAN + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/bbodin/AntMAN +* Source code: https://github.com/cran/AntMAN +* Date/Publication: 2021-07-23 10:00:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "AntMAN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AntMAN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AM_mix_hyperparams_uninorm + > ### Title: univariate Normal mixture hyperparameters + > ### Aliases: AM_mix_hyperparams_uninorm + > + > ### ** Examples + > + > + ... + Press [enter] to continue + Plotting pmf for M,K + NULL + Press [enter] to continue + Plotting traces from M,K + Press [enter] to continue + Plotting values from M,K + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘UnitTest_AM_binder.R’ + Running ‘UnitTest_AM_coclustering.R’ + Running ‘UnitTest_AM_demo.R’ + Running ‘UnitTest_AM_extract.R’ + Running ‘UnitTest_AM_mcmc.R’ + Running the tests in ‘tests/UnitTest_AM_mcmc.R’ failed. + Complete output: + > ####################################################################################### + > ############### + > ############### AntMAN Package : Tests and Examples + ... + Press [enter] to continue + Plotting pmf for M,K + NULL + Press [enter] to continue + Plotting traces from M,K + Press [enter] to continue + Plotting values from M,K + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + libs 6.4Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Rdpack’ ‘mcclust’ + All declared Imports should be used. + ``` + +# APCI + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/APCI +* Date/Publication: 2024-09-02 20:20:06 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "APCI")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘1_tests.R’ + Running the tests in ‘tests/1_tests.R’ failed. + Complete output: + > # install the package and use this script to test the package + > library("APCI") + > # or: remotes::install_github("jiahui1902/APCI") + > test_data <- APCI::women9017 + > test_data$acc <- as.factor(test_data$acc) + > test_data$pcc <- as.factor(test_data$pcc) + > test_data$educc <- as.factor(test_data$educc) + ... + -0.335818939 0.165402344 0.138957101 -0.357703237 0.229441985 + acc8:pcc3 acc9:pcc3 acc1:pcc4 acc2:pcc4 acc3:pcc4 + -0.147848556 0.146360984 -0.436635793 0.062363971 0.289676120 + acc4:pcc4 acc5:pcc4 acc6:pcc4 acc7:pcc4 acc8:pcc4 + 0.266502847 0.199035811 -0.082410026 -0.140171983 -0.274808726 + acc9:pcc4 acc1:pcc5 acc2:pcc5 acc3:pcc5 acc4:pcc5 + 0.070541348 0.052280642 0.320968547 -0.136111903 -0.102002632 + acc5:pcc5 acc6:pcc5 acc7:pcc5 acc8:pcc5 acc9:pcc5 + -0.553458810 -0.333938836 0.340338956 0.670285259 -0.300340437 + Killed + ``` + +# aplot + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/YuLab-SMU/aplot +* Source code: https://github.com/cran/aplot +* Date/Publication: 2024-06-17 09:50:01 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "aplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘aplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: insert_left + > ### Title: plot-insertion + > ### Aliases: insert_left insert_right insert_top insert_bottom + > + > ### ** Examples + > + > library(ggplot2) + ... + > ap + > ap[2, 1] <- ap[2, 1] + theme_bw() + > ap[2, 1] <- ap[2, 1] + + + aes(color = as.factor(am)) + + + scale_color_manual(values = c('steelblue', 'darkgreen')) + > ap[1, 1] <- ap[1, 1] + theme(axis.line.x.bottom=element_line()) + > ap + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# applicable + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/tidymodels/applicable +* Source code: https://github.com/cran/applicable +* Date/Publication: 2024-04-25 00:00:04 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "applicable")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(applicable) + Loading required package: ggplot2 + > + > test_check("applicable") + Loading required package: dplyr + ... + `expected` is a character vector ('percentile') + ── Failure ('test-plot.R:36:3'): output of autoplot.apd_pca is correct when options=distance are provided ── + ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`). + + `actual` is NULL + `expected` is a character vector ('percentile') + + [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ] + Error: Test failures + Execution halted + ``` + +# ASRgenomics + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/ASRgenomics +* Date/Publication: 2024-01-29 21:20:02 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "ASRgenomics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ASRgenomics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kinship.pca + > ### Title: Performs a Principal Component Analysis (PCA) based on a kinship + > ### matrix K + > ### Aliases: kinship.pca + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + ... + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 249 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + data 8.5Mb + ``` + +# autocogs + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/schloerke/autocogs +* Source code: https://github.com/cran/autocogs +* Date/Publication: 2021-05-29 17:00:05 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "autocogs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(autocogs) + > + > test_check("autocogs") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 228 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 8. └─autocogs (local) FUN(X[[i]], ...) + 9. └─base::lapply(...) + 10. └─autocogs (local) FUN(X[[i]], ...) + 11. ├─base::do.call(fn, args) + 12. └─autocogs (local) ``(...) + 13. └─base::do.call(loess, c(core_params, params$method.args)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 228 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’ + All declared Imports should be used. + ``` + +# autoplotly + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/terrytangyuan/autoplotly +* Source code: https://github.com/cran/autoplotly +* Date/Publication: 2021-04-18 06:50:11 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "autoplotly")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘autoplotly-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplotly + > ### Title: Automatic Visualization of Popular Statistical Results Using + > ### 'plotly.js' and 'ggplot2' + > ### Aliases: autoplotly + > + > ### ** Examples + > + > # Automatically generate interactive plot for results produced by `stats::prcomp` + > p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris, + + colour = 'Species', label = TRUE, label.size = 3, frame = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplotly ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(autoplotly) + > + > test_check("autoplotly") + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 5. └─ggfortify::ggbiplot(...) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + Error: Test failures + Execution halted + ``` + +# autoReg + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/cardiomoon/autoReg +* Source code: https://github.com/cran/autoReg +* Date/Publication: 2023-11-14 05:53:27 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "autoReg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘autoReg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adjustedPlot.survreg + > ### Title: Draw predicted survival curve with an object survreg + > ### Aliases: adjustedPlot.survreg + > + > ### ** Examples + > + > library(survival) + > x=survreg(Surv(time, status) ~ rx, data=anderson,dist="exponential") + > adjustedPlot(x) + > adjustedPlot(x,addCox=TRUE) + Warning: Removed 42 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Automatic_Regression_Modeling.Rmd’ + ... + Species setosa (N=50) Mean ± SD 5.0 ± 0.4 + versicolor (N=50) Mean ± SD 5.9 ± 0.5 1.46 (1.24 to 1.68, p<.001) 1.44 (1.16 to 1.71, p<.001) 1.47 (1.23 to 1.70, p<.001) + virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.87 (1.62 to 2.11, p<.001) 1.97 (1.76 to 2.17, p<.001) + ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— + + > modelPlot(fit1, imputed = TRUE) + + ... + + When sourcing ‘Survival.R’: + Error: argument is of length zero + Execution halted + + ‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... failed + ‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK + ‘Getting_started.Rmd’ using ‘UTF-8’... failed + ‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK + ‘Survival.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Automatic_Regression_Modeling.Rmd’ using rmarkdown + + Quitting from lines 142-143 [unnamed-chunk-15] (Automatic_Regression_Modeling.Rmd) + Error: processing vignette 'Automatic_Regression_Modeling.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘Automatic_Regression_Modeling.Rmd’ + + --- re-building ‘Bootstrap_Prediction.Rmd’ using rmarkdown + ``` + +# baggr + +
+ +* Version: 0.7.8 +* GitHub: https://github.com/wwiecek/baggr +* Source code: https://github.com/cran/baggr +* Date/Publication: 2024-02-12 18:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "baggr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘baggr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: baggr_plot + > ### Title: Plotting method in baggr package + > ### Aliases: baggr_plot + > + > ### ** Examples + > + > fit <- baggr(schools, pooling = "none") + Automatically chose Rubin model with aggregate data based on input data. + Setting prior for mean in each group using 10 times the max effect : + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(baggr) + Loading required package: Rcpp + This is baggr; see vignette('baggr') for tutorial, ?baggr for basic help. + For execution on a local, multicore CPU with excess RAM call: + options(mc.cores = parallel::detectCores()) + > + ... + 10. └─bayesplot::mcmc_areas(...) + 11. └─ggplot2:::`+.gg`(...) + 12. └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. ├─ggplot2::ggplot_add(object, p, objectname) + 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 488 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘baggr.Rmd’ + ... + 2.5% 0.4303903 + mean 0.8619752 + 97.5% 0.9998572 + + + > plot(baggr_schools, order = FALSE) + + When sourcing ‘baggr.R’: + Error: argument is of length zero + Execution halted + + ‘baggr.Rmd’ using ‘UTF-8’... failed + ‘baggr_binary.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘baggr.Rmd’ using rmarkdown + + Quitting from lines 272-273 [unnamed-chunk-9] (baggr.Rmd) + Error: processing vignette 'baggr.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘baggr.Rmd’ + + --- re-building ‘baggr_binary.Rmd’ using rmarkdown + --- finished re-building ‘baggr_binary.Rmd’ + + SUMMARY: processing the following file failed: + ‘baggr.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 196.3Mb + sub-directories of 1Mb or more: + libs 194.5Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# banter + +
+ +* Version: 0.9.6 +* GitHub: NA +* Source code: https://github.com/cran/banter +* Date/Publication: 2023-02-12 21:32:29 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "banter")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘banter-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotDetectorTrace + > ### Title: Plot BANTER Detector Traces + > ### Aliases: plotDetectorTrace + > + > ### ** Examples + > + > data(train.data) + ... + > bant.mdl <- addBanterDetector( + + bant.mdl, train.data$detectors, + + ntree = 50, sampsize = 1, num.cores = 1 + + ) + > + > plotDetectorTrace(bant.mdl) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotDetectorTrace ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# bartMan + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/bartMan +* Date/Publication: 2024-07-24 12:10:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "bartMan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bartMan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mdsBart + > ### Title: mdsBart + > ### Aliases: mdsBart + > + > ### ** Examples + > + > if (requireNamespace("dbarts", quietly = TRUE)) { + ... + | + |======================================================================| 100% + Extracting Observation Data... + + Getting proximites... + Getting MDS... + Performing procrustes... + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mdsBart -> suppressMessages -> withCallingHandlers + Execution halted + ``` + +# BasketballAnalyzeR + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/sndmrc/BasketballAnalyzeR +* Source code: https://github.com/cran/BasketballAnalyzeR +* Date/Publication: 2020-06-26 09:00:11 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "BasketballAnalyzeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BasketballAnalyzeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatterplot + > ### Title: Draws a scatter plot or a matrix of scatter plots + > ### Aliases: scatterplot + > + > ### ** Examples + > + > # Single scatter plot + ... + > X <- data.frame(AST=Pbox.sel$AST/Pbox.sel$MIN,TOV=Pbox.sel$TOV/Pbox.sel$MIN) + > X$PTSpm <- Pbox.sel$PTS/Pbox.sel$MIN + > mypal <- colorRampPalette(c("blue","yellow","red")) + > scatterplot(X, data.var=c("AST","TOV"), z.var="PTSpm", labels=1:nrow(X), palette=mypal) + > # Matrix of scatter plots + > data <- Pbox[1:50, c("PTS","P3M","P2M","OREB","Team")] + > scatterplot(data, data.var=1:4, z.var="Team") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.9Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’ + All declared Imports should be used. + ``` + +# bayefdr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/VallejosGroup/bayefdr +* Source code: https://github.com/cran/bayefdr +* Date/Publication: 2022-10-26 19:35:06 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "bayefdr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayefdr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: traceplot + > ### Title: Trace, marginal density histogram, and autocorrelation plot of + > ### MCMC draws. + > ### Aliases: traceplot + > + > ### ** Examples + > + > x <- rnorm(1000) + > traceplot(x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayefdr) + > + > test_check("bayefdr") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 8. └─base::Reduce(`+`, c(list(noGeomPlot), layers)) + 9. └─ggplot2:::`+.gg`(init, x[[i]]) + 10. └─ggplot2:::add_ggplot(e1, e2, e2name) + 11. ├─ggplot2::ggplot_add(object, p, objectname) + 12. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 13. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] + Error: Test failures + Execution halted + ``` + +# bayesAB + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/FrankPortman/bayesAB +* Source code: https://github.com/cran/bayesAB +* Date/Publication: 2021-06-25 00:50:02 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "bayesAB")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayesAB) + > + > test_check("bayesAB") + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-dists.R:34:3'): Success ────────────────────────────────────── + plotNormalInvGamma(3, 1, 1, 1)$labels$y not equal to "sig_sq". + target is NULL, current is character + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + Error: Test failures + Execution halted + ``` + +# BayesGrowth + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/jonathansmart/BayesGrowth +* Source code: https://github.com/cran/BayesGrowth +* Date/Publication: 2023-11-21 18:10:08 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "BayesGrowth")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MCMC-example.Rmd’ + ... + > ggplot(growth_curve, aes(Age, LAA)) + geom_point(data = example_data, + + aes(Age, Length), alpha = 0.3) + geom_lineribbon(aes(ymin = .lower, + + .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘MCMC-example.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 14, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, FALSE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NUL + Execution halted + + ‘MCMC-example.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MCMC-example.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 84.8Mb + sub-directories of 1Mb or more: + data 1.5Mb + libs 82.6Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# BayesianReasoning + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/gorkang/BayesianReasoning +* Source code: https://github.com/cran/BayesianReasoning +* Date/Publication: 2023-11-14 11:33:20 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(BayesianReasoning) + > + > test_check("BayesianReasoning") + + Plot created in: ./FP_10_sens_100_screening_1667_diagnostic_44.png + + ... + `names(expected)` is absent + ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ─────────────── + vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`). + + `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect') + `names(expected)` is absent + + [ FAIL 8 | WARN 56 | SKIP 4 | PASS 115 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPV_NPV.Rmd’ + ... + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Warning in ggforce::geom_mark_rect(aes(label = paste0(translated_labels$label_PPV_NPV, : + All aesthetics have length 1, but the data has 10201 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + + When sourcing ‘PPV_NPV.R’: + Error: object is not coercible to a unit + Execution halted + + ‘PPV_NPV.Rmd’ using ‘UTF-8’... failed + ‘introduction.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPV_NPV.Rmd’ using rmarkdown + ``` + +# BayesMallows + +
+ +* Version: 2.2.2 +* GitHub: https://github.com/ocbe-uio/BayesMallows +* Source code: https://github.com/cran/BayesMallows +* Date/Publication: 2024-08-17 13:00:03 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "BayesMallows")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + `expected` is a character vector ('interaction(chain, cluster)') + ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ── + p$labels$colour (`actual`) not equal to "cluster" (`expected`). + + `actual` is NULL + `expected` is a character vector ('cluster') + + [ FAIL 10 | WARN 0 | SKIP 6 | PASS 435 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 23.7Mb + sub-directories of 1Mb or more: + doc 2.7Mb + libs 20.1Mb + ``` + +# bayesplay + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/bayesplay/bayesplay +* Source code: https://github.com/cran/bayesplay +* Date/Publication: 2023-04-13 12:10:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "bayesplay")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayesplay-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visual_compare + > ### Title: Visually compare two models + > ### Aliases: visual_compare + > + > ### ** Examples + > + > # define two models + ... + > h1_mod <- prior(family = "normal", mean = 0, sd = 10) + > m0 <- extract_predictions(data_model * h0_mod) + > m1 <- extract_predictions(data_model * h1_mod) + > + > # visually compare the model + > visual_compare(m0, m1) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘advanced.Rmd’ + ... + > plot(posterior1, add_prior = TRUE) + labs(title = "prior and posterior distribution", + + subtitle = "for a binomial likelihood and beta prior") + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for + + ... + > visual_compare(d_model1, d_model2) + + When sourcing ‘plots.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘advanced.Rmd’ using ‘UTF-8’... failed + ‘basic.Rmd’ using ‘UTF-8’... OK + ‘default_ttests.Rmd’ using ‘UTF-8’... OK + ‘plots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘advanced.Rmd’ using rmarkdown + ``` + +# bayesplot + +
+ +* Version: 1.11.1 +* GitHub: https://github.com/stan-dev/bayesplot +* Source code: https://github.com/cran/bayesplot +* Date/Publication: 2024-02-15 05:30:11 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "bayesplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayesplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MCMC-intervals + > ### Title: Plot interval estimates from MCMC draws + > ### Aliases: MCMC-intervals mcmc_intervals mcmc_areas mcmc_areas_ridges + > ### mcmc_intervals_data mcmc_areas_data mcmc_areas_ridges_data + > + > ### ** Examples + > + ... + + $Parameter + [1] "alpha" "sigma" "beta[1]" "beta[2]" "beta[3]" "beta[4]" + + > + > color_scheme_set("brightblue") + > mcmc_intervals(x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayesplot) + This is bayesplot version 1.11.1 + - Online documentation and vignettes at mc-stan.org/bayesplot + - bayesplot theme set to bayesplot::theme_default() + * Does _not_ affect other ggplot2 plots + * See ?bayesplot_theme_set for details on theme setting + ... + 5. └─bayesplot::ppc_violin_grouped(y, yrep, group) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 1 | SKIP 73 | PASS 994 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘plotting-mcmc-draws.Rmd’ + ... + + + > color_scheme_set("red") + + > mcmc_intervals(posterior, pars = c("cyl", "drat", + + "am", "sigma")) + + ... + > fit_cp <- sampling(schools_mod_cp, data = schools_dat, + + seed = 803214055, control = list(adapt_delta = 0.9)) + + When sourcing ‘visual-mcmc-diagnostics.R’: + Error: error in evaluating the argument 'object' in selecting a method for function 'sampling': object 'schools_mod_cp' not found + Execution halted + + ‘graphical-ppcs.Rmd’ using ‘UTF-8’... OK + ‘plotting-mcmc-draws.Rmd’ using ‘UTF-8’... failed + ‘visual-mcmc-diagnostics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + R 4.0Mb + doc 3.8Mb + ``` + +# bayestestR + +
+ +* Version: 0.14.0 +* GitHub: https://github.com/easystats/bayestestR +* Source code: https://github.com/cran/bayestestR +* Date/Publication: 2024-07-24 14:10:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "bayestestR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayestestR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bayesfactor_restricted + > ### Title: Bayes Factors (BF) for Order Restricted Models + > ### Aliases: bayesfactor_restricted bf_restricted + > ### bayesfactor_restricted.stanreg bayesfactor_restricted.brmsfit + > ### bayesfactor_restricted.blavaan bayesfactor_restricted.emmGrid + > ### as.logical.bayesfactor_restricted + > + ... + + ) + > + > + > (b <- bayesfactor_restricted(posterior, hypothesis = hyps, prior = prior)) + Bayes Factor (Order-Restriction) + + Hypothesis P(Prior) P(Posterior) BF + A > B & B > C 0.16 0.23 1.39 + A > B & A > C 0.36 0.59 1.61 + C > A 0.46 0.34 0.742 + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayestestR) + > + > test_check("bayestestR") + Starting 2 test processes + [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] + + ... + 14. └─brms:::eval2(call, envir = args, enclos = envir) + 15. └─base::eval(expr, envir, ...) + 16. └─base::eval(expr, envir, ...) + 17. └─rstan (local) .fun(model_code = .x1) + 18. └─rstan:::cxxfunctionplus(...) + 19. └─base::sink(type = "output") + + [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] + Error: Test failures + Execution halted + ``` + +# BCEA + +
+ +* Version: 2.4.6 +* GitHub: https://github.com/n8thangreen/BCEA +* Source code: https://github.com/cran/BCEA +* Date/Publication: 2024-02-16 15:00:08 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "BCEA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BCEA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ceac.plot.bcea + > ### Title: Cost-Effectiveness Acceptability Curve (CEAC) Plot + > ### Aliases: ceac.plot.bcea ceac.plot + > ### Keywords: hplot + > + > ### ** Examples + > + ... + > he <- BCEA::bcea(eff, cost) + No reference selected. Defaulting to first intervention. + > ceac.plot(he) + > + > ceac.plot(he, graph = "base") + > ceac.plot(he, graph = "ggplot2") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(BCEA) + The BCEA version loaded is: 2.4.6 + + Attaching package: 'BCEA' + + The following object is masked from 'package:graphics': + ... + 3. └─BCEA:::eib_plot_ggplot(he, graph_params, ...) + 4. └─ggplot2:::`+.gg`(...) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 7 | PASS 159 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CEriskav.Rmd’ + ... + + > CEriskav(bcea_smoke) <- r + + > plot(bcea_smoke) + + > plot(bcea_smoke, graph = "ggplot") + + ... + + ‘CEriskav.Rmd’ using ‘UTF-8’... failed + ‘bcea.Rmd’ using ‘UTF-8’... failed + ‘ceac.Rmd’ using ‘UTF-8’... failed + ‘ceef.Rmd’ using ‘UTF-8’... OK + ‘ceplane.Rmd’ using ‘UTF-8’... failed + ‘contour.Rmd’ using ‘UTF-8’... failed + ‘eib.Rmd’ using ‘UTF-8’... failed + ‘paired_vs_multiple_comps.Rmd’ using ‘UTF-8’... OK + ‘Set_bcea_parameters.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘CEriskav.Rmd’ using rmarkdown + + Quitting from lines 41-46 [unnamed-chunk-3] (CEriskav.Rmd) + Error: processing vignette 'CEriskav.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘CEriskav.Rmd’ + + --- re-building ‘bcea.Rmd’ using rmarkdown + ``` + +# BDgraph + +
+ +* Version: 2.73 +* GitHub: NA +* Source code: https://github.com/cran/BDgraph +* Date/Publication: 2024-08-23 13:20:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "BDgraph")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘BDgraph-Examples.Rmd’ + ... + Sensitivity 1 0.714 0.714 + MCC 1 0.827 0.827 + + > plotroc(list(bdgraph.obj, bdgraph.mpl.obj), data.sim, + + cut = 200, labels = c("BDgraph", "BDgraph.mpl"), color = c("blue", + + "red")) + + When sourcing ‘BDgraph-Examples.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘BDgraph-Examples.Rmd’ using ‘UTF-8’... failed + ‘Introduction-BDgraph.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘BDgraph-Examples.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + libs 6.8Mb + ``` + +# BEAMR + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/annaSeffernick/BEAMR +* Source code: https://github.com/cran/BEAMR +* Date/Publication: 2024-07-27 16:00:06 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "BEAMR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BEAMR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gen_beam_plot_list + > ### Title: Generate BEAM Plot List + > ### Aliases: gen_beam_plot_list + > + > ### ** Examples + > + > data(beam_stats) + ... + + beam.specs=beam_stats$beam.specs) + > plot.list <- gen_beam_plot_list(beam.result=beam_stats, beam.specs=plot.specs, + + beam.feat.pvals=test.feat.pvals, + + number.pairs=1, set.id="ENSG00000099810", + + feat.id=NULL, title.size=11, + + pair.order="omic", endpt.order=NULL) + Error in if (new_name %in% existing) { : argument is of length zero + Error in plot.temp$plot : $ operator is invalid for atomic vectors + Calls: gen_beam_plot_list + Execution halted + ``` + +# beastt + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/GSK-Biostatistics/beastt +* Source code: https://github.com/cran/beastt +* Date/Publication: 2024-06-20 15:50:16 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "beastt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘beastt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_dist + > ### Title: Plot Distribution + > ### Aliases: plot_dist + > + > ### ** Examples + > + > library(distributional) + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘binary.Rmd’ + ... + + > plot_dist(pwr_prior) + + When sourcing ‘binary.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + When sourcing ‘continuous.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘binary.Rmd’ using ‘UTF-8’... failed + ‘continuous.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘binary.Rmd’ using rmarkdown + ``` + +# BeeGUTS + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/bgoussen/BeeGUTS +* Source code: https://github.com/cran/BeeGUTS +* Date/Publication: 2023-09-18 15:40:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "BeeGUTS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BeeGUTS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: traceplot + > ### Title: Plotting method for traces and densities for 'beeSurvFit' + > ### objects + > ### Aliases: traceplot traceplot.beeSurvFit + > + > ### ** Examples + > + > data(fitBetacyfluthrin_Chronic) + > traceplot(fitBetacyfluthrin_Chronic) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + Chain 1: Elapsed Time: 137.867 seconds (Warm-up) + Chain 1: 75.093 seconds (Sampling) + Chain 1: 212.96 seconds (Total) + Chain 1: + + > traceplot(fit) + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 45-58 [example] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 78.9Mb + sub-directories of 1Mb or more: + data 4.0Mb + libs 74.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# besthr + +
+ +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/besthr +* Date/Publication: 2023-04-14 08:50:08 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "besthr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘besthr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.hrest + > ### Title: plots the 'hrest' object + > ### Aliases: plot.hrest + > + > ### ** Examples + > + > + > d1 <- make_data() + > hr_est <- estimate(d1, score, group) + > plot(hr_est) + Picking joint bandwidth of 0.68 + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic-use.Rmd’ + ... + Confidence Intervals (0.025, 0.975) + 3.7475, 8.2525 + + 100 bootstrap resamples. + > plot(hr_est_1) + Picking joint bandwidth of 0.381 + + When sourcing ‘basic-use.R’: + Error: object is not coercible to a unit + Execution halted + + ‘basic-use.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘basic-use.Rmd’ using rmarkdown + + Quitting from lines 34-44 [unnamed-chunk-2] (basic-use.Rmd) + Error: processing vignette 'basic-use.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘basic-use.Rmd’ + + SUMMARY: processing the following file failed: + ‘basic-use.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# betaclust + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/betaclust +* Date/Publication: 2023-09-29 10:20:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "betaclust")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignettes.Rmd’ + ... + + data = pca.methylation.data[, 2:5], patient_number = 1, plot_type = "ggplot") + + > plot(threshold_out, what = "kernel density", threshold = TRUE, + + data = pca.methylation.data[, 2:5], plot_type = "ggplot") + + > plot(threshold_out, what = "uncertainty") + + When sourcing ‘vignettes.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘vignettes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignettes.Rmd’ using rmarkdown + ``` + +# biclustermd + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/jreisner/biclustermd +* Source code: https://github.com/cran/biclustermd +* Date/Publication: 2021-06-17 15:10:06 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "biclustermd")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(biclustermd) + Loading required package: ggplot2 + Loading required package: tidyr + + Attaching package: 'tidyr' + + ... + ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── + ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. + Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' + ── Failure ('test-autoplot_biclustermd.R:7:3'): autoplot_biclustermd() correctly plots cluster lines ── + ap$data[[4]]$yintercept[-1] not equal to cumsum(colSums(sbc$Q)) + 0.5. + Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘nycflights13’ + All declared Imports should be used. + ``` + +# biodosetools + +
+ +* Version: 3.6.1 +* GitHub: https://github.com/biodosetools-team/biodosetools +* Source code: https://github.com/cran/biodosetools +* Date/Publication: 2022-11-16 16:00:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "biodosetools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(biodosetools) + > + > test_check("biodosetools") + ! Problem with `glm()` -> constraint ML optimization will be used instead + ! Problem with `glm()` -> constraint ML optimization will be used instead + number of iterations= 43 + ... + actual | expected + [2] "Estimation" | "Estimation" [2] + [3] "Dose (Gy)" | "Dose (Gy)" [3] + [4] "Translocations/cells" | "Translocations/cells" [4] + - "yield_low" [5] + - "yield_upp" [6] + + [ FAIL 4 | WARN 0 | SKIP 1 | PASS 232 ] + Error: Test failures + Execution halted + ``` + +# BioPred + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/BioPred +* Date/Publication: 2024-06-06 16:50:09 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "BioPred")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + + > tutorial_data$biogroup = ifelse(tutorial_data$x2 <= + + 0.5, "biomarker_positive", "biomarker_negative") + + > res = subgrp_perf_pred(yvar = "y.time", censorvar = "y.event", + + grpvar = "biogroup", grpname = c("biomarker_positive", "biomarker_negative"), .... [TRUNCATED] + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Tutorial.Rmd’ using rmarkdown + ``` + +# BlandAltmanLeh + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/BlandAltmanLeh +* Date/Publication: 2015-12-23 23:32:17 +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "BlandAltmanLeh")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Intro.Rmd’ + ... + > b <- 0.02 * a + 0.3 * rnorm(150) + + > library(ggExtra) + + > print(ggMarginal(bland.altman.plot(a, b, graph.sys = "ggplot2"), + + type = "histogram", size = 4)) + + When sourcing ‘Intro.R’: + Error: argument is of length zero + Execution halted + + ‘Intro.Rmd’... failed + ``` + +# bmggum + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Naidantu/bmggum +* Source code: https://github.com/cran/bmggum +* Date/Publication: 2021-04-09 08:50:06 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "bmggum")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bmggum-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bayesplot + > ### Title: bayesian convergence diagnosis plotting function + > ### Aliases: bayesplot + > + > ### ** Examples + > + > Data <- c(1,4,2,3) + ... + Chain 1: + Warning: There were 3 divergent transitions after warmup. See + https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup + to find out why this is a problem and how to eliminate them. + Warning: Examine the pairs() plot to diagnose sampling problems + + > bayesplot(mod, 'alpha', 'density', inc_warmup=FALSE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: bayesplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 206.7Mb + sub-directories of 1Mb or more: + libs 206.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# boxly + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Merck/boxly +* Source code: https://github.com/cran/boxly +* Date/Publication: 2023-10-24 02:40:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "boxly")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 16. ├─plotly::add_trace(...) + 17. │ └─plotly::add_data(p, data) + 18. │ └─plotly:::is.plotly(p) + 19. ├─plotly::ggplotly(p, tooltip = "text", dynamicTicks = TRUE) + 20. └─plotly:::ggplotly.ggplot(p, tooltip = "text", dynamicTicks = TRUE) + 21. └─plotly::gg2list(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +# braidReports + +
+ +* Version: 0.5.4 +* GitHub: NA +* Source code: https://github.com/cran/braidReports +* Date/Publication: 2021-01-05 18:20:09 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "braidReports")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘braidReports-Ex.R’ failed + The error most likely occurred in: + + > ### Name: makeBRAIDreport + > ### Title: Make a BRAID Report Page + > ### Aliases: makeBRAIDreport + > ### Keywords: hplot + > + > ### ** Examples + > + ... + 22. │ └─grid::convertUnit(short, "cm", valueOnly = TRUE) + 23. │ ├─grid:::upgradeUnit(x) + 24. │ └─grid:::upgradeUnit.default(x) + 25. │ └─base::stop("Not a unit object") + 26. └─base::.handleSimpleError(``, "Not a unit object", base::quote(upgradeUnit.default(x))) + 27. └─rlang (local) h(simpleError(msg, call)) + 28. └─handlers[[1L]](cnd) + 29. └─cli::cli_abort(...) + 30. └─rlang::abort(...) + Execution halted + ``` + +# BRcal + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/apguthrie/BRcal +* Source code: https://github.com/cran/BRcal +* Date/Publication: 2024-06-25 11:30:08 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "BRcal")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BRcal-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lineplot + > ### Title: Lineplot for LLO-adjusted Probability Predictions + > ### Aliases: lineplot + > + > ### ** Examples + > + > + ... + > # Simulated 100 binary event outcomes using x + > y <- rbinom(100, 1, x) # By construction, x is well calibrated. + > + > # Lineplot show change in probabilities from original to MLE-recalibration to + > # specified Levels of Boldness-Recalibration via t_levels + > # Return a list with dataframe used to construct plot with return_df=TRUE + > lp1 <- lineplot(x, y, t_levels=c(0.98, 0.95), return_df=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: lineplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hockey_vignette.Rmd’ + ... + [841] 0.4804441 0.7670617 0.4668403 0.4104682 0.6058493 0.4249086 0.6581869 + [848] 0.7194199 0.4534938 0.7421488 0.6726924 0.3255808 0.5005185 0.6483056 + [855] 0.7210362 0.6593455 0.4586214 0.7750603 0.5841900 0.4826292 0.4080026 + [862] 0.6701504 0.6561462 0.4814185 0.7421488 0.6786381 0.3255808 0.4814569 + + > lineplot(hockey$x, hockey$y) + + When sourcing ‘hockey_vignette.R’: + Error: argument is of length zero + Execution halted + + ‘hockey_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘hockey_vignette.Rmd’ using rmarkdown + + Quitting from lines 180-181 [unnamed-chunk-11] (hockey_vignette.Rmd) + Error: processing vignette 'hockey_vignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘hockey_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘hockey_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# breathtestcore + +
+ +* Version: 0.8.7 +* GitHub: https://github.com/dmenne/breathtestcore +* Source code: https://github.com/cran/breathtestcore +* Date/Publication: 2024-01-24 15:02:47 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "breathtestcore")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > + > options(Ncpus = parallelly::availableCores(omit = 1)) + > test_check("breathtestcore") + Loading required package: breathtestcore + Starting 1 test process + [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] + ... + `expected`: 10 + ── Failure ('test_plot_breathtestfit.R:81:3'): Plot multiple groups data only (no fit) ── + length(p) (`actual`) not equal to length(ggplot()) (`expected`). + + `actual`: 11 + `expected`: 10 + + [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] + Error: Test failures + Execution halted + ``` + +# brolgar + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/njtierney/brolgar +* Source code: https://github.com/cran/brolgar +* Date/Publication: 2024-05-10 14:50:34 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "brolgar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘brolgar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_sample + > ### Title: Facet data into groups to facilitate exploration + > ### Aliases: facet_sample + > + > ### ** Examples + > + > library(ggplot2) + > ggplot(heights, + + aes(x = year, + + y = height_cm, + + group = country)) + + + geom_line() + + + facet_sample() + Error in if (params$as.table) { : argument is of length zero + Calls: ... -> setup -> -> compute_layout + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exploratory-modelling.Rmd’ + ... + Warning in is.na(non_null_default_aes[[aes_param_name]]) : + is.na() applied to non-(list or vector) of type 'language' + + When sourcing ‘exploratory-modelling.R’: + Error: ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + ... + Error: argument is of length zero + Execution halted + + ‘exploratory-modelling.Rmd’ using ‘UTF-8’... failed + ‘finding-features.Rmd’ using ‘UTF-8’... failed + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK + ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK + ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed + ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown + + Quitting from lines 47-56 [use-gg-highlight] (exploratory-modelling.Rmd) + Error: processing vignette 'exploratory-modelling.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + aes_param_name]])`: + ! 'length = 2' in coercion to 'logical(1)' + --- failed re-building ‘exploratory-modelling.Rmd’ + + --- re-building ‘finding-features.Rmd’ using rmarkdown + ``` + +# calibrationband + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/marius-cp/calibrationband +* Source code: https://github.com/cran/calibrationband +* Date/Publication: 2022-08-09 14:40:02 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "calibrationband")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘calibrationband-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.calibrationband + > ### Title: Plotting monotone confidence bands + > ### Aliases: plot.calibrationband autoplot.calibrationband + > ### autolayer.calibrationband + > + > ### ** Examples + > + ... + > p <- function(x,s){p = 1/(1+((1/x*(1-x))^(s+1)));return(p)} + > dat <- data.frame(pr=x, y=rbinom(n,1,p(x,s))) + > + > cb <- calibration_bands(x=dat$pr, y=dat$y,alpha=0.05, method="round", digits =3) + > + > #simple plotting + > plot(cb) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# cartograflow + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/fbahoken/cartogRaflow +* Source code: https://github.com/cran/cartograflow +* Date/Publication: 2023-10-17 22:40:21 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "cartograflow")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cartograflow-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flowgini + > ### Title: Analysis of flow concentration (Gini coefficient) + > ### Aliases: flowgini + > + > ### ** Examples + > + > library(cartograflow) + ... + ℹ Use `flowcum` instead. + Warning: Use of `x$linkcum` is discouraged. + ℹ Use `linkcum` instead. + Warning: Use of `x$flowcum` is discouraged. + ℹ Use `flowcum` instead. + Warning: Use of `x$flowcum` is discouraged. + ℹ Use `flowcum` instead. + Error in pm[[2]] : subscript out of bounds + Calls: flowgini ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# cases + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/maxwestphal/cases +* Source code: https://github.com/cran/cases +* Date/Publication: 2023-05-18 08:30:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "cases")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example_wdbc.Rmd’ + ... + 13 TRUE FALSE + 14 FALSE FALSE + 15 FALSE FALSE + + + > visualize(results_bm) + + ... + + regu = TRU .... [TRUNCATED] + + > visualize(results_comp) + + When sourcing ‘package_overview.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘example_wdbc.Rmd’ using ‘UTF-8’... failed + ‘package_overview.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘example_wdbc.Rmd’ using rmarkdown + data_wdbc package:cases R Documentation + + _B_r_e_a_s_t _C_a_n_c_e_r _W_i_s_c_o_n_s_i_n (_D_i_a_g_n_o_s_t_i_c) _D_a_t_a _S_e_t + + _D_e_s_c_r_i_p_t_i_o_n: + + Dataset documentation can be found at the source website and + references below. + ... + Quitting from lines 160-168 [viz_comp] (package_overview.Rmd) + Error: processing vignette 'package_overview.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘package_overview.Rmd’ + + SUMMARY: processing the following files failed: + ‘example_wdbc.Rmd’ ‘package_overview.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cats + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/cats +* Date/Publication: 2022-03-11 10:20:07 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "cats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: trial_ocs + > ### Title: Calculates the operating characteristics of the cohort trial + > ### Aliases: trial_ocs + > + > ### ** Examples + > + > + ... + + safety_prob = safety_prob, Bayes_Sup1 = Bayes_Sup1, Bayes_Sup2 = Bayes_Sup2, + + cohort_offset = cohort_offset, sr_first_pos = sr_first_pos, + + missing_prob = missing_prob, cohort_fixed = cohort_fixed, accrual_type = accrual_type, + + accrual_param = accrual_param, hist_lag = hist_lag, analysis_times = analysis_times, + + time_trend = time_trend, cohorts_start = cohorts_start, cohorts_sim = cohorts_sim, + + iter = 2, coresnum = 1, save = FALSE, ret_list = TRUE, plot_ocs = TRUE + + ) + Error in pm[[2]] : subscript out of bounds + Calls: trial_ocs -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘epitools’ ‘forcats’ ‘purrr’ + All declared Imports should be used. + ``` + +# ceterisParibus + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/pbiecek/ceterisParibus +* Source code: https://github.com/cran/ceterisParibus +* Date/Publication: 2020-03-28 03:10:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "ceterisParibus")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ceterisParibus) + Loading required package: ggplot2 + Loading required package: gower + > + > test_check("ceterisParibus") + Welcome to DALEX (version: 2.4.3). + ... + 5. └─ceterisParibus:::plot_interactive.what_if_explainer(wi_rf_all) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘knitr’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# cfda + +
+ +* Version: 0.11.0 +* GitHub: https://github.com/modal-inria/cfda +* Source code: https://github.com/cran/cfda +* Date/Publication: 2023-10-07 15:50:05 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "cfda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cfda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute_duration + > ### Title: Compute duration of individuals + > ### Aliases: compute_duration + > + > ### ** Examples + > + > # Simulate the Jukes-Cantor model of nucleotide replacement + ... + > d_JK <- generate_Markov(n = 10, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10) + > + > + > # compute duration of each individual + > duration <- compute_duration(d_JK) + > + > hist(duration) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: hist ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cfda) + Loading required package: fda + Loading required package: splines + Loading required package: fds + Loading required package: rainbow + Loading required package: MASS + ... + 7. └─cfda:::hist.njump(njump) + 8. └─ggplot2:::`+.gg`(...) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 1 | SKIP 12 | PASS 351 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cfda.Rmd’ + ... + + > head(nJump) + 1 2 3 4 5 6 + 17 9 3 13 10 13 + + > hist(nJump) + + When sourcing ‘cfda.R’: + Error: argument is of length zero + Execution halted + + ‘cfda.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cfda.Rmd’ using rmarkdown + ``` + +# cheem + +
+ +* Version: 0.4.0.0 +* GitHub: https://github.com/nspyrison/cheem +* Source code: https://github.com/cran/cheem +* Date/Publication: 2023-11-08 21:30:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "cheem")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cheem) + -------------------------------------------------------- + cheem --- version 0.4.0.0 + Please share bugs, suggestions, and feature requests at: + https://github.com/nspyrison/cheem/issues/ + -------------------------------------------------------- + ... + 13. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) + 14. │ │ └─base::stopifnot(is.list(x), is.list(val)) + 15. │ └─x %||% list() + 16. ├─plotly::ggplotly(...) + 17. └─plotly:::ggplotly.ggplot(...) + 18. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started-with-cheem.Rmd’ + ... + + > knitr::opts_chunk$set(echo = TRUE, include = TRUE, + + results = "show", eval = FALSE, message = FALSE, warning = FALSE, + + error = FALSE, co .... [TRUNCATED] + + > knitr::include_graphics("../inst/shiny_apps/cheem/www/lime_nonlinear.png") + + When sourcing ‘getting-started-with-cheem.R’: + Error: Cannot find the file(s): "../inst/shiny_apps/cheem/www/lime_nonlinear.png" + Execution halted + + ‘getting-started-with-cheem.Rmd’ using ‘UTF-8’... failed + ``` + +# chillR + +
+ +* Version: 0.75 +* GitHub: NA +* Source code: https://github.com/cran/chillR +* Date/Publication: 2023-11-27 22:20:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "chillR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chillR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_scenarios + > ### Title: Plot historic and future scenarios for climate-related metrics + > ### ('ggplot2' version) + > ### Aliases: plot_scenarios + > + > ### ** Examples + > + ... + > + > # Plot the climate scenarios + > + > plot_scenarios(climate_scenario_list, metric = 'Chill_Portions', + + add_historic = TRUE, size = 2, shape = 3, color = 'blue', + + outlier_shape = 12, historic_color = 'skyblue', + + group_by = c("Year", "Scenario")) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# chronicle + +
+ +* Version: 0.3 +* GitHub: NA +* Source code: https://github.com/cran/chronicle +* Date/Publication: 2021-06-25 05:00:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "chronicle")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chronicle-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_barplot + > ### Title: Create a bar plot from a data frame through ggplotly + > ### Aliases: make_barplot + > + > ### ** Examples + > + > make_barplot(dt = iris, bars = 'Species', value = 'Sepal.Length') + Error in pm[[2]] : subscript out of bounds + Calls: make_barplot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘chronicle.Rmd’ + ... + + filename = "quick_demo", title = "A quick chronicle demo", + + author = .... [TRUNCATED] + + Quitting from lines 34-46 [unnamed-chunk-3] (quick_demo.Rmd) + + When sourcing ‘chronicle.R’: + Error: ℹ In index: 1. + Caused by error in `pm[[2]]`: + ! subscript out of bounds + Execution halted + + ‘chronicle.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘chronicle.Rmd’ using rmarkdown + + Quitting from lines 38-67 [unnamed-chunk-3] (chronicle.Rmd) + Error: processing vignette 'chronicle.Rmd' failed with diagnostics: + ℹ In index: 1. + Caused by error in `pm[[2]]`: + ! subscript out of bounds + --- failed re-building ‘chronicle.Rmd’ + + SUMMARY: processing the following file failed: + ‘chronicle.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’ + All declared Imports should be used. + ``` + +# CINNA + +
+ +* Version: 1.2.2 +* GitHub: NA +* Source code: https://github.com/cran/CINNA +* Date/Publication: 2023-08-08 16:40:02 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "CINNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CINNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pca_centralities + > ### Title: PCA Centrality Measures + > ### Aliases: pca_centralities + > + > ### ** Examples + > + > # Create a data frame with multiple observations + ... + 13. │ └─e1 %+% e2 + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CINNA.Rmd’ + ... + > calc_cent <- calculate_centralities(zachary, include = pr_cent[1:10]) + + > pca_centralities(calc_cent) + + When sourcing ‘CINNA.R’: + Error: ℹ In index: 1. + ℹ With name: contrib. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘CINNA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CINNA.Rmd’ using rmarkdown + + Quitting from lines 231-234 [unnamed-chunk-11] (CINNA.Rmd) + Error: processing vignette 'CINNA.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: contrib. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘CINNA.Rmd’ + + SUMMARY: processing the following file failed: + ‘CINNA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘utils’ + All declared Imports should be used. + ``` + +# circhelp + +
+ +* Version: 1.1 +* GitHub: https://github.com/achetverikov/circhelp +* Source code: https://github.com/cran/circhelp +* Date/Publication: 2024-07-04 17:10:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "circhelp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘circhelp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: remove_cardinal_biases + > ### Title: Remove cardinal biases + > ### Aliases: remove_cardinal_biases + > + > ### ** Examples + > + > + > # Data in orientation domain from Pascucci et al. (2019, PLOS Bio), + > # https://doi.org/10.5281/zenodo.2544946 + > + > ex_data <- Pascucci_et_al_2019_data[observer == 4, ] + > remove_cardinal_biases(ex_data$err, ex_data$orientation, plots = "show") + Error in as.unit(value) : object is not coercible to a unit + Calls: remove_cardinal_biases ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cardinal_biases.Rmd’ + ... + + 90)) + .... [TRUNCATED] + + > ex_subj_data <- data[observer == 4, ] + + > res <- remove_cardinal_biases(ex_subj_data$err, ex_subj_data$orientation, + + plots = "show") + + When sourcing ‘cardinal_biases.R’: + Error: object is not coercible to a unit + Execution halted + + ‘cardinal_biases.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cardinal_biases.Rmd’ using rmarkdown + ``` + +# clifro + +
+ +* Version: 3.2-5 +* GitHub: https://github.com/ropensci/clifro +* Source code: https://github.com/cran/clifro +* Date/Publication: 2021-05-24 05:50:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "clifro")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > library(clifro) + > + > test_check("clifro") + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] + + ... + • On CRAN (4): 'test-cf_find_station.R:4:3', 'test-cf_last_query.R:4:3', + 'test-cf_query.R:4:3', 'test-cf_station.R:4:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-windrose.R:15:3'): windrose ────────────────────────────────── + tt$labels inherits from `'NULL'` not `'character'`. + + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# clinDataReview + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/openanalytics/clinDataReview +* Source code: https://github.com/cran/clinDataReview +* Date/Publication: 2024-06-18 09:10:05 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "clinDataReview")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clinDataReview-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatterplotClinData + > ### Title: Scatterplot of variables of interest for clinical data + > ### visualization. + > ### Aliases: scatterplotClinData + > + > ### ** Examples + > + ... + + data = dataPlot, + + xVar = "ADY", + + yVar = "LBSTRESN", + + aesPointVar = list(color = "TRTP", fill = "TRTP"), + + aesLineVar = list(group = "USUBJID", color = "TRTP"), + + labelVars = labelVars + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatterplotClinData ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(clinDataReview) + > + > test_check("clinDataReview") + adding: report.html (deflated 63%) + adding: report_dependencies169f5c7b66d/ (stored 0%) + adding: report_dependencies169f5c7b66d/file169f105f2e2e.html (deflated 8%) + ... + 11. ├─base::withCallingHandlers(...) + 12. └─ggplot2:::`+.gg`(gg, do.call(layerFunction, argsGeom)) + 13. └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. ├─ggplot2::ggplot_add(object, p, objectname) + 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 35 | WARN 0 | SKIP 31 | PASS 453 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘clinDataReview-dataPreprocessing.Rmd’ using rmarkdown + --- finished re-building ‘clinDataReview-dataPreprocessing.Rmd’ + + --- re-building ‘clinDataReview-dataVisualization.Rmd’ using rmarkdown + + Quitting from lines 167-208 [timeProfiles] (clinDataReview-dataVisualization.Rmd) + Error: processing vignette 'clinDataReview-dataVisualization.Rmd' failed with diagnostics: + argument is of length zero + ... + --- failed re-building ‘clinDataReview-dataVisualization.Rmd’ + + --- re-building ‘clinDataReview-reporting.Rmd’ using rmarkdown + --- finished re-building ‘clinDataReview-reporting.Rmd’ + + SUMMARY: processing the following file failed: + ‘clinDataReview-dataVisualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + doc 4.3Mb + ``` + +# clinUtils + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/openanalytics/clinUtils +* Source code: https://github.com/cran/clinUtils +* Date/Publication: 2024-05-17 14:50:06 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "clinUtils")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘clinUtils-vignette.Rmd’ + ... + + layout + + + > listPlotsInteractiveLB <- sapply(listPlotsLB, function(ggplot) ggplotly(ggplot) %>% + + partial_bundle(), simplify = FALSE) + + When sourcing ‘clinUtils-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘clinUtils-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘clinUtils-vignette.Rmd’ using rmarkdown + ``` + +## Newly fixed + +* checking running R code from vignettes ... WARNING + ``` + Errors in running code in vignettes: + when running code in ‘clinUtils-vignette.Rmd’ + ... + + + + + + Quitting from lines 2-4 [lab-hist-interactive1] + + When sourcing ‘clinUtils-vignette.R’: + Error: there is no package called 'webshot' + Execution halted + + ‘clinUtils-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.7Mb + sub-directories of 1Mb or more: + doc 6.5Mb + ``` + +# cloneRate + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/bdj34/cloneRate +* Source code: https://github.com/cran/cloneRate +* Date/Publication: 2023-09-22 15:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "cloneRate")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cloneRate-dataAnalysis.Rmd’ + ... + + > fitColor <- colorPal[6] + + > ggplot(PD9478_long, aes(x = Age, y = VAF)) + theme_bw() + + + coord_cartesian(xlim = c(min(x), max(x)), ylim = c(-0.01, + + 0.52), expand .... [TRUNCATED] + + When sourcing ‘cloneRate-dataAnalysis.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘cloneRate-dataAnalysis.Rmd’ using ‘UTF-8’... failed + ‘cloneRate-simulate.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cloneRate-dataAnalysis.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 47.4Mb + sub-directories of 1Mb or more: + doc 1.0Mb + libs 45.2Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# clustEff + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/clustEff +* Date/Publication: 2024-01-23 08:52:55 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "clustEff")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clustEff-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clustEff-package + > ### Title: Clusters of effects curves + > ### Aliases: clustEff-package + > ### Keywords: package + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +# ClustImpute + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/ClustImpute +* Date/Publication: 2021-05-31 07:40:11 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "ClustImpute")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Example_on_simulated_data.Rmd’ + ... + > dat4plot$true_clust_fct <- factor(true_clust) + + > p_base <- ggplot(dat4plot, aes(x = x, y = y, color = true_clust_fct)) + + + geom_point() + + > ggExtra::ggMarginal(p_base, groupColour = TRUE, groupFill = TRUE) + + When sourcing ‘Example_on_simulated_data.R’: + Error: argument is of length zero + Execution halted + + ‘Example_on_simulated_data.Rmd’ using ‘UTF-8’... failed + ‘description_of_algorithm.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Example_on_simulated_data.Rmd’ using rmarkdown + + Quitting from lines 49-53 [unnamed-chunk-3] (Example_on_simulated_data.Rmd) + Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Example_on_simulated_data.Rmd’ + + --- re-building ‘description_of_algorithm.Rnw’ using Sweave + Error: processing vignette 'description_of_algorithm.Rnw' failed with diagnostics: + ... + l.6 \usepackage + {Sweave}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘description_of_algorithm.Rnw’ + + SUMMARY: processing the following files failed: + ‘Example_on_simulated_data.Rmd’ ‘description_of_algorithm.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cmstatr + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/cmstatr/cmstatr +* Source code: https://github.com/cran/cmstatr +* Date/Publication: 2024-03-14 14:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "cmstatr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cmstatr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nested_data_plot + > ### Title: Create a plot of nested sources of variation + > ### Aliases: nested_data_plot + > + > ### ** Examples + > + > library(dplyr) + ... + + intersect, setdiff, setequal, union + + > carbon.fabric.2 %>% + + filter(test == "WT" & condition == "RTD") %>% + + nested_data_plot(strength, + + groups = c(batch, panel)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cmstatr) + > + > test_check("cmstatr") + Starting 2 test processes + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] + ... + 6. └─cmstatr:::draw_vert_lines_to_labels(g, elm_list, vline_args) + 7. └─ggplot2:::`+.gg`(...) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cmstatr_Graphing.Rmd’ + ... + + by = "condition") %>% inner_join(a_basis_pooled_results, + + by = "condition") .... [TRUNCATED] + + > carbon.fabric.2 %>% mutate(panel = as.character(panel)) %>% + + filter(test == "WT") %>% nested_data_plot(strength, groups = c(batch, + + pane .... [TRUNCATED] + + When sourcing ‘cmstatr_Graphing.R’: + Error: argument is of length zero + Execution halted + + ‘adktest.Rmd’ using ‘UTF-8’... OK + ‘cmstatr_Graphing.Rmd’ using ‘UTF-8’... failed + ‘cmstatr_Tutorial.Rmd’ using ‘UTF-8’... OK + ‘cmstatr_Validation.Rmd’ using ‘UTF-8’... OK + ‘hk_ext.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘adktest.Rmd’ using rmarkdown + --- finished re-building ‘adktest.Rmd’ + + --- re-building ‘cmstatr_Graphing.Rmd’ using rmarkdown + ``` + +# codaredistlm + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/tystan/codaredistlm +* Source code: https://github.com/cran/codaredistlm +* Date/Publication: 2022-12-22 19:50:06 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "codaredistlm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘codaredistlm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_delta_comp + > ### Title: Plot redistributed time-use predictions from compositional ilr + > ### multiple linear regression model fit + > ### Aliases: plot_delta_comp + > + > ### ** Examples + > + ... + | | x| + |:----|------:| + |0% | 1439.9| + |25% | 1440.0| + |50% | 1440.0| + |75% | 1440.0| + |100% | 1440.1| + --- + + --- + ``` + +# coefplot + +
+ +* Version: 1.2.8 +* GitHub: NA +* Source code: https://github.com/cran/coefplot +* Date/Publication: 2022-01-14 09:42:47 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "coefplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘coefplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: buildModelCI + > ### Title: buildModelCI + > ### Aliases: buildModelCI + > + > ### ** Examples + > + > + ... + cut.C 327.4816 model1 + cut.Q -574.8626 model1 + cut.L 1187.6004 model1 + carat 7843.1229 model1 + (Intercept) -2732.2382 model1 + > coefplot(model1) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# CohortPlat + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/CohortPlat +* Date/Publication: 2022-02-14 09:30:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "CohortPlat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CohortPlat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_trial + > ### Title: Plots the cohort trial study overview given stage data. + > ### Aliases: plot_trial + > + > ### ** Examples + > + > + ... + + stage_data = stage_data, cohort_random = cohort_random, cohorts_max = cohorts_max, + + sr_drugs_pos = sr_drugs_pos, target_rr = target_rr, sharing_type = sharing_type, + + safety_prob = safety_prob, Bayes_Sup = Bayes_Sup, prob_rr_transform = prob_rr_transform, + + cohort_offset = cohort_offset, Bayes_Fut = Bayes_Fut, sr_first_pos = sr_first_pos + + ) + > + > plot_trial(res_list, unit = "n") + Error in pm[[2]] : subscript out of bounds + Calls: plot_trial -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘my-vignette.Rmd’ + ... + + > set.seed(50) + + > ocs1 <- trial_ocs(n_int = n_int, n_fin = n_fin, rr_comb = rr_comb, + + rr_mono = rr_mono, rr_back = rr_back, rr_plac = rr_plac, + + rr_transfo .... [TRUNCATED] + + When sourcing ‘my-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘my-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘my-vignette.Rmd’ using rmarkdown + + Quitting from lines 1043-1073 [unnamed-chunk-20] (my-vignette.Rmd) + Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘my-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘my-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# complmrob + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/dakep/complmrob +* Source code: https://github.com/cran/complmrob +* Date/Publication: 2019-09-17 18:10:02 UTC +* Number of recursive dependencies: 31 + +Run `revdepcheck::cloud_details(, "complmrob")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘complmrob-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.complmrob + > ### Title: Diagnostic plots for the robust regression model with + > ### compositional covariates + > ### Aliases: plot.complmrob + > + > ### ** Examples + > + > data <- data.frame(lifeExp = state.x77[, "Life Exp"], USArrests[ , -3]) + > mUSArr <- complmrob(lifeExp ~ ., data = data) + > plot(mUSArr) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# conjoint + +
+ +* Version: 1.41 +* GitHub: NA +* Source code: https://github.com/cran/conjoint +* Date/Publication: 2018-07-26 13:00:03 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "conjoint")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘conjoint-Ex.R’ failed + The error most likely occurred in: + + > ### Name: caSegmentation + > ### Title: Function caSegmentation divides respondents on clusters + > ### Aliases: caSegmentation + > ### Keywords: multivariate + > + > ### ** Examples + > + ... + Available components: + + [1] "cluster" "centers" "totss" "withinss" "tot.withinss" + [6] "betweenss" "size" "iter" "ifault" + > util<-as.data.frame(segments$util) + > set.seed(123) + > ggplot2::autoplot(kmeans(util,3),data=util,label=TRUE,label.size=4,frame=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# conquestr + +
+ +* Version: 1.3.4 +* GitHub: NA +* Source code: https://github.com/cran/conquestr +* Date/Publication: 2024-07-24 06:00:01 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "conquestr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘plotting.Rmd’ + ... + > myRout <- ConQuestRout() + no rout file provided, loading the example rout file instead + + > myPlot <- plotRout(myRout) + + > myPlot + + ... + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘data-cleaning-functions-in-conquestr.Rmd’ using ‘UTF-8’... OK + ‘generateResponses.Rmd’ using ‘UTF-8’... OK + ‘intro-to-conquestr.Rmd’ using ‘UTF-8’... OK + ‘itanal-in-conquestr.Rmd’ using ‘UTF-8’... OK + ‘plotting.Rmd’ using ‘UTF-8’... failed + ‘responseProbs.Rmd’ using ‘UTF-8’... OK + ‘test_item_review_sheet_markdown.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘data-cleaning-functions-in-conquestr.Rmd’ using rmarkdown + --- finished re-building ‘data-cleaning-functions-in-conquestr.Rmd’ + + --- re-building ‘generateResponses.Rmd’ using rmarkdown + ``` + +# CoreMicrobiomeR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/CoreMicrobiomeR +* Date/Publication: 2024-04-03 20:03:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "CoreMicrobiomeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CoreMicrobiomeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: group_bar_plots + > ### Title: Grouped Bar Plots Based on Sample Size + > ### Aliases: group_bar_plots + > + > ### ** Examples + > + > #To run input data + ... + + top_percentage = 10 # Adjust the percentage as needed for core/non-core OTUs + + ) + Warning encountered during diversity analysis:you have empty rows: their dissimilarities may be + meaningless in method “bray” + > #To run grouped bar plot function + > plot_group_bar <- group_bar_plots(core_1$final_otu_table_bef_filter, + + core_1$final_otu_aft_filter, 10) + Error in pm[[2]] : subscript out of bounds + Calls: group_bar_plots -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# correlationfunnel + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/business-science/correlationfunnel +* Source code: https://github.com/cran/correlationfunnel +* Date/Publication: 2020-06-09 04:40:03 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + + ... + ▆ + 1. ├─correlationfunnel::plot_correlation_funnel(...) at test-plot_correlation_funnel.R:23:1 + 2. └─correlationfunnel:::plot_correlation_funnel.data.frame(...) + 3. ├─plotly::ggplotly(g, tooltip = "text") + 4. └─plotly:::ggplotly.ggplot(g, tooltip = "text") + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 17 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘utils’ + All declared Imports should be used. + ``` + +# corrViz + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/corrViz +* Date/Publication: 2023-06-30 11:40:07 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "corrViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘corrViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: animSolar + > ### Title: animSolar + > ### Aliases: animSolar + > + > ### ** Examples + > + > cm <- cor(mtcars) + ... + All aesthetics have length 1, but the data has 250 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Warning in geom_text(data = solar_system, aes(x = 0, y = 0, label = sun), : + All aesthetics have length 1, but the data has 250 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Error in pm[[2]] : subscript out of bounds + Calls: animSolar -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘corrViz.Rmd’ + ... + > library(corrViz) + + > cm <- cor(mtcars) + + > corrHeatmap(mat = cm, display = "all", reorder = TRUE, + + pal = colorRampPalette(c("darkblue", "white", "darkred"))(100)) + + When sourcing ‘corrViz.R’: + Error: subscript out of bounds + Execution halted + + ‘corrViz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘corrViz.Rmd’ using rmarkdown + + Quitting from lines 76-81 [heatmap] (corrViz.Rmd) + Error: processing vignette 'corrViz.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘corrViz.Rmd’ + + SUMMARY: processing the following file failed: + ‘corrViz.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.2Mb + sub-directories of 1Mb or more: + doc 6.7Mb + ``` + +# corx + +
+ +* Version: 1.0.7.2 +* GitHub: https://github.com/conig/corx +* Source code: https://github.com/cran/corx +* Date/Publication: 2023-06-16 04:10:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "corx")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(corx) + > + > test_check("corx") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] + Error: Test failures + Execution halted + ``` + +# cosinor2 + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/amutak/cosinor2 +* Source code: https://github.com/cran/cosinor2 +* Date/Publication: 2018-10-15 16:10:03 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "cosinor2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cosinor2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cosinor.PR + > ### Title: Percent Rhythm + > ### Aliases: cosinor.PR + > + > ### ** Examples + > + > fit.temperature<-cosinor.lm(Temperature~time(Time), period = 24, data = temperature_zg) + ... + 1 0.9838823 0.9680243 0 + > + > fit.november<-population.cosinor.lm(data = PANAS_november, time = PANAS_time, + + period = 7) + MESOR Amplitude Acrophase + 1 1.435419 0.2662682 -5.544496 + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: population.cosinor.lm ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cosinor2.Rmd’ + ... + Loading required package: cosinor + + > fit.panas.cosinor <- population.cosinor.lm(data = PANAS_november, + + time = PANAS_time, period = 7) + MESOR Amplitude Acrophase + 1 1.435419 0.2662682 -5.544496 + + When sourcing ‘cosinor2.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cosinor2.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cosinor2.Rmd’ using rmarkdown + + Quitting from lines 47-48 [unnamed-chunk-2] (cosinor2.Rmd) + Error: processing vignette 'cosinor2.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘cosinor2.Rmd’ + + SUMMARY: processing the following file failed: + ‘cosinor2.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# CoSMoS + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/TycheLab/CoSMoS +* Source code: https://github.com/cran/CoSMoS +* Date/Publication: 2021-05-29 23:20:08 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "CoSMoS")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette.Rmd’ + ... + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + + > precip_ggamma <- analyzeTS(TS = precip, season = "month", + + dist = "ggamma", acsID = "weibull", lag.max = 12) + + > reportTS(aTS = precip_ggamma, method = "dist") + theme_light() + + When sourcing ‘vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette.Rmd’ using rmarkdown + ``` + +# countfitteR + +
+ +* Version: 1.4 +* GitHub: https://github.com/BioGenies/countfitteR +* Source code: https://github.com/cran/countfitteR +* Date/Publication: 2020-09-30 21:30:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "countfitteR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(countfitteR) + > + > test_check("countfitteR") + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('testing.R:45:3'): plot_fit ──────────────────────────────────────── + p$labels[[1]] not equal to "x". + target is NULL, current is character + + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] + Error: Test failures + Execution halted + ``` + +# coursekata + +
+ +* Version: 0.18.0 +* GitHub: https://github.com/coursekata/coursekata-r +* Source code: https://github.com/cran/coursekata +* Date/Publication: 2024-08-16 20:20:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "coursekata")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘coursekata-Ex.R’ failed + The error most likely occurred in: + + > ### Name: middle + > ### Title: Find a percentage of a distribution + > ### Aliases: middle tails lower upper + > + > ### ** Examples + > + > + ... + > tails(1:10, .5) + [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE + > + > sampling_distribution <- do(1000) * mean(rnorm(100, 5, 10)) + > sampling_distribution %>% + + gf_histogram(~mean, data = sampling_distribution, fill = ~ middle(mean, .68)) %>% + + gf_refine(scale_fill_manual(values = c("blue", "coral"))) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(coursekata) + Loading required package: dslabs + Loading required package: fivethirtyeight + Some larger datasets need to be installed separately, like senators and + house_district_forecast. To install these, we recommend you install the + fivethirtyeightdata package by running: + ... + • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-color.svg + • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-facet.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-color.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-facet.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y.svg + • gf_model-visual/gf-violin-horizontal-mull-mod-y-on-x.svg + • gf_model-visual/gf-violin-mull-mod-y-on-x-2.svg + • gf_model-visual/gf-violin-null-mod-y-on-y.svg + Error: Test failures + Execution halted + ``` + +# covidcast + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/cmu-delphi/covidcast +* Source code: https://github.com/cran/covidcast +* Date/Publication: 2023-07-12 23:40:06 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "covidcast")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(covidcast) + We encourage COVIDcast API users to register on our mailing list: + https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api + We'll send announcements about new data sources, package updates, + server maintenance, and new features. + > + ... + • plot/default-county-choropleth.svg + • plot/default-hrr-choropleth-with-include.svg + • plot/default-msa-choropleth-with-include.svg + • plot/default-state-choropleth-with-include.svg + • plot/default-state-choropleth-with-range.svg + • plot/state-choropleth-with-no-metadata.svg + • plot/state-line-graph-with-range.svg + • plot/state-line-graph-with-stderrs.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘external-data.Rmd’ + ... + Warning: Metadata for signal mean and standard deviation not available; defaulting to observed mean and standard deviation to set plot range. + Warning in ggplot2::guide_colorbar(title = NULL, horizontal = TRUE, barheight = legend_height, : + Arguments in `...` must be used. + ✖ Problematic argument: + • horizontal = TRUE + ℹ Did you misspell an argument name? + + ... + Error: Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. + ℹ Message from server: + ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form + Execution halted + + ‘correlation-utils.Rmd’ using ‘UTF-8’... OK + ‘covidcast.Rmd’ using ‘UTF-8’... OK + ‘external-data.Rmd’ using ‘UTF-8’... failed + ‘multi-signals.Rmd’ using ‘UTF-8’... OK + ‘plotting-signals.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘correlation-utils.Rmd’ using rmarkdown + --- finished re-building ‘correlation-utils.Rmd’ + + --- re-building ‘covidcast.Rmd’ using rmarkdown + + Quitting from lines 38-45 [unnamed-chunk-1] (covidcast.Rmd) + Error: processing vignette 'covidcast.Rmd' failed with diagnostics: + Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. + ℹ Message from server: + ... + ℹ Message from server: + ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form + --- failed re-building ‘plotting-signals.Rmd’ + + SUMMARY: processing the following files failed: + ‘covidcast.Rmd’ ‘external-data.Rmd’ ‘multi-signals.Rmd’ + ‘plotting-signals.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 20 marked UTF-8 strings + ``` + +# Coxmos + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/BiostatOmics/Coxmos +* Source code: https://github.com/cran/Coxmos +* Date/Publication: 2024-03-25 20:32:38 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::cloud_details(, "Coxmos")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Coxmos-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getAutoKM + > ### Title: getAutoKM + > ### Aliases: getAutoKM + > + > ### ** Examples + > + > data("X_proteomic") + ... + > X_train <- X_proteomic[index_train,1:50] + > Y_train <- Y_proteomic[index_train,] + > X_test <- X_proteomic[-index_train,1:50] + > Y_test <- Y_proteomic[-index_train,] + > splsicox.model <- splsicox(X_train, Y_train, n.comp = 2, penalty = 0.5, x.center = TRUE, + + x.scale = TRUE) + > getAutoKM(type = "LP", model = splsicox.model) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: getAutoKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Coxmos-MO-pipeline.Rmd’ + ... + + $proteomic + + + > LST_KM_RES_LP <- getAutoKM(type = "LP", model = lst_models$`SB.sPLS-DRCOX`, + + comp = 1:4, top = 10, ori_data = T, BREAKTIME = NULL, only_sig = .... [TRUNCATED] + + ... + Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found + + > X <- X_proteomic + + When sourcing ‘Coxmos-pipeline.R’: + Error: object 'X_proteomic' not found + Execution halted + + ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... failed + ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.5Mb + doc 2.9Mb + ``` + +# cpr + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/dewittpe/cpr +* Source code: https://github.com/cran/cpr +* Date/Publication: 2024-02-15 15:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "cpr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cpr.Rmd’ + ... + Warning: Removed 25 rows containing missing values or values outside the scale range + (`geom_rug()`). + Warning: Removed 26 rows containing missing values or values outside the scale range + (`geom_rug()`). + Warning: Removed 38 rows containing missing values or values outside the scale range + (`geom_rug()`). + + When sourcing ‘cpr.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cnr.Rmd’ using ‘UTF-8’... OK + ‘cpr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cnr.Rmd’ using rmarkdown + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘test-bsplineD.R’ + Running ‘test-bsplines.R’ + Running ‘test-btensor.R’ + Running ‘test-build_tensor.R’ + Running ‘test-cn.R’ + Running ‘test-cnr.R’ + Running ‘test-coef_vcov.R’ + Running the tests in ‘tests/test-coef_vcov.R’ failed. + Complete output: + > # Tests for extracting coefficients and vcov matrix from regression fits + ... + + stopifnot(identical(names(COEF_VCOV), c("theta", "coef", "vcov_theta", "vcov"))) + + stopifnot(identical(COEF_VCOV$theta, numeric(0))) + + stopifnot(identical(COEF_VCOV$coef, fixef(fit))) + + stopifnot(identical(COEF_VCOV$vcov_theta, matrix(0)[FALSE, FALSE])) + + stopifnot(identical(COEF_VCOV$vcov, as.matrix(vcov(fit)))) + + }) + Error in initializePtr() : + function 'cholmod_factor_ldetA' not provided by package 'Matrix' + Calls: with ... initialize -> -> initializePtr -> .Call + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 4.1Mb + ``` + +# cpsvote + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Reed-EVIC/cpsvote +* Source code: https://github.com/cran/cpsvote +* Date/Publication: 2020-11-05 16:00:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "cpsvote")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘voting.Rmd’ + ... + + .... [TRUNCATED] + + > library(usmap) + + > cps16 %>% as_survey_design(weights = turnout_weight) %>% + + mutate(state = STATE) %>% group_by(state) %>% summarize(turnout = survey_mean(hurach .... [TRUNCATED] + + When sourcing ‘voting.R’: + Error: argument is of length zero + Execution halted + + ‘add-variables.Rmd’ using ‘UTF-8’... OK + ‘background.Rmd’ using ‘UTF-8’... OK + ‘basics.Rmd’ using ‘UTF-8’... OK + ‘voting.Rmd’ using ‘UTF-8’... failed + ``` + +# crimeutils + +
+ +* Version: 0.5.1 +* GitHub: https://github.com/jacobkap/crimeutils +* Source code: https://github.com/cran/crimeutils +* Date/Publication: 2022-12-07 15:10:07 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "crimeutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crimeutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scale_linetype_crim + > ### Title: A set of linetypes + > ### Aliases: scale_linetype_crim + > + > ### ** Examples + > + > ggplot2::ggplot(mtcars, ggplot2::aes(x = mpg, y = hp, linetype = as.character(cyl))) + + + ggplot2::geom_line(size = 1) + + + scale_linetype_crim() + + + theme_crim() + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# crmPack + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/openpharma/crmPack +* Source code: https://github.com/cran/crmPack +* Date/Publication: 2024-06-26 15:00:14 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "crmPack")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crmPack-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DataMixture-class + > ### Title: Class for the data with mixture sharing + > ### Aliases: DataMixture-class .DataMixture + > ### Keywords: classes + > + > ### ** Examples + > + ... + + refDose = 50) + > + > nodata <- Data(doseGrid=doseGrid) + > + > priorSamples <- mcmc(nodata, model, options) + > plot(priorSamples, model, nodata) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example.Rnw’ + ... + [1] -5.070681 + + > newDLTmodel@phi2 + [1] 1.125107 + + > print(plot(samples, model, data)) + + When sourcing ‘example.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘guidelines.Rmd’ using ‘UTF-8’... OK + ‘example.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘guidelines.Rmd’ using rmarkdown + --- finished re-building ‘guidelines.Rmd’ + + --- re-building ‘example.Rnw’ using Sweave + Loading required package: ggplot2 + Registered S3 method overwritten by 'crmPack': + method from + print.gtable gtable + Type crmPackHelp() to open help browser + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building ‘example.Rnw’ + + SUMMARY: processing the following file failed: + ‘example.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# crosshap + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/jacobimarsh/crosshap +* Source code: https://github.com/cran/crosshap +* Date/Publication: 2024-03-31 15:40:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "crosshap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crosshap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: build_bot_halfeyeplot + > ### Title: Bot hap-pheno raincloud plot + > ### Aliases: build_bot_halfeyeplot + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# ctrialsgov + +
+ +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/ctrialsgov +* Date/Publication: 2021-10-18 16:00:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ctrialsgov) + > + > test_check("ctrialsgov") + [NCT04553939] ible Local Advanved |Bladder| Cancer + [NCT03517995] of Sulforaphane in |Bladder| Cancer Chemoprevent + [NCT04210479] Comparison of |Bladder| Filling vs. Non-Fil + ... + ▆ + 1. ├─ctrialsgov::ctgov_to_plotly(p) at test-plot.R:12:3 + 2. └─ctrialsgov:::ctgov_to_plotly.ctgov_bar_plot(p) + 3. ├─plotly::ggplotly(p, tooltip = "text") + 4. └─plotly:::ggplotly.ggplot(p, tooltip = "text") + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 43 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1350 marked UTF-8 strings + ``` + +# cubble + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/huizezhang-sherry/cubble +* Source code: https://github.com/cran/cubble +* Date/Publication: 2024-08-27 15:20:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "cubble")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cb5match.Rmd’ + ... + > p2 <- ggplot(res_tm_long, aes(x = date, y = matched, + + group = type, color = type)) + geom_line() + facet_wrap(vars(group)) + + + scale_colo .... [TRUNCATED] + + > (p1 | p2) + patchwork::plot_layout(guides = "collect") + + + plot_annotation(tag_levels = "a") & theme(legend.position = "bottom") + + ... + Error: subscript out of bounds + Execution halted + + ‘cb1class.Rmd’ using ‘UTF-8’... OK + ‘cb2create.Rmd’ using ‘UTF-8’... OK + ‘cb3tsibblesf.Rmd’ using ‘UTF-8’... OK + ‘cb4glyph.Rmd’ using ‘UTF-8’... OK + ‘cb5match.Rmd’ using ‘UTF-8’... failed + ‘cb6interactive.Rmd’ using ‘UTF-8’... failed + ‘cb7misc.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cb1class.Rmd’ using rmarkdown + --- finished re-building ‘cb1class.Rmd’ + + --- re-building ‘cb2create.Rmd’ using rmarkdown + --- finished re-building ‘cb2create.Rmd’ + + --- re-building ‘cb3tsibblesf.Rmd’ using rmarkdown + --- finished re-building ‘cb3tsibblesf.Rmd’ + + --- re-building ‘cb4glyph.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + data 3.0Mb + doc 1.4Mb + ``` + +# curtailment + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/martinlaw/curtailment +* Source code: https://github.com/cran/curtailment +* Date/Publication: 2023-10-25 15:50:04 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "curtailment")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘curtailment-Ex.R’ failed + The error most likely occurred in: + + > ### Name: drawDiagramGeneric + > ### Title: drawDiagramGeneric + > ### Aliases: drawDiagramGeneric + > + > ### ** Examples + > + > go <- cbind(6:8, rep(8,3)) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +# dabestr + +
+ +* Version: 2023.9.12 +* GitHub: https://github.com/ACCLAB/dabestr +* Source code: https://github.com/cran/dabestr +* Date/Publication: 2023-10-13 11:50:06 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "dabestr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tutorial_deltadelta.Rmd’ + ... + > paired_delta2.mean_diff <- load(df, x = Treatment, + + y = Measurement, experiment = Genotype, colour = Rep, delta2 = TRUE, + + idx = list(c(" ..." ... [TRUNCATED] + + > dabest_plot(paired_delta2.mean_diff, raw_marker_size = 0.5, + + raw_marker_alpha = 0.3) + + ... + Error: argument is of length zero + Execution halted + + ‘datasets.Rmd’ using ‘UTF-8’... OK + ‘plot_aesthetics.Rmd’ using ‘UTF-8’... OK + ‘tutorial_basics.Rmd’ using ‘UTF-8’... OK + ‘tutorial_deltadelta.Rmd’ using ‘UTF-8’... failed + ‘tutorial_minimeta.Rmd’ using ‘UTF-8’... failed + ‘tutorial_proportion_plots.Rmd’ using ‘UTF-8’... OK + ‘tutorial_repeated_measures.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘datasets.Rmd’ using rmarkdown + --- finished re-building ‘datasets.Rmd’ + + --- re-building ‘plot_aesthetics.Rmd’ using rmarkdown + ``` + +# DAISIEprep + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/joshwlambert/DAISIEprep +* Source code: https://github.com/cran/DAISIEprep +* Date/Publication: 2024-04-02 11:30:06 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(DAISIEprep) + > + > test_check("DAISIEprep") + [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + + ══ Skipped tests (14) ══════════════════════════════════════════════════════════ + ... + ── Failure ('test-plot_phylod.R:8:3'): plot_phylod runs silent without error ─── + `plot_phylod(phylod = phylod, node_pies = FALSE)` produced warnings. + ── Failure ('test-plot_phylod.R:13:3'): plot_phylod runs silent without error ── + `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings. + ── Failure ('test-plot_phylod.R:18:3'): plot_phylod runs silent without error ── + `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings. + + [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + Error: Test failures + Execution halted + ``` + +# dbmss + +
+ +* Version: 2.9-2 +* GitHub: https://github.com/EricMarcon/dbmss +* Source code: https://github.com/cran/dbmss +* Date/Publication: 2024-08-24 11:00:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "dbmss")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dbmss-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DEnvelope + > ### Title: Estimation of the confidence envelope of the D function under + > ### its null hypothesis + > ### Aliases: DEnvelope + > + > ### ** Examples + > + ... + > r <- 0:30 + > NumberOfSimulations <- 20 + > Alpha <- .05 + > # Plot the envelope (after normalization by pi.r^2) + > autoplot(DEnvelope(X, r, NumberOfSimulations, Alpha, + + "V. Americana", "Q. Rosea", Intertype = TRUE), ./(pi*r^2) ~ r) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dbmss.Rmd’ + ... + + > autoplot(paracou16, labelSize = expression("Basal area (" ~ + + cm^2 ~ ")"), labelColor = "Species") + + > autoplot(Mhat(paracou16, ReferenceType = "V. Americana", + + NeighborType = "Q. Rosea"), main = "") + + When sourcing ‘dbmss.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘dbmss.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dbmss.Rmd’ using rmarkdown + ``` + +# deeptime + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/willgearty/deeptime +* Source code: https://github.com/cran/deeptime +* Date/Publication: 2024-08-19 07:00:43 UTC +* Number of recursive dependencies: 197 + +Run `revdepcheck::cloud_details(, "deeptime")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(deeptime) + > + > test_check("deeptime") + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + ... + • patterns/geo-pattern2-new.svg + • patterns/scale-fill-geopattern-labels-new.svg + • patterns/scale-fill-geopattern-limits-new.svg + • patterns/scale-fill-geopattern-na-new.svg + • patterns/scale-fill-geopattern-na2-new.svg + • points_range/geom-points-range-aes-new.svg + • points_range/geom-points-range-bg-new.svg + • points_range/geom-points-range-h-new.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘coord_geo.Rmd’ + ... + + y = n)) + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + + + coord_geo(xlim = .... [TRUNCATED] + + > ggplot(coral_div) + geom_line(aes(x = stage_age, y = n)) + + + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + coord_geo(dat = "periods", + + .... [TRUNCATED] + + ... + Error: argument is of length zero + Execution halted + + ‘coord.Rmd’ using ‘UTF-8’... OK + ‘coord_geo.Rmd’ using ‘UTF-8’... failed + ‘geo.Rmd’ using ‘UTF-8’... OK + ‘ggarrange2.Rmd’ using ‘UTF-8’... OK + ‘phylogenies.Rmd’ using ‘UTF-8’... OK + ‘time.Rmd’ using ‘UTF-8’... failed + ‘traits.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘coord.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + R 2.8Mb + doc 1.8Mb + help 1.1Mb + ``` + +# descriptio + +
+ +* Version: 1.3 +* GitHub: https://github.com/nicolas-robette/descriptio +* Source code: https://github.com/cran/descriptio +* Date/Publication: 2024-03-07 11:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "descriptio")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘descriptio-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggassoc_crosstab + > ### Title: Proportional area plot + > ### Aliases: ggassoc_crosstab + > ### Keywords: multivariate aplot + > + > ### ** Examples + > + > data(Movies) + > ggassoc_crosstab(data=Movies, mapping=ggplot2::aes(Genre, Country)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggassoc_crosstab ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘FactoMineR’, ‘vcd’ + ``` + +# directlabels + +
+ +* Version: 2024.1.21 +* GitHub: https://github.com/tdhock/directlabels +* Source code: https://github.com/cran/directlabels +* Date/Publication: 2024-01-24 19:20:07 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "directlabels")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘examples.Rmd’ + ... + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + + When sourcing ‘examples.R’: + Error: Problem while computing stat. + ℹ Error occurred in the 3rd layer. + Caused by error in `get()`: + ! object 'last.qp' of mode 'function' was not found + Execution halted + + ‘examples.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘examples.Rmd’ using knitr + ``` + +# disto + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/talegari/disto +* Source code: https://github.com/cran/disto +* Date/Publication: 2018-08-02 12:50:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "disto")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘disto-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.disto + > ### Title: Plot a disto object + > ### Aliases: plot.disto + > + > ### ** Examples + > + > temp <- stats::dist(iris[,1:4]) + ... + > dio <- disto(objectname = "temp") + > plot(dio, type = "heatmap") + > plot(dio, type = "dendrogram") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the factoextra package. + Please report the issue at . + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette_disto.Rmd’ + ... + + > plot(dio, type = "dendrogram") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the factoextra package. + Please report the issue at . + + When sourcing ‘vignette_disto.R’: + Error: argument is of length zero + Execution halted + + ‘vignette_disto.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette_disto.Rmd’ using rmarkdown + + Quitting from lines 42-72 [unnamed-chunk-1] (vignette_disto.Rmd) + Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘vignette_disto.Rmd’ + + SUMMARY: processing the following file failed: + ‘vignette_disto.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘proxy’ + All declared Imports should be used. + ``` + +# distributional + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/mitchelloharawild/distributional +* Source code: https://github.com/cran/distributional +* Date/Publication: 2024-02-07 13:30:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "distributional")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘distributional-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dist_truncated + > ### Title: Truncate a distribution + > ### Aliases: dist_truncated + > + > ### ** Examples + > + > dist <- dist_truncated(dist_normal(2,1), lower = 0) + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# dittoViz + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/dtm2451/dittoViz +* Source code: https://github.com/cran/dittoViz +* Date/Publication: 2024-02-02 00:00:12 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "dittoViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dittoViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: barPlot + > ### Title: Outputs a stacked bar plot to show the percent composition of + > ### samples, groups, clusters, or other groupings + > ### Aliases: barPlot + > + > ### ** Examples + > + ... + 15 3 D 12 32 0.3750000 + 16 4 D 8 32 0.2500000 + > # through hovering the cursor over the relevant parts of the plot + > if (requireNamespace("plotly", quietly = TRUE)) { + + barPlot(example_df, "clustering", group.by = "groups", + + do.hover = TRUE) + + } + Error in pm[[2]] : subscript out of bounds + Calls: barPlot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dittoViz) + Loading required package: ggplot2 + > test_check("dittoViz") + [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 6. └─dittoViz:::.yPlot_add_data_y_direction(...) + 7. └─ggplot2:::`+.gg`(p, do.call(geom_boxplot, boxplot.args)) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] + Error: Test failures + Execution halted + ``` + +# dotwhisker + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/fsolt/dotwhisker +* Source code: https://github.com/cran/dotwhisker +* Date/Publication: 2024-06-07 12:20:06 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "dotwhisker")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dotwhisker-Ex.R’ failed + The error most likely occurred in: + + > ### Name: small_multiple + > ### Title: Generate a 'Small Multiple' Plot of Regression Results + > ### Aliases: small_multiple + > + > ### ** Examples + > + > library(broom) + ... + + m[[i]] <- update(m[[i-1]], paste(". ~ . +", ordered_vars[i])) + + m123456_df <- rbind(m123456_df, m[[i]] %>% tidy %>% by_2sd(mtcars) %>% + + mutate(model = paste("Model", i))) + + } + > + > # Generate a 'small multiple' plot + > small_multiple(m123456_df) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: small_multiple ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dotwhisker-vignette.Rmd’ + ... + + wt = "Weight", cyl = "Cylinders", disp = "Displacement", + + .... [TRUNCATED] + + > small_multiple(m123456_df) + theme_bw(base_size = 4) + + + ylab("Coefficient Estimate") + geom_hline(yintercept = 0, + + colour = "grey60", li .... [TRUNCATED] + + ... + + > small_multiple(results_df, show_stats = FALSE) + scale_x_discrete(limits = model_names) + + + theme_bw() + ylab("Coefficient Estimate") + geom_hl .... [TRUNCATED] + + When sourcing ‘kl2007_examples.R’: + Error: argument is of length zero + Execution halted + + ‘dotwhisker-vignette.Rmd’ using ‘UTF-8’... failed + ‘kl2007_examples.Rmd’ using ‘ASCII’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown + ``` + +# DRomics + +
+ +* Version: 2.5-2 +* GitHub: https://github.com/aursiber/DRomics +* Source code: https://github.com/cran/DRomics +* Date/Publication: 2024-01-31 09:30:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "DRomics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DRomics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PCAdataplot + > ### Title: Performs and plots the results of a PCA on omic data + > ### Aliases: PCAdataplot + > + > ### ** Examples + > + > + ... + Number of items: 100 + Identifiers of the first 20 items: + [1] "1" "2" "3" "4" "5.1" "6.1" "7.1" "8.1" "9.1" "10.1" + [11] "11.1" "12.1" "13.1" "14.1" "15" "16.1" "17.1" "18.1" "19.1" "20.1" + Data were normalized between arrays using the following method: cyclicloess + > plot(o) + > PCAdataplot(o) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PCAdataplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘DRomics_vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘DRomics_vignette.Rmd’ + ... + [16] "ENSDARG00000100660" "ENSDARG00000113107" "ENSDARG00000099787" + [19] "ENSDARG00000112451" "ENSDARG00000070546" + Data were normalized with respect to library size and tranformed using + the following method: rlog + + > PCAdataplot(o, batch = zebraf$batch) + theme_bw() + + When sourcing ‘DRomics_vignette.R’: + Error: argument is of length zero + Execution halted + + ‘DRomics_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + doc 2.9Mb + ``` + +# dtwclust + +
+ +* Version: 6.0.0 +* GitHub: https://github.com/asardaes/dtwclust +* Source code: https://github.com/cran/dtwclust +* Date/Publication: 2024-07-23 08:50:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "dtwclust")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(dtwclust) + Loading required package: proxy + + Attaching package: 'proxy' + + The following objects are masked from 'package:stats': + + ... + 7. └─dtwclust (local) .local(x, y = y, ...) + 8. └─ggplot2:::`+.gg`(gg, do_call(ggrepel::geom_label_repel, labels)) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 15 | PASS 1930 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘parallelization-considerations.Rmd’ using rmarkdown_notangle + --- finished re-building ‘parallelization-considerations.Rmd’ + + --- re-building ‘timing-experiments.Rmd’ using rmarkdown_notangle + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.5Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 2.1Mb + libs 11.1Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# duke + +
+ +* Version: 0.0.3 +* GitHub: https://github.com/aidangildea/duke +* Source code: https://github.com/cran/duke +* Date/Publication: 2023-12-15 21:50:16 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "duke")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 2. │ └─testthat:::expect_condition_matching(...) + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─testthat::expect_equal(ggplot2::layer_data(p3)$fill[9], "#B5B5B5") + + [ FAIL 1 | WARN 9 | SKIP 0 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +# easysurv + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/Maple-Health-Group/easysurv +* Source code: https://github.com/cran/easysurv +* Date/Publication: 2024-06-21 10:30:06 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::cloud_details(, "easysurv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘easysurv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_km + > ### Title: Generate Kaplan-Meier estimates + > ### Aliases: get_km + > + > ### ** Examples + > + > km_results <- get_km( + ... + Poor Poor 228 145 3.101736 0.1772520 2.183562 1.978082 2.619178 + Median follow-up + Good 4.452055 + Medium 4.712329 + Poor 4.115068 + + Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = "{n.risk}", : + argument "risktable_height" is missing, with no default + Calls: ... ggsurvfit_build -> -> .construct_risktable + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘easysurv.Rmd’ + ... + Median follow-up + Tab+Vis 2.217659 + Tab->Vis 2.220397 + Tab 2.308008 + Vis 2.198494 + + + When sourcing ‘easysurv.R’: + Error: argument "risktable_height" is missing, with no default + Execution halted + + ‘easysurv.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘easysurv.Rmd’ using rmarkdown + + Quitting from lines 149-157 [km] (easysurv.Rmd) + Error: processing vignette 'easysurv.Rmd' failed with diagnostics: + argument "risktable_height" is missing, with no default + --- failed re-building ‘easysurv.Rmd’ + + SUMMARY: processing the following file failed: + ‘easysurv.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EGAnet + +
+ +* Version: 2.0.7 +* GitHub: https://github.com/hfgolino/EGAnet +* Source code: https://github.com/cran/EGAnet +* Date/Publication: 2024-09-02 20:00:01 UTC +* Number of recursive dependencies: 190 + +Run `revdepcheck::cloud_details(, "EGAnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EGAnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dimensionStability + > ### Title: Dimension Stability Statistics from 'bootEGA' + > ### Aliases: dimensionStability + > + > ### ** Examples + > + > # Load data + ... + 16. │ └─e1 %+% e2 + 17. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 18. │ ├─ggplot2::ggplot_add(object, p, objectname) + 19. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 20. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 3.5Mb + ``` + +# EGM + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/shah-in-boots/EGM +* Source code: https://github.com/cran/EGM +* Date/Publication: 2024-05-23 16:10:05 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "EGM")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(EGM) + Loading required package: vctrs + Loading required package: data.table + > EGM::set_wfdb_path("/usr/local/bin") + > + > test_check("EGM") + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-ggm.R:63:2'): theming works ────────────────────────────────── + g$labels$x (`actual`) not equal to "sample" (`expected`). + + `actual` is NULL + `expected` is a character vector ('sample') + + [ FAIL 1 | WARN 0 | SKIP 19 | PASS 43 ] + Error: Test failures + Execution halted + ``` + +# emmeans + +
+ +* Version: 1.10.4 +* GitHub: https://github.com/rvlenth/emmeans +* Source code: https://github.com/cran/emmeans +* Date/Publication: 2024-08-21 03:00:01 UTC +* Number of recursive dependencies: 159 + +Run `revdepcheck::cloud_details(, "emmeans")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘emmeans-Ex.R’ failed + The error most likely occurred in: + + > ### Name: auto.noise + > ### Title: Auto Pollution Filter Noise + > ### Aliases: auto.noise + > ### Keywords: datasets + > + > ### ** Examples + > + > # (Based on belief that noise/10 is in decibel units) + > noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise) + > + > # Interaction plot of predictions + > emmip(noise.lm, type ~ size | side) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: emmip ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basics.Rmd’ + ... + 'emmGrid' object with variables: + source = fish, soy, skim + percent = 9, 12, 15, 18 + Transformation: “inverse” + + > emmip(RG4, source ~ percent, style = "factor") + + ... + ‘messy-data.Rmd’ using ‘UTF-8’... failed + ‘models.Rmd’ using ‘UTF-8’... OK + ‘predictions.Rmd’ using ‘UTF-8’... failed + ‘re-engineering-clds.rmd’ using ‘UTF-8’... OK + ‘sophisticated.Rmd’ using ‘UTF-8’... failed + ‘transformations.Rmd’ using ‘UTF-8’... failed + ‘utilities.Rmd’ using ‘UTF-8’... OK + ‘vignette-topics.Rmd’ using ‘UTF-8’... OK + ‘xplanations.Rmd’ using ‘UTF-8’... failed + ‘xtending.Rmd’ using ‘UTF-8’... OK + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'CARBayes', 'coxme', 'gee', 'geepack', 'MCMCglmm', 'MCMCpack', + 'mice', 'pscl', 'rstanarm', 'sommer' + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘AQuickStart.Rmd’ using rmarkdown + --- finished re-building ‘AQuickStart.Rmd’ + + --- re-building ‘FAQs.Rmd’ using rmarkdown + --- finished re-building ‘FAQs.Rmd’ + + --- re-building ‘basics.Rmd’ using rmarkdown + + Quitting from lines 260-262 [unnamed-chunk-13] (basics.Rmd) + Error: processing vignette 'basics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘basics.Rmd’ + + --- re-building ‘comparisons.Rmd’ using rmarkdown + ``` + +# EMMIXmfa + +
+ +* Version: 2.0.14 +* GitHub: https://github.com/suren-rathnayake/EMMIXmfa +* Source code: https://github.com/cran/EMMIXmfa +* Date/Publication: 2024-01-25 20:30:02 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "EMMIXmfa")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EMMIXmfa-Ex.R’ failed + The error most likely occurred in: + + > ### Name: factor_scores + > ### Title: Computes Factor Scores + > ### Aliases: factor_scores factor_scores.mcfa factor_scores.mctfa + > ### plot.emmix + > ### Keywords: cluster multivariate models + > + > ### ** Examples + ... + > Y <- iris[-c(sel_subset), -5] + > Y <- as.matrix(Y) + > clust <- predict(model, Y) + > + > fa_scores <- factor_scores(model, Y) + > # Visualizing new data in factor space + > plot_factors(fa_scores, type = "Umean", clust = clust) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_factors ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# entropart + +
+ +* Version: 1.6-15 +* GitHub: https://github.com/EricMarcon/entropart +* Source code: https://github.com/cran/entropart +* Date/Publication: 2024-08-26 19:30:09 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "entropart")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘entropart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Accumulation + > ### Title: Diversity accumulation. + > ### Aliases: DivAC EntAC as.AccumCurve is.AccumCurve autoplot.AccumCurve + > ### plot.AccumCurve + > + > ### ** Examples + > + ... + 11. │ └─base::withCallingHandlers(...) + 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. └─l$compute_geom_2(d, theme = plot$theme) + 14. └─ggplot2 (local) compute_geom_2(..., self = self) + 15. └─self$geom$use_defaults(...) + 16. └─ggplot2 (local) use_defaults(..., self = self) + 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘entropart.Rmd’ + ... + + > autoplot(Abd18, Distribution = "lnorm") + + When sourcing ‘entropart.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (149). + ✖ Fix the following mappings: `shape`, `colour`, and `size`. + Execution halted + + ‘entropart.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘entropart.Rmd’ using rmarkdown + + Quitting from lines 53-55 [PlotN18] (entropart.Rmd) + Error: processing vignette 'entropart.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (149). + ✖ Fix the following mappings: `shape`, `colour`, and `size`. + --- failed re-building ‘entropart.Rmd’ + + SUMMARY: processing the following file failed: + ‘entropart.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EnvStats + +
+ +* Version: 3.0.0 +* GitHub: https://github.com/alexkowa/EnvStats +* Source code: https://github.com/cran/EnvStats +* Date/Publication: 2024-08-24 23:10:05 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "EnvStats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EnvStats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_stripchart + > ### Title: 1-D Scatter Plots with Confidence Intervals Using ggplot2 + > ### Aliases: geom_stripchart + > ### Keywords: hplot htest + > + > ### ** Examples + > + ... + > + > p + geom_stripchart() + + + labs(x = "Number of Cylinders", y = "Miles per Gallon") + Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0. + ℹ Please use the `fun` argument instead. + ℹ The deprecated feature was likely used in the EnvStats package. + Please report the issue to the authors. + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.8Mb + sub-directories of 1Mb or more: + R 3.5Mb + help 3.5Mb + ``` + +# epiCleanr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/truenomad/epiCleanr +* Source code: https://github.com/cran/epiCleanr +* Date/Publication: 2023-09-28 12:20:05 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "epiCleanr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epiCleanr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: handle_outliers + > ### Title: Detect and Handle Outliers in Dataset + > ### Aliases: handle_outliers + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + doc 2.9Mb + help 2.5Mb + ``` + +# epiphy + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/chgigot/epiphy +* Source code: https://github.com/cran/epiphy +* Date/Publication: 2023-11-16 11:20:10 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "epiphy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epiphy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clump + > ### Title: Regroup observational data into even clumps of individuals. + > ### Aliases: clump clump.intensity + > + > ### ** Examples + > + > my_incidence <- incidence(tomato_tswv$field_1929) + ... + 18. │ └─ggplot2 (local) setup_params(...) + 19. │ └─ggplot2:::make_summary_fun(...) + 20. │ └─rlang::as_function(fun.data) + 21. │ └─base::get(x, envir = env, mode = "function") + 22. └─base::.handleSimpleError(...) + 23. └─rlang (local) h(simpleError(msg, call)) + 24. └─handlers[[1L]](cnd) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + Execution halted + ``` + +# EQUALSTATS + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/EQUALSTATS +* Date/Publication: 2024-09-06 16:10:15 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "EQUALSTATS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EQUALSTATS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: function.Survival_Analysis + > ### Title: Perform Survival Analysis + > ### Aliases: function.Survival_Analysis + > + > ### ** Examples + > + > # Create simulated data #### + ... + > rv$second_menu_choice <- NA + > rv$entry[[1]] <- "Admission to care home" + > rv$entry[[2]] <- "Follow-up" + > rv$entry[[3]] <- "Treatment" + > # Final function #### + > Results <- function.Survival_Analysis(Predefined_lists, rv) + Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", : + argument "risktable_height" is missing, with no default + Calls: function.Survival_Analysis + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘lmerTest’ + ``` + +# ergm.multi + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/statnet/ergm.multi +* Source code: https://github.com/cran/ergm.multi +* Date/Publication: 2024-02-20 23:20:05 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ergm.multi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ergm.multi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gofN + > ### Title: Linear model diagnostics for multinetwork linear models + > ### Aliases: gofN [.gofN augment.gofN summary.gofN + > + > ### ** Examples + > + > data(samplk) + ... + > + > ### If 'ggplot2' and 'ggrepel' are installed, illustrate the autoplot() method. + > if(require("ggplot2") && requireNamespace("ggrepel")){ + + autoplot(fit.gof) + + } + Loading required package: ggplot2 + Loading required namespace: ggrepel + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Goeyvaerts_reproduction.Rmd’ + ... + [1] 0.9763295 + + + + > autoplot(gof.wd) + Loading required namespace: ggrepel + + When sourcing ‘Goeyvaerts_reproduction.R’: + Error: argument is of length zero + Execution halted + + ‘Goeyvaerts_reproduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Goeyvaerts_reproduction.Rmd’ using rmarkdown + + Quitting from lines 157-158 [unnamed-chunk-16] (Goeyvaerts_reproduction.Rmd) + Error: processing vignette 'Goeyvaerts_reproduction.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Goeyvaerts_reproduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘Goeyvaerts_reproduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# esci + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/rcalinjageman/esci +* Source code: https://github.com/cran/esci +* Date/Publication: 2024-07-08 21:40:10 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "esci")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘esci-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimate_mdiff_2x2_between + > ### Title: Estimates for a 2x2 between-subjects design with a continuous + > ### outcome variable + > ### Aliases: estimate_mdiff_2x2_between + > + > ### ** Examples + > + ... + + estimates_from_summary$interaction, + + effect_size = "mean" + + ) + Warning: Using size for a discrete variable is not advised. + Warning: Using alpha for a discrete variable is not advised. + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(esci) + > + > test_check("esci") + Loading required package: Matrix + Loading required package: metadat + Loading required package: numDeriv + ... + 17. │ └─self$geom$use_defaults(...) + 18. └─base::.handleSimpleError(...) + 19. └─rlang (local) h(simpleError(msg, call)) + 20. └─handlers[[1L]](cnd) + 21. └─cli::cli_abort(...) + 22. └─rlang::abort(...) + + [ FAIL 14 | WARN 0 | SKIP 0 | PASS 3182 ] + Error: Test failures + Execution halted + ``` + +# evalITR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/MichaelLLi/evalITR +* Source code: https://github.com/cran/evalITR +* Date/Publication: 2023-08-25 23:10:06 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "evalITR")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cv_multiple_alg.Rmd’ + ... + intersect, setdiff, setequal, union + + + > load("../data/star.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' + + ... + Execution halted + + ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed + ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed + ‘install.Rmd’ using ‘UTF-8’... OK + ‘paper_alg1.Rmd’ using ‘UTF-8’... OK + ‘sample_split.Rmd’ using ‘UTF-8’... failed + ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed + ‘user_itr.Rmd’ using ‘UTF-8’... failed + ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘forcats’ ‘rqPen’ ‘utils’ + All declared Imports should be used. + ``` + +# eventstudyr + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/JMSLab/eventstudyr +* Source code: https://github.com/cran/eventstudyr +* Date/Publication: 2024-03-04 15:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "eventstudyr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(eventstudyr) + > + > test_check("eventstudyr") + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + ... + `expected` is a character vector ('ci_lower') + ── Failure ('test-EventStudyPlot.R:128:5'): confidence intervals are appropriately present or absent ── + p_ci$labels$ymax (`actual`) not equal to "ci_upper" (`expected`). + + `actual` is NULL + `expected` is a character vector ('ci_upper') + + [ FAIL 6 | WARN 0 | SKIP 0 | PASS 258 ] + Error: Test failures + Execution halted + ``` + +# EvoPhylo + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/tiago-simoes/EvoPhylo +* Source code: https://github.com/cran/EvoPhylo +* Date/Publication: 2022-11-03 17:00:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "EvoPhylo")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EvoPhylo-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_clusters + > ### Title: Estimate and plot character partitions + > ### Aliases: make_clusters plot.cluster_df + > + > ### ** Examples + > + > # See vignette("char-part") for how to use this + ... + > # tSNE (3 dimensions; default is 2) + > cluster_df_tsne <- make_clusters(Dmatrix, k = 3, tsne = TRUE, + + tsne_dim = 2) + > + > # Plot clusters, plots divided into 2 rows, and increasing + > # overlap of text labels (default = 10) + > plot(cluster_df_tsne, nrow = 2, max.overlaps = 20) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘char-part.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘char-part.Rmd’ + ... + + collapse = TRUE, dpi = 300) + + > devtools::load_all(".") + + When sourcing ‘char-part.R’: + Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in + '/tmp/Rtmp6FtfyP/file1a7972246c9b/vignettes'. + ... + ℹ Are you in your project directory and does your project have a 'DESCRIPTION' + file? + Execution halted + + ‘char-part.Rmd’ using ‘UTF-8’... failed + ‘data_treatment.Rmd’ using ‘UTF-8’... OK + ‘fbd-params.Rmd’ using ‘UTF-8’... failed + ‘offset_handling.Rmd’ using ‘UTF-8’... failed + ‘rates-selection_BEAST2.Rmd’ using ‘UTF-8’... failed + ‘rates-selection_MrBayes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 1.6Mb + extdata 2.4Mb + ``` + +# expirest + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/piusdahinden/expirest +* Source code: https://github.com/cran/expirest +* Date/Publication: 2024-03-25 16:30:02 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "expirest")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(expirest) + > + > test_check("expirest") + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1122 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Failure ('test-plot_expirest_wisle.R:260:3'): plot_expirest_wisle_succeeds ── + tmp4l2[["Graph"]]$labels has length 0, not length 8. + ── Failure ('test-plot_expirest_wisle.R:264:3'): plot_expirest_wisle_succeeds ── + tmp4b1[["Graph"]]$labels has length 0, not length 5. + ── Failure ('test-plot_expirest_wisle.R:269:3'): plot_expirest_wisle_succeeds ── + tmp4b2[["Graph"]]$labels has length 0, not length 5. + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1122 ] + Error: Test failures + Execution halted + ``` + +# explainer + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/PERSIMUNE/explainer +* Source code: https://github.com/cran/explainer +* Date/Publication: 2024-04-18 09:00:02 UTC +* Number of recursive dependencies: 183 + +Run `revdepcheck::cloud_details(, "explainer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘explainer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: eDecisionCurve + > ### Title: Decision Curve Plot + > ### Aliases: eDecisionCurve + > + > ### ** Examples + > + > library("explainer") + ... + > mylrn$train(maintask, splits$train) + > myplot <- eDecisionCurve( + + task = maintask, + + trained_model = mylrn, + + splits = splits, + + seed = seed + + ) + Error in pm[[2]] : subscript out of bounds + Calls: eDecisionCurve -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘ggpmisc’ + All declared Imports should be used. + ``` + +# exuber + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/kvasilopoulos/exuber +* Source code: https://github.com/cran/exuber +* Date/Publication: 2023-03-22 23:10:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "exuber")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exuber.Rmd’ + ... + 370 1 1 1 0 + 371 1 1 0 0 + 372 1 1 0 0 + + > autoplot(est_stocks) + Using `radf_crit` for `cv`. + + ... + + > autoplot(estimation, crit_values) + + When sourcing ‘plotting.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘exuber.Rmd’ using ‘UTF-8’... failed + ‘plotting.Rmd’ using ‘UTF-8’... failed + ‘simulation.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘exuber.Rmd’ using rmarkdown + + Quitting from lines 73-74 [plot-radf] (exuber.Rmd) + Error: processing vignette 'exuber.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘exuber.Rmd’ + + --- re-building ‘plotting.Rmd’ using rmarkdown + + Quitting from lines 58-59 [autoplot-basic] (plotting.Rmd) + Error: processing vignette 'plotting.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘plotting.Rmd’ + + --- re-building ‘simulation.Rmd’ using rmarkdown + ``` + +# ezEDA + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/kviswana/ezEDA +* Source code: https://github.com/cran/ezEDA +* Date/Publication: 2021-06-29 04:40:10 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "ezEDA")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ezEDA) + > + > test_check("ezEDA") + [ FAIL 22 | WARN 0 | SKIP 0 | PASS 57 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Error ('test_two_measures_relationship.R:19:3'): y axis is labeled 'hwy' ──── + Error in `expect_match(p$labels$y, "hwy")`: is.character(act$val) is not TRUE + Backtrace: + ▆ + 1. └─testthat::expect_match(p$labels$y, "hwy") at test_two_measures_relationship.R:19:3 + 2. └─base::stopifnot(is.character(act$val)) + + [ FAIL 22 | WARN 0 | SKIP 0 | PASS 57 ] + Error: Test failures + Execution halted + ``` + +# ezplot + +
+ +* Version: 0.7.13 +* GitHub: NA +* Source code: https://github.com/cran/ezplot +* Date/Publication: 2024-01-28 11:30:05 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "ezplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ezplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: model_plot + > ### Title: model_plot + > ### Aliases: model_plot + > + > ### ** Examples + > + > y = rnorm(26) + > df = data.frame(ID = 1:26, actual = y + rnorm(26), fitted = y, id = letters) + > model_plot(df, "ID", "actual", "fitted") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# fable.prophet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mitchelloharawild/fable.prophet +* Source code: https://github.com/cran/fable.prophet +* Date/Publication: 2020-08-20 09:30:03 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "fable.prophet")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘intro.Rmd’ + ... + 9 Domestic mdl 2019 Dec sample[5000] 5338093. + 10 Domestic mdl 2020 Jan sample[5000] 4888643. + # ℹ 62 more rows + + > fc %>% autoplot(lax_passengers) + + When sourcing ‘intro.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL + Execution halted + + ‘intro.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# fabletools + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/tidyverts/fabletools +* Source code: https://github.com/cran/fabletools +* Date/Publication: 2024-04-22 11:22:41 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "fabletools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fabletools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.fbl_ts + > ### Title: Plot a set of forecasts + > ### Aliases: autoplot.fbl_ts autolayer.fbl_ts + > + > ### ** Examples + > + > ## Don't show: + ... + > library(fable) + > library(tsibbledata) + > fc <- aus_production %>% model(ets = ETS(log(Beer) ~ error("M") + trend("Ad") + + + season("A"))) %>% forecast(h = "3 years") + > fc %>% autoplot(aus_production) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + + ... + 28. └─ggplot2 (local) compute_geom_2(..., self = self) + 29. └─self$geom$use_defaults(...) + ── Failure ('test-graphics.R:327:3'): autoplot_dcmp_ts() ─────────────────────── + `print(p)` produced warnings. + ── Failure ('test-graphics.R:346:3'): autoplot_dcmp_ts() ─────────────────────── + `print(p)` produced warnings. + + [ FAIL 4 | WARN 5 | SKIP 1 | PASS 267 ] + Error: Test failures + Execution halted + ``` + +# factoextra + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/kassambara/factoextra +* Source code: https://github.com/cran/factoextra +* Date/Publication: 2020-04-01 21:20:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "factoextra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘factoextra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: eclust + > ### Title: Visual enhancement of clustering analysis + > ### Aliases: eclust + > + > ### ** Examples + > + > # Load and scale data + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# fairmodels + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/ModelOriented/fairmodels +* Source code: https://github.com/cran/fairmodels +* Date/Publication: 2022-08-23 19:50:06 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "fairmodels")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(fairmodels) + > + > + > test_check("fairmodels") + Welcome to DALEX (version: 2.4.3). + Find examples and detailed introduction at: http://ema.drwhy.ai/ + ... + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_plot_density.R:14:3'): Test plot_density ───────────────────── + plt$labels$x not equal to "probability". + target is NULL, current is character + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + Error: Test failures + Execution halted + ``` + +# fastR2 + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/rpruim/fastR2 +* Source code: https://github.com/cran/fastR2 +* Date/Publication: 2023-11-09 06:30:03 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "fastR2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fastR2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ACTgpa + > ### Title: ACT scores and GPA + > ### Aliases: ACTgpa + > ### Keywords: datasets + > + > ### ** Examples + > + > + > gf_point(GPA ~ ACT, data = ACTgpa) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + data 2.0Mb + snippet 3.7Mb + ``` + +# faux + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/debruine/faux +* Source code: https://github.com/cran/faux +* Date/Publication: 2023-04-20 07:00:11 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "faux")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘codebook.Rmd’ using rmarkdown + --- finished re-building ‘codebook.Rmd’ + + --- re-building ‘continuous.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘faux-Ex.R’ failed + The error most likely occurred in: + + > ### Name: beta2norm + > ### Title: Convert beta to normal + > ### Aliases: beta2norm + > + > ### ** Examples + > + > + > x <- rbeta(10000, 2, 3) + > y <- beta2norm(x) + shape1 was set to 1.96704823352025 + shape2 was set to 2.94110338061547 + > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y)) + > ggExtra::ggMarginal(g, type = "histogram") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(faux) + + ************ + Welcome to faux. For support and examples visit: + https://debruine.github.io/faux/ + - Get and set global package options with: faux_options() + ... + 6. └─methods (local) ``(...) + 7. └─methods::new(def, ...) + 8. ├─methods::initialize(value, ...) + 9. └─methods::initialize(value, ...) + 10. └─.Object$initialize(...) + 11. └─lme4 (local) initializePtr() + + [ FAIL 20 | WARN 6 | SKIP 14 | PASS 1331 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘norta.Rmd’ + ... + + > p <- ggplot(dat, aes(uniform_var, poisson_var)) + + + geom_point() + geom_smooth() + + > ggMarginal(p, type = "histogram") + `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")' + + ... + Error: argument is of length zero + Execution halted + + ‘codebook.Rmd’ using ‘UTF-8’... OK + ‘continuous.Rmd’ using ‘UTF-8’... OK + ‘contrasts.Rmd’ using ‘UTF-8’... OK + ‘norta.Rmd’ using ‘UTF-8’... failed + ‘rnorm_multi.Rmd’ using ‘UTF-8’... OK + ‘sim_design.Rmd’ using ‘UTF-8’... OK + ‘sim_df.Rmd’ using ‘UTF-8’... OK + ``` + +# fddm + +
+ +* Version: 1.0-2 +* GitHub: https://github.com/rtdists/fddm +* Source code: https://github.com/cran/fddm +* Date/Publication: 2024-07-02 16:00:07 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fddm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘benchmark.Rmd’ + ... + > mi <- min(bm_vec[, -seq_len(t_idx)]) + + > ma <- max(bm_vec[, (t_idx + 1):(ncol(bm_vec) - 4)]) + + > ggplot(mbm_vec, aes(x = factor(FuncName, levels = Names_vec), + + y = time, color = factor(FuncName, levels = Names_vec), fill = factor(FuncName, .... [TRUNCATED] + + ... + + When sourcing ‘pfddm.R’: + Error: Not a unit object + Execution halted + + ‘benchmark.Rmd’ using ‘UTF-8’... failed + ‘example.Rmd’ using ‘UTF-8’... OK + ‘math.Rmd’ using ‘UTF-8’... OK + ‘pfddm.Rmd’ using ‘UTF-8’... failed + ‘validity.Rmd’ using ‘UTF-8’... OK + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 16.6Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 14.1Mb + ``` + +# feasts + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/tidyverts/feasts +* Source code: https://github.com/cran/feasts +* Date/Publication: 2024-03-15 09:10:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "feasts")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(feasts) + Loading required package: fabletools + > + > test_check("feasts") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + + ... + ── Error ('test-graphics.R:192:3'): gg_tsdisplay() plots ─────────────────────── + Error in `p + ggplot2::labs(x = "x", y = "y", title = "title")`: non-numeric argument to binary operator + ── Failure ('test-graphics.R:273:3'): gg_arma() plots ────────────────────────── + p_built$plot$labels[c("x", "y")] not equivalent to list(x = "Re(1/root)", y = "Im(1/root)"). + Component "x": 1 string mismatch + Component "y": 1 string mismatch + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + Error: Test failures + Execution halted + ``` + +# fergm + +
+ +* Version: 1.1.4 +* GitHub: https://github.com/benjamin-w-campbell/fergm +* Source code: https://github.com/cran/fergm +* Date/Publication: 2018-10-17 22:20:11 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "fergm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fergm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: coef_posterior_density + > ### Title: Plots the posterior density for FERGM model terms. + > ### Aliases: coef_posterior_density + > ### Keywords: FERGM interpret summary + > + > ### ** Examples + > + ... + > data("ergm.fit") + > data("fergm.fit") + > data("mesa") + > + > # rstan functions + > # Histogram of the posterior + > rstan::stan_hist(fergm.fit$stan.fit, par = "beta") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ffp + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/Reckziegel/FFP +* Source code: https://github.com/cran/ffp +* Date/Publication: 2022-09-29 15:10:06 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "ffp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ffp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scenario_density + > ### Title: Plot Scenarios + > ### Aliases: scenario_density scenario_histogram + > + > ### ** Examples + > + > x <- diff(log(EuStockMarkets))[, 1] + > p <- exp_decay(x, 0.005) + > + > scenario_density(x, p, 500) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +# fic + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/chjackson/fic +* Source code: https://github.com/cran/fic +* Date/Publication: 2019-04-13 08:32:39 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "fic")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘linear.Rnw’ + ... + + > library(ggplot2) + + > if (requireNamespace("GGally", quietly = TRUE)) { + + GGally::ggpairs(mtcars[, c("mpg", "am", "wt", "qsec", "disp", + + "hp")], aes(colour .... [TRUNCATED] + + ... + When sourcing 'linear.R': + Error: argument is of length zero + Execution halted + + ‘fic.Rnw’ using ‘UTF-8’... OK + ‘linear.Rnw’ using ‘UTF-8’... failed + ‘loss.Rnw’ using ‘UTF-8’... OK + ‘multistate.Rnw’ using ‘UTF-8’... OK + ‘skewnormal.Rnw’ using ‘UTF-8’... OK + ‘survival.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘numDeriv’ + All declared Imports should be used. + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘fic.Rnw’ using knitr + Error: processing vignette 'fic.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'fic.tex' failed. + LaTeX errors: + ! LaTeX Error: File `grfext.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + --- finished re-building ‘skewnormal.Rnw’ + + --- re-building ‘survival.Rnw’ using knitr + --- finished re-building ‘survival.Rnw’ + + SUMMARY: processing the following files failed: + ‘fic.Rnw’ ‘linear.Rnw’ ‘multistate.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# fido + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/jsilve24/fido +* Source code: https://github.com/cran/fido +* Date/Publication: 2024-06-05 21:30:06 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "fido")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fido-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.pibblefit + > ### Title: Plot Summaries of Posterior Distribution of pibblefit Parameters + > ### Aliases: plot.pibblefit + > + > ### ** Examples + > + > sim <- pibble_sim(N=10, D=4, Q=3) + > fit <- pibble(sim$Y, sim$X) + > plot(fit, par="Lambda") + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(fido) + > + > #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE") + > test_check("fido") + [1] 0.27980164 -0.69169550 -0.53205652 0.11488451 -0.42419872 2.20261388 + [7] -1.62190133 -0.90893172 0.07891428 0.75060681 0.43593605 0.26819442 + ... + 21. └─base::Map(...) + 22. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 23. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 24. └─layer$compute_geom_2(key, single_params, theme) + 25. └─ggplot2 (local) compute_geom_2(..., self = self) + 26. └─self$geom$use_defaults(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 114 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘non-linear-models.Rmd’ + ... + + The following object is masked from ‘package:dplyr’: + + select + + + When sourcing ‘non-linear-models.R’: + Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + Execution halted + + ‘introduction-to-fido.Rmd’ using ‘UTF-8’... OK + ‘mitigating-pcrbias.Rmd’ using ‘UTF-8’... OK + ‘non-linear-models.Rmd’ using ‘UTF-8’... failed + ‘orthus.Rmd’ using ‘UTF-8’... OK + ‘picking_priors.Rmd’ using ‘UTF-8’... OK + ``` + +* checking installed package size ... NOTE + ``` + installed size is 106.5Mb + sub-directories of 1Mb or more: + data 4.0Mb + libs 100.6Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction-to-fido.Rmd’ using rmarkdown + --- finished re-building ‘introduction-to-fido.Rmd’ + + --- re-building ‘mitigating-pcrbias.Rmd’ using rmarkdown + --- finished re-building ‘mitigating-pcrbias.Rmd’ + + --- re-building ‘non-linear-models.Rmd’ using rmarkdown + ``` + +# fitdistrplus + +
+ +* Version: 1.2-1 +* GitHub: https://github.com/lbbe-software/fitdistrplus +* Source code: https://github.com/cran/fitdistrplus +* Date/Publication: 2024-07-12 12:20:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "fitdistrplus")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fitdistrplus-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CIcdfplot + > ### Title: Empirical cumulative distribution function with pointwise + > ### confidence intervals on probabilities or on quantiles + > ### Aliases: CIcdfplot + > ### Keywords: distribution + > + > ### ** Examples + ... + > f1 <- fitdist(s1, "exp") + > b1 <- bootdist(f1, niter= 11) #voluntarily low to decrease computation time + > + > # plot 95 percent bilateral confidence intervals on y values (probabilities) + > CIcdfplot(b1, CI.level= 95/100, CI.output = "probability") + > if (ggplotEx) CIcdfplot(b1, CI.level= 95/100, CI.output = "probability", plotstyle = "ggplot") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘t-CIcdfplot.R’ + Running the tests in ‘tests/t-CIcdfplot.R’ failed. + Complete output: + > library(fitdistrplus) + Loading required package: MASS + Loading required package: survival + > + > nbboot <- 201 + > nbboot <- 10 + > ggplotEx <- requireNamespace("ggplot2", quietly = TRUE) + ... + 97.5 % 2.152084 2.778622 + > + > par(mfrow=c(1,2)) + > CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black") + > CIcdfplot(b1, CI.level=95/100, CI.output = "quantile", datacol="blue") + > if(ggplotEx) CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black", plotstyle = "ggplot") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘FAQ.Rmd’ + ... + + > dcomp <- denscomp(list(fitW, fitln, fitg), legendtext = c("Weibull", + + "lognormal", "gamma"), xlab = "serving sizes (g)", xlim = c(0, + + 25 .... [TRUNCATED] + + > dcomp + ggplot2::theme_minimal() + ggplot2::ggtitle("Ground beef fits") + + When sourcing ‘FAQ.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘FAQ.Rmd’ using ‘UTF-8’... failed + ‘Optimalgo.Rmd’ using ‘UTF-8’... OK + ‘fitdistrplus_vignette.Rmd’ using ‘UTF-8’... OK + ‘starting-values.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘FAQ.Rmd’ using rmarkdown + ``` + +# fitlandr + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Sciurus365/fitlandr +* Source code: https://github.com/cran/fitlandr +* Date/Publication: 2023-02-10 10:40:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "fitlandr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fitlandr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fit_2d_vf + > ### Title: Estimate a 2D vector field + > ### Aliases: fit_2d_vf + > + > ### ** Examples + > + > # generate data + > single_output_grad <- simlandr::sim_fun_grad(length = 200, seed = 1614) + > # fit the vector field + > v2 <- fit_2d_vf(single_output_grad, x = "x", y = "y", method = "MVKE") + > plot(v2) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# flexsurv + +
+ +* Version: 2.3.2 +* GitHub: https://github.com/chjackson/flexsurv +* Source code: https://github.com/cran/flexsurv +* Date/Publication: 2024-08-17 05:50:02 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "flexsurv")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘standsurv.Rmd’ + ... + 5 0 967 Good 2.649315 68.74975 25110 1986-05-18 female Good + 6 0 629 Good 1.723288 64.53328 23570 1987-03-07 female Good + + > km <- survfit(Surv(recyrs, censrec) ~ group2, data = bc) + + > kmsurvplot <- ggsurvplot(km) + + When sourcing ‘standsurv.R’: + Error: argument is of length zero + Execution halted + + ‘standsurv.Rmd’ using ‘UTF-8’... failed + ‘flexsurv.Rnw’ using ‘UTF-8’... OK + ‘multistate.Rnw’ using ‘UTF-8’... OK + ‘distributions.Rnw’ using ‘UTF-8’... OK + ‘flexsurv-examples.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.9Mb + libs 3.4Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘standsurv.Rmd’ using rmarkdown + + Quitting from lines 113-116 [unnamed-chunk-4] (standsurv.Rmd) + Error: processing vignette 'standsurv.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘standsurv.Rmd’ + + --- re-building ‘flexsurv.Rnw’ using knitr + --- finished re-building ‘flexsurv.Rnw’ + ... + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘flexsurv-examples.Rnw’ + + SUMMARY: processing the following files failed: + ‘standsurv.Rmd’ ‘multistate.Rnw’ ‘distributions.Rnw’ + ‘flexsurv-examples.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# flipr + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/LMJL-Alea/flipr +* Source code: https://github.com/cran/flipr +* Date/Publication: 2023-08-23 09:00:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "flipr")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘alternative.Rmd’ using rmarkdown + --- finished re-building ‘alternative.Rmd’ + + --- re-building ‘exactness.Rmd’ using rmarkdown + + Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) + Error: processing vignette 'exactness.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘exactness.Rmd’ + + --- re-building ‘flipr.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exactness.Rmd’ + ... + + > library(flipr) + + > load("../R/sysdata.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' + + ... + cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' + + When sourcing ‘plausibility.R’: + Error: cannot open the connection + Execution halted + + ‘alternative.Rmd’ using ‘UTF-8’... OK + ‘exactness.Rmd’ using ‘UTF-8’... failed + ‘flipr.Rmd’ using ‘UTF-8’... failed + ‘plausibility.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 11.2Mb + sub-directories of 1Mb or more: + doc 9.1Mb + libs 1.4Mb + ``` + +# FLOPART + +
+ +* Version: 2024.6.19 +* GitHub: NA +* Source code: https://github.com/cran/FLOPART +* Date/Publication: 2024-06-20 21:30:10 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "FLOPART")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘comparison.Rmd’ + ... + + > if (require("ggplot2")) { + + ggplot() + ggtitle("Models with label constraints (FLOPART) and without (penalty values)") + + + scale_fill_m .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘comparison.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘comparison.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘comparison.Rmd’ using knitr + ``` + +# fmesher + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/inlabru-org/fmesher +* Source code: https://github.com/cran/fmesher +* Date/Publication: 2024-07-01 13:00:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fmesher")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fmesher-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fm_mesh_1d + > ### Title: Make a 1D mesh object + > ### Aliases: fm_mesh_1d + > + > ### ** Examples + > + > if (require("ggplot2")) { + ... + + boundary = c("neumann", "free"), + + degree = 2 + + ) + + ggplot() + + + geom_fm(data = m, xlim = c(0.5, 10.5)) + + } + Loading required package: ggplot2 + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic_use.Rmd’ + ... + + > plot(mesh2) + + > suppressPackageStartupMessages(library(ggplot2)) + + > ggplot() + geom_fm(data = mesh2) + + When sourcing ‘basic_use.R’: + Error: argument is of length zero + Execution halted + + ‘basic_use.Rmd’ using ‘UTF-8’... failed + ‘fmesher_library.Rmd’ using ‘UTF-8’... OK + ‘inla_conversion.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basic_use.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + libs 10.5Mb + ``` + +# fmf + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/fmf +* Date/Publication: 2020-09-03 07:32:12 UTC +* Number of recursive dependencies: 175 + +Run `revdepcheck::cloud_details(, "fmf")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fmf-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot + > ### Title: PCA Plot of the Noise Score of Each Individual + > ### Aliases: plot + > + > ### ** Examples + > + > + ... + 17. │ └─ggplot2:::`+.gg`(...) + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 22. └─base::.handleSimpleError(...) + 23. └─purrr (local) h(simpleError(msg, call)) + 24. └─cli::cli_abort(...) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# forestly + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Merck/forestly +* Source code: https://github.com/cran/forestly +* Date/Publication: 2024-07-08 19:40:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "forestly")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘forest-plot-static.Rmd’ + ... + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <86> + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <92> + + When sourcing ‘forest-plot-static.R’: + Error: object is not a unit + Execution halted + + ‘forest-plot-static.Rmd’ using ‘UTF-8’... failed + ‘forestly-cran.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘forest-plot-static.Rmd’ using rmarkdown + ``` + +# FossilSim + +
+ +* Version: 2.4.0 +* GitHub: NA +* Source code: https://github.com/cran/FossilSim +* Date/Publication: 2024-09-05 19:40:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "FossilSim")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FossilSim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.fbdrange + > ### Title: Plot oriented tree with stratigraphic ranges + > ### Aliases: plot.fbdrange + > + > ### ** Examples + > + > tree_file <- system.file("extdata", "fbdrange.trees", package = "FossilSim") + > fbdr <- get_fbdrange_from_file(tree_file) + > p <- plot(fbdr, smart.labels = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# FPDclustering + +
+ +* Version: 2.3.1 +* GitHub: NA +* Source code: https://github.com/cran/FPDclustering +* Date/Publication: 2024-01-30 00:10:06 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "FPDclustering")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FPDclustering-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GPDC + > ### Title: Gaussian PD-Clustering + > ### Aliases: GPDC + > + > ### ** Examples + > + > #Load the data + ... + > #Results + > table(res$label,ais$sex) + + f m + 1 95 1 + 2 5 101 + > plot(res) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# frailtyEM + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/tbalan/frailtyEM +* Source code: https://github.com/cran/frailtyEM +* Date/Publication: 2019-09-22 13:00:10 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "frailtyEM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘frailtyEM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: summary.emfrail + > ### Title: Summary for 'emfrail' objects + > ### Aliases: summary.emfrail + > + > ### ** Examples + > + > data("bladder") + ... + filter + + The following object is masked from ‘package:graphics’: + + layout + + > ggplotly(pl2) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘frailtyEM_manual.Rnw’ using Sweave + Loading required package: survival + Loading required package: gridExtra + Warning: The `` argument of `guides()` cannot be `FALSE`. Use + "none" instead as of ggplot2 3.3.4. + Warning: Removed 2 rows containing missing values or values outside + the scale range (`geom_path()`). + Warning in data("kidney") : data set ‘kidney’ not found + Warning in emfrail(Surv(time, status) ~ age + sex + cluster(id), data = kidney, : + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘frailtyEM_manual.Rnw’ + + SUMMARY: processing the following file failed: + ‘frailtyEM_manual.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# funcharts + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/unina-sfere/funcharts +* Source code: https://github.com/cran/funcharts +* Date/Publication: 2024-07-19 12:00:31 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "funcharts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘funcharts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pca_mfd + > ### Title: Multivariate functional principal components analysis + > ### Aliases: pca_mfd + > + > ### ** Examples + > + > library(funcharts) + > mfdobj <- data_sim_mfd() + > pca_obj <- pca_mfd(mfdobj) + > plot_pca_mfd(pca_obj) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# FunnelPlotR + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/nhs-r-community/FunnelPlotR +* Source code: https://github.com/cran/FunnelPlotR +* Date/Publication: 2024-04-12 08:40:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "FunnelPlotR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FunnelPlotR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: funnel_plot + > ### Title: Funnel plots for comparing institutional performance + > ### Aliases: funnel_plot + > + > ### ** Examples + > + > # We will use the 'medpar' dataset from the 'COUNT' package. + ... + > # Draw plot, returning just the plot object + > fp<-funnel_plot(medpar, denominator=prds, numerator=los, + + group = provnum, limit=95, title="An example funnel plot") + > + > # Methods for viewing/extracting + > print(fp) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘changing_funnel_plot_options.Rmd’ + ... + + family = "poisson", data = medpar) + + > medpar$prds <- predict(mod, newdata = medpar, type = "response") + + > funnel_plot(medpar, denominator = prds, numerator = los, + + group = provnum, limit = 99, label = "outlier", draw_unadjusted = TRUE) + + ... + + group = provnum, title = "Length of Stay Funnel plot for `medpar` data", + + draw .... [TRUNCATED] + Plotting using unadjusted limits + + When sourcing ‘funnel_plots.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘changing_funnel_plot_options.Rmd’ using ‘UTF-8’... failed + ‘funnel_plots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘changing_funnel_plot_options.Rmd’ using rmarkdown + + Quitting from lines 33-49 [dtsetup] (changing_funnel_plot_options.Rmd) + Error: processing vignette 'changing_funnel_plot_options.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘changing_funnel_plot_options.Rmd’ + + --- re-building ‘funnel_plots.Rmd’ using rmarkdown + ``` + +# genekitr + +
+ +* Version: 1.2.8 +* GitHub: https://github.com/GangLiLab/genekitr +* Source code: https://github.com/cran/genekitr +* Date/Publication: 2024-09-06 13:00:06 UTC +* Number of recursive dependencies: 202 + +Run `revdepcheck::cloud_details(, "genekitr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘genekitr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotVenn + > ### Title: Venn plot for groups of genes + > ### Aliases: plotVenn + > + > ### ** Examples + > + > k1 = requireNamespace("ComplexUpset",quietly = TRUE) + ... + + use_venn = FALSE, + + main_text_size = 15, + + legend_text_size = 8, + + legend_position = 'left' + + ) + + } + Color length should be same with venn_list, auto assign colors... + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotVenn ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# geoheatmap + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/geoheatmap +* Date/Publication: 2024-09-05 15:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "geoheatmap")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘geoheatmap.Rmd’ + ... + + facet_col = "state", value_col = "teams", merge_col = "name_de", + + .... [TRUNCATED] + + > geoheatmap(facet_data = football_teams, grid_data = de_states_grid1, + + facet_col = "state", value_col = "teams", merge_col = "name_de", + + .... [TRUNCATED] + + When sourcing ‘geoheatmap.R’: + Error: subscript out of bounds + Execution halted + + ‘geoheatmap.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘geoheatmap.Rmd’ using rmarkdown + ``` + +# geomtextpath + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/AllanCameron/geomtextpath +* Source code: https://github.com/cran/geomtextpath +* Date/Publication: 2024-06-13 06:40:02 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "geomtextpath")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geomtextpath-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_textsf + > ### Title: Visualise sf objects with labels + > ### Aliases: geom_textsf geom_labelsf + > + > ### ** Examples + > + > ggplot(waterways) + + ... + 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 20. │ └─self$draw_panel(data, panel_params, coord, na.rm = FALSE, legend = "other") + 21. │ └─geomtextpath (local) draw_panel(...) + 22. │ └─geomtextpath:::sf_textgrob(...) + 23. └─base::.handleSimpleError(...) + 24. └─rlang (local) h(simpleError(msg, call)) + 25. └─handlers[[1L]](cnd) + 26. └─cli::cli_abort(...) + 27. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(geomtextpath) + Loading required package: ggplot2 + > + > test_check("geomtextpath") + [ FAIL 1 | WARN 0 | SKIP 4 | PASS 463 ] + + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-sf.R:91:3'): We can make grobs from sf features ──────────────── + Error in `(x$boxlinewidth %||% defaults$linewidth[type_ind]) * 3.779528`: non-numeric argument to binary operator + Backtrace: + ▆ + 1. └─geomtextpath:::sf_textgrob(river, as_textbox = TRUE) at test-sf.R:91:3 + + [ FAIL 1 | WARN 0 | SKIP 4 | PASS 463 ] + Error: Test failures + Execution halted + ``` + +# geostan + +
+ +* Version: 0.6.2 +* GitHub: https://github.com/ConnorDonegan/geostan +* Source code: https://github.com/cran/geostan +* Date/Publication: 2024-06-04 09:45:37 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "geostan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geostan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.geostan_fit + > ### Title: print or plot a fitted geostan model + > ### Aliases: print.geostan_fit plot.geostan_fit + > + > ### ** Examples + > + > data(georgia) + ... + log(income) -1.013 0.001 0.019 -1.049 -1.029 -1.014 -0.998 -0.974 188 1.003 + + Samples were drawn using NUTS(diag_e) at Tue Sep 10 09:34:29 2024. + For each parameter, n_eff is a crude measure of effective sample size, + and Rhat is the potential scale reduction factor on split chains (at + convergence, Rhat=1). + > plot(fit) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 129.8Mb + sub-directories of 1Mb or more: + libs 127.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# GGally + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/ggobi/ggally +* Source code: https://github.com/cran/GGally +* Date/Publication: 2024-02-14 00:53:32 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "GGally")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GGally-Ex.R’ failed + The error most likely occurred in: + + > ### Name: +.gg + > ### Title: Modify a 'ggmatrix' object by adding an 'ggplot2' object to all + > ### plots + > ### Aliases: +.gg add_to_ggmatrix + > + > ### ** Examples + > + ... + > p_ <- GGally::print_if_interactive + > data(tips) + > + > pm <- ggpairs(tips[, 2:4], ggplot2::aes(color = sex)) + > ## change to black and white theme + > pm + ggplot2::theme_bw() + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (requireNamespace("testthat", quietly = TRUE)) { + + library(testthat) + + library(GGally) + + + + test_check("GGally") + + } + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 20 | WARN 1 | SKIP 22 | PASS 426 ] + Error: Test failures + Execution halted + ``` + +# gganimate + +
+ +* Version: 1.0.9 +* GitHub: https://github.com/thomasp85/gganimate +* Source code: https://github.com/cran/gganimate +* Date/Publication: 2024-02-27 14:00:03 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "gganimate")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gganimate) + Loading required package: ggplot2 + > + > test_check("gganimate") + [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] + + ... + 3. ├─gganimate::animate(p, nframes = 2) at test-anim_save.R:14:5 + 4. └─gganimate:::animate.gganim(p, nframes = 2) + 5. └─args$renderer(frames_vars$frame_source, args$fps) + 6. └─gganimate:::png_dim(frames[1]) + 7. └─cli::cli_abort("Provided file ({file}) does not exist") + 8. └─rlang::abort(...) + + [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gganimate.Rmd’ + ... + Theme element `panel.grid.major.y` is missing + Theme element `panel.grid.major.x` is missing + Warning: Failed to plot frame + Caused by error in `UseMethod()`: + ! no applicable method for 'element_grob' applied to an object of class "NULL" + + When sourcing ‘gganimate.R’: + Error: Provided file (/tmp/RtmpPBufaF/165c2292cd97/gganim_plot0001.png) does + not exist + Execution halted + + ‘gganimate.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘gganimate.Rmd’ using rmarkdown + ``` + +# ggbrain + +
+ +* Version: 0.8.1 +* GitHub: https://github.com/michaelhallquist/ggbrain +* Source code: https://github.com/cran/ggbrain +* Date/Publication: 2023-03-21 18:00:05 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "ggbrain")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggbrain_introduction.Rmd’ + ... + + > gg_obj <- gg_base + geom_brain(definition = "underlay", + + fill_scale = scale_fill_gradient(low = "grey8", high = "grey62"), + + show_legend .... [TRUNCATED] + + > gg_obj$render() + + ... + + > plot(gg_obj) + + When sourcing ‘ggbrain_labels.R’: + Error: argument is of length zero + Execution halted + + ‘ggbrain_aesthetics.Rmd’ using ‘UTF-8’... OK + ‘ggbrain_introduction.Rmd’ using ‘UTF-8’... failed + ‘ggbrain_labels.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggbrain_aesthetics.Rmd’ using rmarkdown + --- finished re-building ‘ggbrain_aesthetics.Rmd’ + + --- re-building ‘ggbrain_introduction.Rmd’ using rmarkdown + + Quitting from lines 238-239 [unnamed-chunk-16] (ggbrain_introduction.Rmd) + Error: processing vignette 'ggbrain_introduction.Rmd' failed with diagnostics: + argument is of length zero + ... + Quitting from lines 47-54 [unnamed-chunk-2] (ggbrain_labels.Rmd) + Error: processing vignette 'ggbrain_labels.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggbrain_labels.Rmd’ + + SUMMARY: processing the following files failed: + ‘ggbrain_introduction.Rmd’ ‘ggbrain_labels.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.8Mb + sub-directories of 1Mb or more: + doc 3.0Mb + extdata 1.6Mb + libs 5.5Mb + ``` + +# ggbreak + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/YuLab-SMU/ggbreak +* Source code: https://github.com/cran/ggbreak +* Date/Publication: 2023-06-26 05:40:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "ggbreak")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggbreak-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scale_wrap + > ### Title: scale-wrap + > ### Aliases: scale_wrap + > + > ### ** Examples + > + > library(ggplot2) + > library(ggbreak) + > p <- ggplot(economics, aes(x=date, y = unemploy, colour = uempmed)) + + + geom_line() + > p + scale_wrap(n=4) + Error in identicalUnits(x) : object is not a unit + Calls: -> print.ggwrap + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggbreak.Rmd’ + ... + > p1 + p2 + + > p2 + scale_x_break(c(18, 21)) + + > p1 + scale_x_break(c(7, 17), scales = 1.5) + scale_x_break(c(18, + + 21), scales = 2) + + When sourcing ‘ggbreak.R’: + Error: second argument must be a list + Execution halted + + ‘ggbreak.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggbreak.Rmd’ using rmarkdown + ``` + +# ggcharts + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/thomas-neitmann/ggcharts +* Source code: https://github.com/cran/ggcharts +* Date/Publication: 2020-05-20 00:40:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "ggcharts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggcharts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bar_chart + > ### Title: Bar Chart + > ### Aliases: bar_chart column_chart + > + > ### ** Examples + > + > data(biomedicalrevenue) + > revenue2018 <- biomedicalrevenue[biomedicalrevenue$year == 2018, ] + > revenue_roche <- biomedicalrevenue[biomedicalrevenue$company == "Roche", ] + > + > ## By default bar_chart() creates a horizontal and sorted plot + > bar_chart(revenue2018, company, revenue) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: bar_chart ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggcharts) + Loading required package: ggplot2 + > + > test_check("ggcharts") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] + + ... + 4. └─ggcharts::bar_chart(revenue_2018, company, revenue) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘customize.Rmd’ + ... + > dreaded_lang <- tibble::tribble(~language, ~pct, "VBA", + + 75.2, "Objective-C", 68.7, "Assembly", 64.4, "C", 57.5, "PHP", + + 54.2, "Erlang", .... [TRUNCATED] + + > (chart <- lollipop_chart(dreaded_lang, language, pct, + + highlight = "R")) + + ... + + > lollipop_chart(diamonds, cut, highlight = "Good") + + When sourcing ‘themes.R’: + Error: argument is of length zero + Execution halted + + ‘customize.Rmd’ using ‘UTF-8’... failed + ‘highlight.Rmd’ using ‘UTF-8’... failed + ‘themes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘customize.Rmd’ using rmarkdown + + Quitting from lines 25-44 [unnamed-chunk-2] (customize.Rmd) + Error: processing vignette 'customize.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘customize.Rmd’ + + --- re-building ‘highlight.Rmd’ using rmarkdown + + Quitting from lines 37-44 [unnamed-chunk-2] (highlight.Rmd) + Error: processing vignette 'highlight.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘highlight.Rmd’ + + --- re-building ‘themes.Rmd’ using rmarkdown + ``` + +# ggdark + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/ggdark +* Date/Publication: 2019-01-11 17:30:06 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "ggdark")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggdark-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dark_mode + > ### Title: Activate dark mode on a 'ggplot2' theme + > ### Aliases: dark_mode + > + > ### ** Examples + > + > library(ggplot2) + ... + > + > p1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species)) + + + geom_point() + > + > p1 # theme returned by theme_get() + > p1 + dark_mode() # activate dark mode on theme returned by theme_get() + Error in match(x, table, nomatch = 0L) : + 'match' requires vector arguments + Calls: dark_mode -> %in% + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggdark) + > + > test_check("ggdark") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Error ('test_dark_mode.R:10:1'): (code run outside of `test_that()`) ──────── + Error in `match(x, table, nomatch = 0L)`: 'match' requires vector arguments + Backtrace: + ▆ + 1. └─ggdark::dark_mode(light_theme) at test_dark_mode.R:10:1 + 2. └─geoms[["GeomPoint"]]$default_aes$colour %in% ... + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggdist + +
+ +* Version: 3.3.2 +* GitHub: https://github.com/mjskay/ggdist +* Source code: https://github.com/cran/ggdist +* Date/Publication: 2024-03-05 05:30:23 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ggdist")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggdist-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Pr_ + > ### Title: Probability expressions in ggdist aesthetics + > ### Aliases: Pr_ p_ + > + > ### ** Examples + > + > library(ggplot2) + ... + + ) + > + > # map density onto alpha of the fill + > ggplot(df, aes(y = name, xdist = d)) + + + stat_slabinterval(aes(alpha = !!p_(x))) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + • test.stat_sample_slabinterval/nas-with-na-rm-true.svg + • test.subguide/dots-subguide-with-side-vertical.svg + • test.subguide/integer-subguide-with-zero-range.svg + • test.subguide/slab-subguide-with-inside-labels-vertical.svg + • test.subguide/slab-subguide-with-outside-labels-vert.svg + • test.subguide/slab-subguide-with-outside-labels.svg + • test.subguide/slab-subguide-with-side-vertical.svg + • test.theme_ggdist/facet-titles-on-left.svg + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dotsinterval.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + + Quitting from lines 49-161 [dotsinterval_components] (dotsinterval.Rmd) + Error: processing vignette 'dotsinterval.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ... + + --- re-building ‘freq-uncertainty-vis.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dotsinterval.Rmd’ + ... + + xdist = dist)) + geom_hline(yintercept = 0:1, color = "gray95") + + + stat_dotsin .... [TRUNCATED] + + When sourcing ‘dotsinterval.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 2nd layer. + Caused by error in `use_defaults()`: + ... + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), + Execution halted + + ‘dotsinterval.Rmd’ using ‘UTF-8’... failed + ‘freq-uncertainty-vis.Rmd’ using ‘UTF-8’... failed + ‘lineribbon.Rmd’ using ‘UTF-8’... failed + ‘slabinterval.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.3Mb + help 1.5Mb + ``` + +# ggeasy + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/jonocarroll/ggeasy +* Source code: https://github.com/cran/ggeasy +* Date/Publication: 2023-03-12 10:00:23 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "ggeasy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggeasy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: easy_labs + > ### Title: Easily add ggplot labels using label attribute of 'data.frame' + > ### column + > ### Aliases: easy_labs + > + > ### ** Examples + > + ... + + ggplot2::geom_line(ggplot2::aes(colour=Species)) + > + > p + > + > p + easy_labs() + > p + easy_labs(title = "Plot Title", subtitle = 'Plot Subtitle', x = 'x axis label') + Error in utils::modifyList(p_labs, as.list(unlist(man_labs))) : + is.list(x) is not TRUE + Calls: +.gg ... ggplot_add.easy_labs -> easy_update_labs -> -> stopifnot + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggeasy) + > + > test_check("ggeasy") + [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + 1. └─ggeasy (local) expect_eqNe(easy_res$labels[sort(names(easy_res$labels))], hard_res$labels[sort(names(hard_res$labels))]) at test-labs.R:76:3 + 2. └─testthat::expect_equal(..., check.environment = FALSE) at test-labs.R:6:16 + + [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] + Deleting unused snapshots: + • labs/labels-attrib.svg + • labs/labels-manual.svg + • labs/labels-mytitle.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘shortcuts.Rmd’ + ... + + > p1 <- p + labs(title = "default labels") + + > p2 <- p + easy_labs() + labs(title = "Replace titles with column labels") + + > p3 <- p + easy_labs(x = "My x axis") + labs(title = "Manually add x axis label") + + When sourcing ‘shortcuts.R’: + Error: is.list(x) is not TRUE + Execution halted + + ‘shortcuts.Rmd’ using ‘UTF-8’... failed + ‘tests_and_coverage.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘shortcuts.Rmd’ using rmarkdown + ``` + +# ggedit + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/yonicd/ggedit +* Source code: https://github.com/cran/ggedit +* Date/Publication: 2024-03-04 14:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "ggedit")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggedit-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dput.ggedit + > ### Title: Convert ggplot object to a string call + > ### Aliases: dput.ggedit + > + > ### ** Examples + > + > + > pList$pointSmooth #original compiled plot + `geom_smooth()` using formula = 'y ~ x' + Error in compute_geom_2(..., self = self) : + unused arguments (list(6), list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, + Calls: ... get_layer_key -> Map -> mapply -> -> + Execution halted + ``` + +# ggESDA + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/kiangkiangkiang/ggESDA +* Source code: https://github.com/cran/ggESDA +* Date/Publication: 2022-08-19 08:40:10 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "ggESDA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggESDA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BLOOD + > ### Title: BLOOD data example + > ### Aliases: BLOOD + > ### Keywords: datasets + > + > ### ** Examples + > + > data(BLOOD) + > ggInterval_minmax(BLOOD, aes(x = Hematocrit)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggInterval_minmax ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggESDA.Rmd’ + ... + [1] "knit_image_paths" "knit_asis" + + > CONCEPT <- rep(c("FRA", "HUS", "INC", "ISA", "JPL", + + "KHA", "LOT", "PHI", "ROM"), each = 3) + + > p <- ggInterval_PCA(facedata, poly = T, concepts_group = CONCEPT) + + When sourcing ‘ggESDA.R’: + Error: argument is of length zero + Execution halted + + ‘ggESDA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggESDA.Rmd’ using rmarkdown + + Quitting from lines 390-406 [ggInterval_PCA] (ggESDA.Rmd) + Error: processing vignette 'ggESDA.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggESDA.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggESDA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggExtra + +
+ +* Version: 0.10.1 +* GitHub: https://github.com/daattali/ggExtra +* Source code: https://github.com/cran/ggExtra +* Date/Publication: 2023-08-21 14:40:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "ggExtra")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggExtra.Rmd’ + ... + + > p1 <- ggplot(df1, aes(x, y)) + geom_point() + theme_bw() + + > p1 + + > ggMarginal(p1) + + When sourcing ‘ggExtra.R’: + Error: argument is of length zero + Execution halted + + ‘ggExtra.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggExtra.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘R6’ ‘scales’ ‘utils’ + All declared Imports should be used. + ``` + +# ggfacto + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/BriceNocenti/ggfacto +* Source code: https://github.com/cran/ggfacto +* Date/Publication: 2024-08-30 15:00:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "ggfacto")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggfacto-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MCA2 + > ### Title: Multiple Correspondence Analysis + > ### Aliases: MCA2 + > + > ### ** Examples + > + > data(tea, package = "FactoMineR") + > res.mca <- MCA2(tea, active_vars = 1:18) + > + > res.mca %>% + + ggmca(tea, sup_vars = c("SPC"), ylim = c(NA, 1.2), text_repel = TRUE) %>% + + ggi() #to make the graph interactive + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ggfixest + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/grantmcdermott/ggfixest +* Source code: https://github.com/cran/ggfixest +* Date/Publication: 2023-12-14 08:00:06 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "ggfixest")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > ## Throttle CPU threads if R CMD check (for CRAN) + > + > if (any(grepl("_R_CHECK", names(Sys.getenv()), fixed = TRUE))) { + + # fixest + + if (requireNamespace("fixest", quietly = TRUE)) { + + library(fixest) + + setFixest_nthreads(1) + ... + ----- FAILED[]: test_ggiplot.R<192--192> + call| expect_snapshot_plot(p19a, label = "ggiplot_multi_complex_kitchen_iid") + diff| 1774 + info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png + ----- FAILED[]: test_ggiplot.R<193--193> + call| expect_snapshot_plot(p19b, label = "ggiplot_multi_complex_kitchen_iid") + diff| 1774 + info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png + Error: 16 out of 101 tests failed + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggiplot.Rmd’ + ... + > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), + + ref.line = -1, main = "Staggered treatment: Split mutli-sample") + The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. + Note that you can provide the argument `df.t` directly. + + When sourcing ‘ggiplot.R’: + Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: + The 1st element of 'object' raises and error: + Error in nb * sd : non-numeric argument to binary operator + Execution halted + + ‘ggiplot.Rmd’ using ‘UTF-8’... failed + ``` + +# ggfocus + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/Freguglia/ggfocus +* Source code: https://github.com/cran/ggfocus +* Date/Publication: 2020-01-23 13:20:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "ggfocus")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction_to_ggfocus.Rmd’ + ... + + geom_point() + scale_alpha_focus(c("A", "B"), alpha_other = 0.5) + + + scale_c .... [TRUNCATED] + + > ggplot(datasets::airquality, aes(x = Day, y = Temp, + + linetype = factor(Month), group = factor(Month))) + geom_line() + + + scale_linetype_f .... [TRUNCATED] + + When sourcing ‘introduction_to_ggfocus.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘introduction_to_ggfocus.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction_to_ggfocus.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggforce + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/thomasp85/ggforce +* Source code: https://github.com/cran/ggforce +* Date/Publication: 2024-02-19 11:00:02 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "ggforce")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggforce-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_row + > ### Title: One-dimensional facets + > ### Aliases: facet_row facet_col + > + > ### ** Examples + > + > # Standard use + > ggplot(mtcars) + + + geom_point(aes(disp, mpg)) + + + facet_col(~gear) + Error in space$x : $ operator is invalid for atomic vectors + Calls: ... -> draw_panels -> -> init_gtable + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 27.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + help 1.2Mb + libs 25.0Mb + ``` + +# ggformula + +
+ +* Version: 0.12.0 +* GitHub: https://github.com/ProjectMOSAIC/ggformula +* Source code: https://github.com/cran/ggformula +* Date/Publication: 2023-11-09 12:30:07 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "ggformula")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggformula-Ex.R’ failed + The error most likely occurred in: + + > ### Name: discrete_breaks + > ### Title: Discrete Breaks + > ### Aliases: discrete_breaks + > + > ### ** Examples + > + > x <- rbinom(100, 100, 0.4) + > p <- gf_bar( ~ x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_bar ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggformula) + Loading required package: ggplot2 + Loading required package: scales + Loading required package: ggridges + + New to ggformula? Try the tutorials: + ... + • layer-factory/gf-text1.svg + • layer-factory/gf-text2.svg + • layer-factory/gf-tile1.svg + • layer-factory/proportions-within-all-dodge.svg + • layer-factory/proportions-within-fill-dodge.svg + • layer-factory/proportions-within-fill-facet-grid-and-group.svg + • layer-factory/proportions-within-fill-facet-grid.svg + • layer-factory/proportions-within-group-facet-grid.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggformula.Rmd’ + ... + + > theme_set(theme_light()) + + > library(ggformula) + + > gf_point(mpg ~ hp, data = mtcars) + + When sourcing ‘ggformula.R’: + Error: argument is of length zero + Execution halted + + ‘ggformula.Rmd’ using ‘UTF-8’... failed + ``` + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'gf_abline': + gf_hline + Code: function(object = NULL, gformula = NULL, data = NULL, ..., + yintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, position = "identity", + show.legend = NA, show.help = NULL, inherit = FALSE, + environment = parent.frame()) + Docs: function(object = NULL, gformula = NULL, data = NULL, ..., + yintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, show.legend = NA, + ... + xintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, show.legend = NA, + show.help = NULL, inherit = FALSE, environment = + parent.frame()) + Argument names in code not in docs: + position + Mismatches in argument names (first 3): + Position: 15 Code: position Docs: show.legend + Position: 16 Code: show.legend Docs: show.help + Position: 17 Code: show.help Docs: inherit + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggformula.Rmd’ using rmarkdown + + Quitting from lines 106-109 [simple-example] (ggformula.Rmd) + Error: processing vignette 'ggformula.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggformula.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggformula.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘akima’, ‘ggforce’ + ``` + +# ggfortify + +
+ +* Version: 0.4.17 +* GitHub: https://github.com/sinhrks/ggfortify +* Source code: https://github.com/cran/ggfortify +* Date/Publication: 2024-04-17 04:30:04 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "ggfortify")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggfortify-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.cv.glmnet + > ### Title: Autoplot 'glmnet::cv.glmnet' + > ### Aliases: autoplot.cv.glmnet + > + > ### ** Examples + > + > if (requireNamespace("survival", quietly = TRUE)) { + + autoplot(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3]))) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > + > suppressWarnings(RNGversion("3.5.0")) + > set.seed(1, sample.kind = "Rejection") + > + > test_check('ggfortify') + Loading required package: ggfortify + ... + 3. └─ggfortify:::autoplot.ts(original.data, columns = "Data", ...) + 4. └─ggplot2:::`+.gg`(p, do.call(geom_factory, args)) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 32 | WARN 10 | SKIP 47 | PASS 358 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basics.Rmd’ + ... + + warning = FALSE) + + > library(ggfortify) + Loading required package: ggplot2 + + > autoplot(AirPassengers) + + ... + Error: argument is of length zero + Execution halted + + ‘basics.Rmd’ using ‘UTF-8’... failed + ‘plot_dist.Rmd’ using ‘UTF-8’... failed + ‘plot_lm.Rmd’ using ‘UTF-8’... OK + ‘plot_map.Rmd’ using ‘UTF-8’... failed + ‘plot_pca.Rmd’ using ‘UTF-8’... OK + ‘plot_surv.Rmd’ using ‘UTF-8’... failed + ‘plot_ts.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basics.Rmd’ using knitr + + Attaching package: 'zoo' + + The following objects are masked from 'package:base': + + as.Date, as.Date.numeric + + + ... + + Quitting from lines 20-22 [unnamed-chunk-1] (plot_dist.Rmd) + Error: processing vignette 'plot_dist.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘plot_dist.Rmd’ + + --- re-building ‘plot_lm.Rmd’ using knitr + --- finished re-building ‘plot_lm.Rmd’ + + --- re-building ‘plot_map.Rmd’ using knitr + ``` + +# gggenomes + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/thackl/gggenomes +* Source code: https://github.com/cran/gggenomes +* Date/Publication: 2024-08-30 11:40:02 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "gggenomes")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gggenomes-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flip + > ### Title: Flip bins and sequences + > ### Aliases: flip flip_seqs sync + > + > ### ** Examples + > + > library(patchwork) + ... + > p4 <- p %>% + + add_clusters(emale_cogs) %>% + + sync() + labs(caption = "shared orthologs") + Joining with `by = join_by(feat_id)` + Flipping: E4-10_086,E4-10_112,RCC970_016B + > + > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘flip.Rmd’ + ... + > p4 <- p %>% add_clusters(emale_cogs) %>% sync() + + + labs(caption = "shared orthologs") + Joining with `by = join_by(feat_id)` + Flipping: E4-10_086,E4-10_112,RCC970_016B + + > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") + + When sourcing ‘flip.R’: + Error: object is not coercible to a unit + Execution halted + + ‘emales.Rmd’ using ‘UTF-8’... OK + ‘flip.Rmd’ using ‘UTF-8’... failed + ‘gggenomes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘emales.Rmd’ using rmarkdown + --- finished re-building ‘emales.Rmd’ + + --- re-building ‘flip.Rmd’ using rmarkdown + + Quitting from lines 17-44 [unnamed-chunk-2] (flip.Rmd) + Error: processing vignette 'flip.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘flip.Rmd’ + ... + virophages) + emale_tirs Terminal inverted repeats of 6 EMALE genomes + + --- finished re-building ‘gggenomes.Rmd’ + + SUMMARY: processing the following file failed: + ‘flip.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggh4x + +
+ +* Version: 0.2.8 +* GitHub: https://github.com/teunbrand/ggh4x +* Source code: https://github.com/cran/ggh4x +* Date/Publication: 2024-01-23 21:00:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "ggh4x")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggh4x) + Loading required package: ggplot2 + > + > test_check("ggh4x") + [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] + + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-facet_wrap2.R:64:3'): facet_wrap2() can some repeat axes ───── + sum(ctrl) (`actual`) not equal to 4L (`expected`). + + `actual`: 3 + `expected`: 4 + + [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Facets.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Statistics.Rmd’ + ... + > incorrect$x[15] <- sqrt(2) + + > ggplot(incorrect, aes(x, colour = group)) + stat_theodensity(distri = "nbinom") + + When sourcing ‘Statistics.R’: + Error: Problem while computing stat. + ℹ Error occurred in the 1st layer. + Caused by error in `setup_params()`: + ! A discrete 'nbinom' distribution cannot be fitted to continuous data. + Execution halted + + ‘Facets.Rmd’ using ‘UTF-8’... OK + ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK + ‘PositionGuides.Rmd’ using ‘UTF-8’... OK + ‘Statistics.Rmd’ using ‘UTF-8’... failed + ‘ggh4x.Rmd’ using ‘UTF-8’... OK + ``` + +# gghighlight + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/yutannihilation/gghighlight +* Source code: https://github.com/cran/gghighlight +* Date/Publication: 2023-12-16 01:00:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "gghighlight")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gghighlight-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gghighlight + > ### Title: Highlight Data With Predicate + > ### Aliases: gghighlight + > + > ### ** Examples + > + > d <- data.frame( + ... + 8. │ ├─purrr:::with_indexed_errors(...) + 9. │ │ └─base::withCallingHandlers(...) + 10. │ ├─purrr:::call_with_cleanup(...) + 11. │ └─gghighlight (local) .f(.x[[i]], .y[[i]], ...) + 12. │ └─gghighlight:::get_default_aes_param(nm, layer$geom, layer$mapping) + 13. └─base::.handleSimpleError(...) + 14. └─purrr (local) h(simpleError(msg, call)) + 15. └─cli::cli_abort(...) + 16. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gghighlight) + Loading required package: ggplot2 + > + > test_check("gghighlight") + label_key: type + label_key: type + ... + 15. └─cli::cli_abort(...) + 16. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 1 | PASS 178 ] + Deleting unused snapshots: + • vdiffr/simple-bar-chart-with-facet.svg + • vdiffr/simple-line-chart.svg + • vdiffr/simple-point-chart.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gghighlight.Rmd’ + ... + Warning in is.na(non_null_default_aes[[aes_param_name]]) : + is.na() applied to non-(list or vector) of type 'language' + + When sourcing ‘gghighlight.R’: + Error: ℹ In index: 1. + ℹ With name: geom_point. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + aes_param_name]])`: + ! 'length = 2' in coercion to 'logical(1)' + Execution halted + + ‘gghighlight.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘gghighlight.Rmd’ using rmarkdown + ``` + +# ggHoriPlot + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/rivasiker/ggHoriPlot +* Source code: https://github.com/cran/ggHoriPlot +* Date/Publication: 2022-10-11 16:22:33 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "ggHoriPlot")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggHoriPlot.Rmd’ + ... + > mid <- sum(range(dat_tab$y, na.rm = T))/2 + + > b <- plotAllLayers(dat_tab, mid, cutpoints$cuts, cutpoints$color) + + > b/a + plot_layout(guides = "collect", heights = c(6, + + 1)) + + When sourcing ‘ggHoriPlot.R’: + Error: object is not a unit + Execution halted + + ‘examples.Rmd’ using ‘UTF-8’... OK + ‘ggHoriPlot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘examples.Rmd’ using rmarkdown + ``` + +# ggiraph + +
+ +* Version: 0.8.10 +* GitHub: https://github.com/davidgohel/ggiraph +* Source code: https://github.com/cran/ggiraph +* Date/Publication: 2024-05-17 12:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "ggiraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggiraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate_interactive + > ### Title: Create interactive annotations + > ### Aliases: annotate_interactive + > + > ### ** Examples + > + > # add interactive annotation to a ggplot ------- + ... + > + > gg <- ggplot(mtcars, aes(x = disp, y = qsec )) + + + geom_point(size=2) + + + annotate_interactive( + + "rect", xmin = 100, xmax = 400, fill = "red", + + data_id = "an_id", tooltip = "a tooltip", + + ymin = 18, ymax = 20, alpha = .5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > if (requireNamespace("tinytest", quietly = TRUE)) { + + tinytest::test_package("ggiraph") + + } + + test-annotate_interactive.R... 0 tests + test-annotate_interactive.R... 0 tests + test-annotate_interactive.R... 0 tests + ... + test-geom_density_interactive.R 8 tests OK 8ms + + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 8 tests OK Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 7.1Mb + ``` + +# ggiraphExtra + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/cardiomoon/ggiraphExtra +* Source code: https://github.com/cran/ggiraphExtra +* Date/Publication: 2020-10-06 07:00:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggiraphExtra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggAncova + > ### Title: Make an interactive plot for an ANCOVA model + > ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm + > + > ### ** Examples + > + > require(moonBook) + ... + addLabelDf, getMapping + + > require(ggplot2) + Loading required package: ggplot2 + > require(ggiraph) + Loading required package: ggiraph + > ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggAncova ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggPredict.Rmd’ + ... + + + > require(plyr) + Loading required package: plyr + + > ggPredict(fit, se = TRUE, interactive = TRUE) + + ... + + > ggPoints(aes(x = wt, y = mpg, color = am), data = mtcars, + + method = "lm", interactive = TRUE) + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘ggPredict.Rmd’ using ‘UTF-8’... failed + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggPredict.Rmd’ using rmarkdown + ``` + +# ggmatplot + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/xuan-liang/ggmatplot +* Source code: https://github.com/cran/ggmatplot +* Date/Publication: 2022-05-17 02:20:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ggmatplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggmatplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggmatplot + > ### Title: ggmatplot + > ### Aliases: ggmatplot + > + > ### ** Examples + > + > + > # Define a data set + > iris_sub <- subset(iris, Species == "setosa") + > ggmatplot(iris_sub[, c(1, 3)], iris_sub[, c(2, 4)]) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggmatplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggmatplot) + Loading required package: ggplot2 + > library(tibble) + > library(stats) + > + > test_check("ggmatplot") + ... + • ggmatplot_parameters/single-color-scatterplot.svg + • ggmatplot_parameters/single-fill-density-plot.svg + • ggmatplot_parameters/single-linetype-line-plot.svg + • ggmatplot_parameters/single-shape-scatterplot.svg + • ggmatplot_parameters/three-color-violin-plot.svg + • ggmatplot_parameters/three-fill-color-violin-plot.svg + • ggmatplot_parameters/three-linetype-line-plot.svg + • ggmatplot_parameters/three-shape-scatterplot.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggmatplot.Rmd’ + ... + 6 -0.5325916 -0.54457006 + + > library(ggmatplot) + Loading required package: ggplot2 + + > ggmatplot(x, z) + + When sourcing ‘ggmatplot.R’: + Error: argument is of length zero + Execution halted + + ‘ggmatplot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggmatplot.Rmd’ using rmarkdown + + Quitting from lines 47-50 [point-plot] (ggmatplot.Rmd) + Error: processing vignette 'ggmatplot.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggmatplot.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggmatplot.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggmice + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/amices/ggmice +* Source code: https://github.com/cran/ggmice +* Date/Publication: 2023-08-07 14:20:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "ggmice")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘old_friends.Rmd’ + ... + layout + + + > p <- plot_flux(dat) + + > ggplotly(p) + + When sourcing ‘old_friends.R’: + Error: subscript out of bounds + Execution halted + + ‘ggmice.Rmd’ using ‘UTF-8’... OK + ‘old_friends.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggmice.Rmd’ using rmarkdown + ``` + +# ggmulti + +
+ +* Version: 1.0.7 +* GitHub: NA +* Source code: https://github.com/cran/ggmulti +* Date/Publication: 2024-04-09 09:40:05 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "ggmulti")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggmulti-Ex.R’ failed + The error most likely occurred in: + + > ### Name: coord_radial + > ### Title: Radial axes + > ### Aliases: coord_radial + > + > ### ** Examples + > + > if(require("dplyr")) { + ... + + The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > + > + > library(testthat) + > library(ggmulti) + Loading required package: ggplot2 + + Attaching package: 'ggmulti' + ... + 16. └─base::Map(...) + 17. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 18. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 19. └─layer$compute_geom_2(key, single_params, theme) + 20. └─ggplot2 (local) compute_geom_2(..., self = self) + 21. └─self$geom$use_defaults(...) + + [ FAIL 4 | WARN 5 | SKIP 0 | PASS 30 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘glyph.Rmd’ + ... + + Sepal.Width, colour = Species), serialaxes.data = iris, axes.layout = "radia ..." ... [TRUNCATED] + + When sourcing ‘glyph.R’: + Error: Base operators are not defined for quosures. Do you need to unquote the + quosure? + + # Bad: myquosure / rhs + ... + + > p + + When sourcing ‘highDim.R’: + Error: argument is of length zero + Execution halted + + ‘glyph.Rmd’ using ‘UTF-8’... failed + ‘highDim.Rmd’ using ‘UTF-8’... failed + ‘histogram-density-.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘glyph.Rmd’ using rmarkdown + ``` + +# ggpackets + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/dgkf/ggpackets +* Source code: https://github.com/cran/ggpackets +* Date/Publication: 2022-10-10 23:30:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "ggpackets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpackets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggpacket + > ### Title: A container for lazy ggplot layers + > ### Aliases: ggpacket + > + > ### ** Examples + > + > library(ggplot2) + > + > # create a ggpacket directly, setting some fixed argument settings + > ggpk_simple <- ggpacket() %+% geom_line(color = "red") %+% geom_point() + > ggplot(mtcars, aes(x = wt, y = mpg)) + ggpk_simple() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > library(ggplot2) + > library(ggpackets) + + Attaching package: 'ggpackets' + + ... + 10. └─ggpackets (local) f(init, x[[i]]) + 11. └─ggplot2:::`+.gg`(gg, ggpk_i) + 12. └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. ├─ggplot2::ggplot_add(object, p, objectname) + 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 4 | WARN 1 | SKIP 0 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘composing-functions.Rmd’ + ... + + geom_point(size = 3) + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + > ggplot(Loblolly) + aes(x = age, y = height, color = Seed) + + + ggpk_my_template() + ggtitle("Growth of Loblolly Pines") + + ... + > diamonds %>% sample_frac(0.01) %>% arrange(cut) %>% + + ggplot() + aes(color = cut) + ggpk_dot_matrix(size = 3, width = 30) + + When sourcing ‘miscellaneous-examples.R’: + Error: argument is of length zero + Execution halted + + ‘composing-functions.Rmd’ using ‘UTF-8’... failed + ‘ggpackets.Rmd’ using ‘UTF-8’... failed + ‘miscellaneous-examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘composing-functions.Rmd’ using rmarkdown + + Quitting from lines 58-62 [simple_ggpacket_output] (composing-functions.Rmd) + Error: processing vignette 'composing-functions.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘composing-functions.Rmd’ + + --- re-building ‘ggpackets.Rmd’ using rmarkdown + ``` + +# ggparallel + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/heike/ggparallel +* Source code: https://github.com/cran/ggparallel +* Date/Publication: 2024-03-09 22:00:02 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "ggparallel")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 12. └─self$get_layer_key(params, layers[include], data[include], theme) + 13. └─ggplot2 (local) get_layer_key(...) + 14. └─base::Map(...) + 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 17. └─layer$compute_geom_2(key, single_params, theme) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# ggparty + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/martin-borkovec/ggparty +* Source code: https://github.com/cran/ggparty +* Date/Publication: 2019-07-18 10:54:06 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggparty")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggparty-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_node_label + > ### Title: Draw (multi-line) labels at nodes + > ### Aliases: geom_node_label geom_node_info geom_node_splitvar + > + > ### ** Examples + > + > library(ggparty) + ... + 30. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 31. │ ├─ggplot2::ggplot_add(object, p, objectname) + 32. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 33. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggparty-graphic-partying.Rmd’ + ... + + 0.55 .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘ggparty-graphic-partying.R’: + Error: Problem while converting geom to grob. + ℹ Error occurred in the 5th layer. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘ggparty-graphic-partying.Rmd’ using ‘UTF-8’... failed + ‘on-the-edge.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggparty-graphic-partying.Rmd’ using rmarkdown + + Quitting from lines 42-122 [unnamed-chunk-2] (ggparty-graphic-partying.Rmd) + Error: processing vignette 'ggparty-graphic-partying.Rmd' failed with diagnostics: + Problem while converting geom to grob. + ℹ Error occurred in the 5th layer. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘ggparty-graphic-partying.Rmd’ + + --- re-building ‘on-the-edge.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘survival’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggpicrust2 + +
+ +* Version: 1.7.3 +* GitHub: https://github.com/cafferychen777/ggpicrust2 +* Source code: https://github.com/cran/ggpicrust2 +* Date/Publication: 2023-11-08 16:10:02 UTC +* Number of recursive dependencies: 231 + +Run `revdepcheck::cloud_details(, "ggpicrust2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpicrust2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pathway_pca + > ### Title: Perform Principal Component Analysis (PCA) on functional pathway + > ### abundance data and create visualizations of the PCA results. + > ### Aliases: pathway_pca + > + > ### ** Examples + > + ... + > + > # Create example metadata + > # Please ensure the sample IDs in the metadata have the column name "sample_name" + > metadata_example <- data.frame(sample_name = colnames(kegg_abundance_example), + + group = factor(rep(c("Control", "Treatment"), each = 5))) + > + > pca_plot <- pathway_pca(kegg_abundance_example, metadata_example, "group") + Error in identicalUnits(x) : object is not a unit + Calls: pathway_pca ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ComplexHeatmap’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + R 2.1Mb + data 2.0Mb + ``` + +# ggplotlyExtra + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/ggplotlyExtra +* Date/Publication: 2019-12-02 16:20:06 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "ggplotlyExtra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggplotlyExtra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplotly_histogram + > ### Title: Clean 'ggplot2' Histogram to be Converted to 'Plotly' + > ### Aliases: ggplotly_histogram + > + > ### ** Examples + > + > + ... + + xlab("len") + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + Warning in geom_bar(data = layerdata, mapping = aes(x = .data$x, y = .data$count, : + Ignoring unknown aesthetics: label1, label2, and label3 + > + > # convert `ggplot` object to `plotly` object + > ggplotly(p, tooltip = c("Range", "count", "density")) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggPMX + +
+ +* Version: 1.2.11 +* GitHub: https://github.com/ggPMXdevelopment/ggPMX +* Source code: https://github.com/cran/ggPMX +* Date/Publication: 2023-11-30 16:10:06 UTC +* Number of recursive dependencies: 181 + +Run `revdepcheck::cloud_details(, "ggPMX")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggPMX-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pmx_config + > ### Title: This function can be used to define the pmx configuration used + > ### in plots. e.g. Monolix/Nonmem + > ### Aliases: pmx_config + > + > ### ** Examples + > + ... + + cats = c("SEX"), + + conts = c("WT0", "AGE0"), + + strats = "STUD" + + ) + NO FINEGRID FILE: + we will use instead predictions.txt for individual plots + Warning: Duplicated aesthetics after name standardisation: colour + Error in if (new_name %in% existing) { : argument is of length zero + Calls: pmx_mlx ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggPMX-guide.Rmd’ + ... + + > work_dir <- file.path(theophylline, "Monolix") + + > input_data <- file.path(theophylline, "data_pk.csv") + + > ctr <- theophylline() + + When sourcing ‘ggPMX-guide.R’: + Error: argument is of length zero + Execution halted + + ‘ggPMX-guide.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggPMX-guide.Rmd’ using rmarkdown + + Quitting from lines 25-37 [load_package] (ggPMX-guide.Rmd) + Error: processing vignette 'ggPMX-guide.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggPMX-guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggPMX-guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘lixoftConnectors’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + doc 1.1Mb + help 2.4Mb + testdata 4.8Mb + ``` + +# ggpol + +
+ +* Version: 0.0.7 +* GitHub: https://github.com/erocoar/ggpol +* Source code: https://github.com/cran/ggpol +* Date/Publication: 2020-11-08 13:40:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "ggpol")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpol-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GeomConfmat + > ### Title: Confusion Matrix + > ### Aliases: GeomConfmat geom_confmat stat_confmat + > + > ### ** Examples + > + > x <- sample(LETTERS[seq(4)], 50, replace = TRUE) + ... + 21. │ └─ggpol (local) draw_panel(...) + 22. │ └─base::lapply(GeomText$default_aes[missing_aes], rlang::eval_tidy) + 23. │ └─rlang (local) FUN(X[[i]], ...) + 24. ├─ggplot2::from_theme(fontsize) + 25. └─base::.handleSimpleError(...) + 26. └─rlang (local) h(simpleError(msg, call)) + 27. └─handlers[[1L]](cnd) + 28. └─cli::cli_abort(...) + 29. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘grDevices’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggprism + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/csdaw/ggprism +* Source code: https://github.com/cran/ggprism +* Date/Publication: 2024-03-21 10:50:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "ggprism")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggprism-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_pvalue + > ### Title: Add p-values to a ggplot + > ### Aliases: add_pvalue + > + > ### ** Examples + > + > library(ggplot2) + ... + + "OJ", "VC", 0.0606, 36 + + ) + > + > # boxplot (or another geom...) + > ggplot(tg, aes(x = supp, y = len)) + + + geom_boxplot() + + + add_pvalue(two.means) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("ggprism") + + } + + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + ... + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggprism.Rmd’ + ... + + p.adj = 0.0606, y.position = 36) + + > p1 <- ggplot(ToothGrowth, aes(x = factor(supp), y = len)) + + + geom_boxplot(aes(fill = factor(supp))) + scale_fill_prism(palette = "candy_bright ..." ... [TRUNCATED] + + > p2 <- p1 + add_pvalue(df_p_val) + + ... + + When sourcing ‘pvalues.R’: + Error: argument is of length zero + Execution halted + + ‘axes.Rmd’ using ‘UTF-8’... OK + ‘colours.Rmd’ using ‘UTF-8’... OK + ‘ggprism.Rmd’ using ‘UTF-8’... failed + ‘pvalues.Rmd’ using ‘UTF-8’... failed + ‘themes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘axes.Rmd’ using rmarkdown + ``` + +# ggpubr + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/kassambara/ggpubr +* Source code: https://github.com/cran/ggpubr +* Date/Publication: 2023-02-10 16:20:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "ggpubr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpubr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_summary + > ### Title: Add Summary Statistics onto a ggplot. + > ### Aliases: add_summary mean_se_ mean_sd mean_ci mean_range median_iqr + > ### median_hilow_ median_q1q3 median_mad median_range + > + > ### ** Examples + > + ... + 10. │ └─ggplot2:::`+.gg`(...) + 11. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 12. │ ├─ggplot2::ggplot_add(object, p, objectname) + 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 15. └─base::.handleSimpleError(...) + 16. └─purrr (local) h(simpleError(msg, call)) + 17. └─cli::cli_abort(...) + 18. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggpubr) + Loading required package: ggplot2 + > + > test_check("ggpubr") + [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + + ... + 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 15. └─base::.handleSimpleError(...) + 16. └─purrr (local) h(simpleError(msg, call)) + 17. └─cli::cli_abort(...) + 18. └─rlang::abort(...) + + [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + Error: Test failures + Execution halted + ``` + +# ggrain + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/njudd/ggrain +* Source code: https://github.com/cran/ggrain +* Date/Publication: 2024-01-23 11:50:02 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "ggrain")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggrain-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_rain + > ### Title: Raincloud Plots + > ### Aliases: geom_rain + > + > ### ** Examples + > + > e1 <- ggplot(iris, aes(Species, Sepal.Width, fill = Species)) + > e1 + geom_rain() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggrain.Rmd’ + ... + > library(ggrain) + Loading required package: ggplot2 + + > ggplot(iris, aes(1, Sepal.Width)) + geom_rain() + + + theme_classic() + theme(axis.title.x = element_blank(), axis.text.x = element_blank(), + + .... [TRUNCATED] + + When sourcing ‘ggrain.R’: + Error: argument is of length zero + Execution halted + + ‘ggrain.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggrain.Rmd’ using rmarkdown + + Quitting from lines 36-41 [most basic raincloud possible] (ggrain.Rmd) + Error: processing vignette 'ggrain.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggrain.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggrain.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggraph + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/thomasp85/ggraph +* Source code: https://github.com/cran/ggraph +* Date/Publication: 2024-03-07 12:40:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_conn_bundle + > ### Title: Create hierarchical edge bundles between node connections + > ### Aliases: geom_conn_bundle geom_conn_bundle2 geom_conn_bundle0 + > + > ### ** Examples + > + > # Create a graph of the flare class system + ... + + ) + + + geom_node_point(aes(filter = leaf, colour = class)) + + + scale_edge_colour_distiller('', direction = 1, guide = 'edge_direction') + + + coord_fixed() + + + ggforce::theme_no_axes() + Error in get_layer_key(...) : + unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, + Calls: ... -> -> process_layers -> + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Edges.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Edges.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + ... + font family 'Arial' not found in PostScript font database + + When sourcing ‘tidygraph.R’: + Error: invalid font type + Execution halted + + ‘Edges.Rmd’ using ‘UTF-8’... failed + ‘Layouts.Rmd’ using ‘UTF-8’... failed + ‘Nodes.Rmd’ using ‘UTF-8’... failed + ‘tidygraph.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 3.9Mb + libs 2.8Mb + ``` + +# ggredist + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/alarm-redist/ggredist +* Source code: https://github.com/cran/ggredist +* Date/Publication: 2022-11-23 11:20:02 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "ggredist")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggredist-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_district_text + > ### Title: Label Map Regions + > ### Aliases: geom_district_text geom_district_label + > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText + > ### Keywords: datasets + > + > ### ** Examples + ... + 22. │ └─coord$transform(data, panel_params) + 23. │ └─ggplot2 (local) transform(..., self = self) + 24. │ └─ggplot2:::sf_rescale01(...) + 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) + 26. └─base::.handleSimpleError(...) + 27. └─rlang (local) h(simpleError(msg, call)) + 28. └─handlers[[1L]](cnd) + 29. └─cli::cli_abort(...) + 30. └─rlang::abort(...) + Execution halted + ``` + +# ggRtsy + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ggRtsy +* Date/Publication: 2023-09-15 19:12:05 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "ggRtsy")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggplot2) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + ... + 13. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) + 14. │ └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call) + 15. └─vctrs (local) ``() + 16. └─vctrs:::stop_subscript_oob(...) + 17. └─vctrs:::stop_subscript(...) + 18. └─rlang::abort(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Vignette.Rmd’ + ... + |Antique White |(238, 223, 204) |#eedfcc | + + > RectangleFiller(plotExample, c("#e32636", "#9966cc", + + "#f4c2c2", "#e16827")) + + When sourcing ‘Vignette.R’: + Error: Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. + Execution halted + + ‘Vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Vignette.Rmd’ using rmarkdown + + Quitting from lines 48-49 [unnamed-chunk-2] (Vignette.Rmd) + Error: processing vignette 'Vignette.Rmd' failed with diagnostics: + Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. + --- failed re-building ‘Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 19 marked UTF-8 strings + ``` + +# ggseqplot + +
+ +* Version: 0.8.4 +* GitHub: https://github.com/maraab23/ggseqplot +* Source code: https://github.com/cran/ggseqplot +* Date/Publication: 2024-05-17 21:40:03 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "ggseqplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggseqplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggseqrfplot + > ### Title: Relative Frequency Sequence Plot + > ### Aliases: ggseqrfplot + > + > ### ** Examples + > + > # Load additional library for fine-tuning the plots + ... + [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 + > + > # ... with ggseqrfplot + > ggseqrfplot(biofam.seq, weighted = FALSE, diss = diss, k = 12, grp.meth="first") + [>] Using k=12 frequency groups with grp.meth='first' + [>] Pseudo/medoid-based-R2: 0.4620155 + [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggseqplot) + Loading required package: TraMineR + + TraMineR stable version 2.2-10 (Built: 2024-05-22) + Website: http://traminer.unige.ch + Please type 'citation("TraMineR")' for citation information. + ... + Backtrace: + ▆ + 1. ├─testthat::expect_s3_class(ggseqtrplot(biofam.seq), "ggplot") at test-ggseqtrplot.R:35:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─ggseqplot::ggseqtrplot(biofam.seq) + + [ FAIL 1 | WARN 1045 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggseqplot.Rmd’ + ... + > p1 + p2 + plot_layout(guides = "collect") & scale_fill_manual(values = canva_palettes$`Fun and tropical`[1:4]) & + + theme_ipsum(base_family = "" .... [TRUNCATED] + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + + When sourcing ‘ggseqplot.R’: + Error: object is not coercible to a unit + Execution halted + + ‘ggseqplot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggseqplot.Rmd’ using rmarkdown + ``` + +# ggside + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/jtlandis/ggside +* Source code: https://github.com/cran/ggside +* Date/Publication: 2024-03-01 09:12:37 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "ggside")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggplot2) + > library(ggside) + Registered S3 method overwritten by 'ggside': + method from + +.gg ggplot2 + > + ... + • ops_meaningful/alpha-0-5-from-function.svg + • side_layers/boxplot2.svg + • vdiff_irisScatter/collapsed-histo.svg + • vdiff_irisScatter/facetgrid-collapsed-density.svg + • vdiff_irisScatter/facetgrid-histo.svg + • vdiff_irisScatter/facetgrid-side-density.svg + • vdiff_irisScatter/stacked-side-density.svg + • vdiff_irisScatter/yside-histo.svg + Error: Test failures + Execution halted + ``` + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'geom_xsideabline': + geom_xsidehline + Code: function(mapping = NULL, data = NULL, position = "identity", + ..., yintercept, na.rm = FALSE, show.legend = NA) + Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = + FALSE, show.legend = NA) + Argument names in code not in docs: + position + Mismatches in argument names (first 3): + Position: 3 Code: position Docs: ... + ... + Docs: function(mapping = NULL, data = NULL, stat = "identity", + position = "identity", ..., lineend = "butt", linejoin + = "round", linemitre = 10, arrow = NULL, na.rm = + FALSE, show.legend = NA, inherit.aes = TRUE) + Argument names in code not in docs: + arrow.fill + Mismatches in argument names: + Position: 10 Code: arrow.fill Docs: na.rm + Position: 11 Code: na.rm Docs: show.legend + Position: 12 Code: show.legend Docs: inherit.aes + ``` + +# ggsmc + +
+ +* Version: 0.1.2.0 +* GitHub: https://github.com/richardgeveritt/ggsmc +* Source code: https://github.com/cran/ggsmc +* Date/Publication: 2024-07-27 17:00:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "ggsmc")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Visualising.Rmd’ + ... + 20 /tmp/RtmpuaCJEi/100d113de41a/gganim_plot0020.png + + > data(lv_output) + + > animate_reveal_time_series(lv_output, parameters = c("X", + + "Y"), alpha = 0.5, ylimits = c(0, 600), duration = 10) + + When sourcing ‘Visualising.R’: + Error: argument "theme" is missing, with no default + Execution halted + + ‘Visualising.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 175 marked UTF-8 strings + ``` + +# ggspatial + +
+ +* Version: 1.1.9 +* GitHub: https://github.com/paleolimbot/ggspatial +* Source code: https://github.com/cran/ggspatial +* Date/Publication: 2023-08-17 15:32:38 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "ggspatial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggspatial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotation_spatial_hline + > ### Title: Projected horizontal and vertical lines + > ### Aliases: annotation_spatial_hline annotation_spatial_vline + > ### GeomSpatialXline + > ### Keywords: datasets + > + > ### ** Examples + ... + 25. │ └─grid:::validGP(list(...)) + 26. │ └─grid (local) numnotnull("fontsize") + 27. │ └─grid (local) check.length(gparname) + 28. │ └─base::stop(...) + 29. └─base::.handleSimpleError(...) + 30. └─rlang (local) h(simpleError(msg, call)) + 31. └─handlers[[1L]](cnd) + 32. └─cli::cli_abort(...) + 33. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggspatial) + > + > test_check("ggspatial") + Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] + + ... + 33. │ └─base::stop(...) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) + + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] + Error: Test failures + Execution halted + ``` + +# ggstatsplot + +
+ +* Version: 0.12.4 +* GitHub: https://github.com/IndrajeetPatil/ggstatsplot +* Source code: https://github.com/cran/ggstatsplot +* Date/Publication: 2024-07-06 16:22:07 UTC +* Number of recursive dependencies: 174 + +Run `revdepcheck::cloud_details(, "ggstatsplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggstatsplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggscatterstats + > ### Title: Scatterplot with marginal distributions and statistical results + > ### Aliases: ggscatterstats + > + > ### ** Examples + > + > set.seed(123) + ... + + iris, + + x = Sepal.Width, + + y = Petal.Length, + + label.var = Species, + + label.expression = Sepal.Length > 7.6 + + ) + + + ggplot2::geom_rug(sides = "b") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggscatterstats ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggstatsplot.Rmd’ + ... + author = {Indrajeet Patil}, + title = {{Visualizations with statistical details: The {'ggstatsplot'} approach}}, + journal = {{Journal of Open Source Software}}, + } + + > ggbetweenstats(iris, Species, Sepal.Length) + + When sourcing ‘ggstatsplot.R’: + Error: argument is of length zero + Execution halted + + ‘additional.Rmd’ using ‘UTF-8’... OK + ‘ggstatsplot.Rmd’ using ‘UTF-8’... failed + ``` + +# ggtern + +
+ +* Version: 3.5.0 +* GitHub: NA +* Source code: https://github.com/cran/ggtern +* Date/Publication: 2024-03-24 21:50:02 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "ggtern")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggtern-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate + > ### Title: Create an annotation layer (ggtern version). + > ### Aliases: annotate + > + > ### ** Examples + > + > ggtern() + + ... + 3. ├─ggtern::ggplot_build(x) + 4. └─ggtern:::ggplot_build.ggplot(x) + 5. └─ggtern:::layers_add_or_remove_mask(plot) + 6. └─ggint$plot_theme(plot) + 7. └─ggplot2:::validate_theme(theme) + 8. └─base::mapply(...) + 9. └─ggplot2 (local) ``(...) + 10. └─cli::cli_abort(...) + 11. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘sp’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘chemometrics’ + ``` + +# ggupset + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/const-ae/ggupset +* Source code: https://github.com/cran/ggupset +* Date/Publication: 2024-06-24 10:10:04 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "ggupset")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggupset-Ex.R’ failed + The error most likely occurred in: + + > ### Name: axis_combmatrix + > ### Title: Convert delimited text labels into a combination matrix axis + > ### Aliases: axis_combmatrix + > + > ### ** Examples + > + > library(ggplot2) + ... + Datsun 710 Cyl: 4_Gears: 4 + Hornet 4 Drive Cyl: 6_Gears: 3 + Hornet Sportabout Cyl: 8_Gears: 3 + Valiant Cyl: 6_Gears: 3 + > ggplot(mtcars, aes(x=combined)) + + + geom_bar() + + + axis_combmatrix(sep = "_") + Error in as.unit(e2) : object is not coercible to a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit + Execution halted + ``` + +# ggVennDiagram + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/gaospecial/ggVennDiagram +* Source code: https://github.com/cran/ggVennDiagram +* Date/Publication: 2024-02-20 08:10:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "ggVennDiagram")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘fully-customed.Rmd’ + ... + [1] "b" "c" "e" "h" "k" "q" "s" "y" + + + > ggVennDiagram(y, show_intersect = TRUE, set_color = "black") + Warning in geom_text(aes(label = .data$count, text = .data$item), data = region_label) : + Ignoring unknown aesthetics: text + + ... + Ignoring unknown aesthetics: text + + When sourcing ‘using-ggVennDiagram.R’: + Error: subscript out of bounds + Execution halted + + ‘VennCalculator.Rmd’ using ‘UTF-8’... OK + ‘fully-customed.Rmd’ using ‘UTF-8’... failed + ‘using-ggVennDiagram.Rmd’ using ‘UTF-8’... failed + ‘using-new-shapes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘VennCalculator.Rmd’ using rmarkdown + --- finished re-building ‘VennCalculator.Rmd’ + + --- re-building ‘fully-customed.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.1Mb + sub-directories of 1Mb or more: + doc 9.5Mb + help 1.1Mb + ``` + +# GimmeMyPlot + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/GimmeMyPlot +* Date/Publication: 2023-10-18 16:10:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GimmeMyPlot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_violin + > ### Title: Violin plot + > ### Aliases: plot_violin + > + > ### ** Examples + > + > library(RColorBrewer) + ... + + width_text = 5, + + pch_colour = "gray30", + + pch_alpha = 0.5, + + width_title = 30, + + lwd = 1.25, + + digits = 2 + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_violin ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 4. └─GimmeMyPlot::plot_violin(df) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + > df[, 3] <- runif(10, 1, 2) + + > colnames(df) <- paste0("X", seq(3)) + + > plot_violin(df, title = "Some random variables", colour = brewer.pal(9, + + "Set1")[seq(3)]) + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 24-57 [violin] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# giniVarCI + +
+ +* Version: 0.0.1-3 +* GitHub: NA +* Source code: https://github.com/cran/giniVarCI +* Date/Publication: 2024-01-08 10:30:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "giniVarCI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘giniVarCI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fcompareCI + > ### Title: Comparisons of variance estimates and confidence intervals for + > ### the Gini index in finite populations + > ### Aliases: fcompareCI + > + > ### ** Examples + > + ... + > data(eusilc, package="laeken") + > y <- eusilc$eqIncome[eusilc$db040 == "Burgenland"] + > w <- eusilc$rb050[eusilc$db040 == "Burgenland"] + > + > # Estimation of the Gini index and confidence intervals using different methods. + > fcompareCI(y, w) + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: fcompareCI + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + libs 12.0Mb + ``` + +# gMCPLite + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/Merck/gMCPLite +* Source code: https://github.com/cran/gMCPLite +* Date/Publication: 2024-01-11 19:30:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "gMCPLite")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘GraphicalMultiplicity.Rmd’ + ... + 0.8600 + 0.1400 + + + + > plot(os, plottype = "HR", xlab = "Events") + + When sourcing ‘GraphicalMultiplicity.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘GraphicalMultiplicity.Rmd’ using ‘UTF-8’... failed + ‘hGraph.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘GraphicalMultiplicity.Rmd’ using rmarkdown + ``` + +# gMOIP + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/relund/gMOIP +* Source code: https://github.com/cran/gMOIP +* Date/Publication: 2024-02-21 21:30:05 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "gMOIP")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gMOIP-Ex.R’ failed + The error most likely occurred in: + + > ### Name: convexHull + > ### Title: Find the convex hull of a set of points. + > ### Aliases: convexHull + > + > ### ** Examples + > + > ## 1D + ... + + $pts + p1 p2 pt vtx + 1 1 1 1 TRUE + 2 2 2 1 TRUE + + > plotHull2D(pts, drawPoints = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotHull2D ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘bi-objective_2x.Rmd’ + ... + + > b <- c(3, 27, 90) + + > obj <- matrix(c(7, -10, -10, -10), nrow = 2) + + > plotBiObj2D(A, b, obj, addTriangles = FALSE) + + ... + When sourcing ‘polytope_2d.R’: + Error: argument is of length zero + Execution halted + + ‘bi-objective_2x.Rmd’ using ‘UTF-8’... failed + ‘bi-objective_3x_ex1.Rmd’ using ‘UTF-8’... OK + ‘intro.Rmd’ using ‘UTF-8’... failed + ‘polytope_2d.Rmd’ using ‘UTF-8’... failed + ‘polytope_3d_ex1.Rmd’ using ‘UTF-8’... OK + ‘tri-objective.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘bi-objective_2x.Rmd’ using rmarkdown + + Quitting from lines 73-78 [2DLP] (bi-objective_2x.Rmd) + Error: processing vignette 'bi-objective_2x.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘bi-objective_2x.Rmd’ + + --- re-building ‘bi-objective_3x_ex1.Rmd’ using rmarkdown + ``` + +# GofCens + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/GofCens +* Date/Publication: 2024-07-29 08:40:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "GofCens")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GofCens-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kmPlot + > ### Title: Plot of the Kaplen-Meier and parametric estimations + > ### Aliases: kmPlot kmPlot.default kmPlot.formula kmPlot.probPlot + > ### kmPlot.probPlot + > + > ### ** Examples + > + ... + Scale: 10.039 + + > + > # Plots for censored data using ggplot2 + > data(colon) + Warning in data(colon) : data set ‘colon’ not found + > kmPlot(Surv(time, status) ~ 1, colon, distr= "lognormal", ggp = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: kmPlot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# greatR + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/ruthkr/greatR +* Source code: https://github.com/cran/greatR +* Date/Publication: 2024-04-09 22:40:07 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "greatR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘process-results.Rmd’ + ... + + > reg_summary$non_registered_genes + [1] "BRAA02G018970.3C" + + > plot(reg_summary, type = "registered", scatterplot_size = c(4, + + 3.5)) + + When sourcing ‘process-results.R’: + Error: object is not a unit + Execution halted + + ‘data-requirement.Rmd’ using ‘UTF-8’... OK + ‘process-results.Rmd’ using ‘UTF-8’... failed + ‘register-data-manually.Rmd’ using ‘UTF-8’... OK + ‘register-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘data-requirement.Rmd’ using rmarkdown + --- finished re-building ‘data-requirement.Rmd’ + + --- re-building ‘process-results.Rmd’ using rmarkdown + + Quitting from lines 76-81 [plot-summary-results] (process-results.Rmd) + Error: processing vignette 'process-results.Rmd' failed with diagnostics: + object is not a unit + ... + --- finished re-building ‘register-data-manually.Rmd’ + + --- re-building ‘register-data.Rmd’ using rmarkdown + --- finished re-building ‘register-data.Rmd’ + + SUMMARY: processing the following file failed: + ‘process-results.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Greymodels + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/havishaJ/Greymodels +* Source code: https://github.com/cran/Greymodels +* Date/Publication: 2022-12-05 12:42:35 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "Greymodels")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Greymodels-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Plots + > ### Title: plots + > ### Aliases: plots plotrm plotsmv1 plotsmv2 plotsigndgm plots_mdbgm12 + > + > ### ** Examples + > + > # Plots - EPGM (1, 1) model + ... + + geom_point(data = set4, aes(x = CI, y = y), shape = 23, color = "black") + + + geom_line(data = xy1, aes(x = x, y = y,color = "Raw Data")) + + + geom_line(data = xy2, aes(x = x, y = y,color = "Fitted&Forecasts")) + + + geom_line(data = set3, aes(x = CI, y = y,color = "LowerBound"), linetype=2) + + + geom_line(data = set4, aes(x = CI, y = y,color = "UpperBound"), linetype=2) + + + scale_color_manual(name = "Label",values = colors) + > r <- ggplotly(p) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# gsDesign + +
+ +* Version: 3.6.4 +* GitHub: https://github.com/keaven/gsDesign +* Source code: https://github.com/cran/gsDesign +* Date/Publication: 2024-07-26 23:20:10 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "gsDesign")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gsDesign-Ex.R’ failed + The error most likely occurred in: + + > ### Name: summary.gsDesign + > ### Title: Bound Summary and Z-transformations + > ### Aliases: summary.gsDesign print.gsDesign gsBoundSummary xprint + > ### print.gsBoundSummary gsBValue gsDelta gsRR gsHR gsCPz + > ### Keywords: design + > + > ### ** Examples + ... + ~RR at bound 0.6605 0.6605 + P(Cross) if RR=1 0.0239 0.9761 + P(Cross) if RR=0.5 0.9000 0.1000 + > gsRR(z = xp$lower$bound, i = 1:3, xrr) + [1] 1.0732500 0.8211496 NA + > plot(xrr, plottype = "RR") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gsDesign) + > + > test_check("gsDesign") + Linear spending function with none = [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] + + ══ Skipped tests (98) ══════════════════════════════════════════════════════════ + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ConditionalPowerPlot.Rmd’ + ... + + > cp <- gsCP(x = update, i = 1, zi = -qnorm(p), theta = theta) + + > plot(cp, xval = hr, xlab = "Future HR", ylab = "Conditional Power/Error", + + main = "Conditional probability of crossing future bound", + + o .... [TRUNCATED] + + ... + ‘PoissonMixtureModel.Rmd’ using ‘UTF-8’... OK + ‘SpendingFunctionOverview.Rmd’ using ‘UTF-8’... OK + ‘SurvivalOverview.Rmd’ using ‘UTF-8’... OK + ‘VaccineEfficacy.Rmd’ using ‘UTF-8’... OK + ‘binomialSPRTExample.Rmd’ using ‘UTF-8’... OK + ‘gsDesignPackageOverview.Rmd’ using ‘UTF-8’... failed + ‘gsSurvBasicExamples.Rmd’ using ‘UTF-8’... failed + ‘hGraph.Rmd’ using ‘UTF-8’... OK + ‘nNormal.Rmd’ using ‘UTF-8’... OK + ‘toInteger.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ConditionalErrorSpending.Rmd’ using rmarkdown + ``` + +# gtExtras + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/jthomasmock/gtExtras +* Source code: https://github.com/cran/gtExtras +* Date/Publication: 2023-09-15 22:32:06 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "gtExtras")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gtExtras) + Loading required package: gt + + Attaching package: 'gt' + + The following object is masked from 'package:testthat': + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── + `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). + + `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" + `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" + + [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] + Error: Test failures + Execution halted + ``` + +# HaploCatcher + +
+ +* Version: 1.0.4 +* GitHub: NA +* Source code: https://github.com/cran/HaploCatcher +* Date/Publication: 2023-04-21 23:32:39 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "HaploCatcher")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘An_Intro_to_HaploCatcher.Rmd’ + ... + > set.seed(NULL) + + > results1 <- auto_locus(geno_mat = geno_mat, gene_file = gene_comp, + + gene_name = "sst1_solid_stem", marker_info = marker_info, + + chromosom .... [TRUNCATED] + Loading required package: lattice + + When sourcing ‘An_Intro_to_HaploCatcher.R’: + Error: object is not a unit + Execution halted + + ‘An_Intro_to_HaploCatcher.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘An_Intro_to_HaploCatcher.Rmd’ using rmarkdown + + Quitting from lines 242-253 [example_models_1] (An_Intro_to_HaploCatcher.Rmd) + Error: processing vignette 'An_Intro_to_HaploCatcher.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘An_Intro_to_HaploCatcher.Rmd’ + + SUMMARY: processing the following file failed: + ‘An_Intro_to_HaploCatcher.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# healthyR + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/spsanderson/healthyR +* Source code: https://github.com/cran/healthyR +* Date/Publication: 2024-07-01 13:20:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "healthyR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started.Rmd’ + ... + + .by = "month", .interactive = FALSE) + Warning: Ignoring unknown labels: + • `colour = "Legend"` + + > ts_alos_plt(.data = df_tbl, .date_col = Date, .value_col = Values, + + .by = "month", .interactive = TRUE) + + When sourcing ‘getting-started.R’: + Error: subscript out of bounds + Execution halted + + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘getting-started.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 3.7Mb + ``` + +# healthyR.ts + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/spsanderson/healthyR.ts +* Source code: https://github.com/cran/healthyR.ts +* Date/Publication: 2023-11-15 06:00:05 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "healthyR.ts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘healthyR.ts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tidy_fft + > ### Title: Tidy Style FFT + > ### Aliases: tidy_fft + > + > ### ** Examples + > + > suppressPackageStartupMessages(library(dplyr)) + ... + > a <- tidy_fft( + + .data = data_tbl, + + .value_col = value, + + .date_col = date_col, + + .harmonics = 3, + + .frequency = 12 + + ) + Error in pm[[2]] : subscript out of bounds + Calls: tidy_fft -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘using-tidy-fft.Rmd’ + ... + $ value 112, 118, 132, 129, 121, 135, 148, 148, 136, 119, 104, 118, 1… + + > suppressPackageStartupMessages(library(timetk)) + + > data_tbl %>% plot_time_series(.date_var = date_col, + + .value = value) + + When sourcing ‘using-tidy-fft.R’: + Error: subscript out of bounds + Execution halted + + ‘getting-started.Rmd’ using ‘UTF-8’... OK + ‘using-tidy-fft.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘getting-started.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + doc 5.2Mb + ``` + +# heatmaply + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/talgalili/heatmaply +* Source code: https://github.com/cran/heatmaply +* Date/Publication: 2023-10-06 20:50:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "heatmaply")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(heatmaply) + Loading required package: plotly + Loading required package: ggplot2 + + Attaching package: 'plotly' + + ... + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─heatmaply:::predict_colors(ggplotly(g), plot_method = "ggplot") + 7. ├─plotly::ggplotly(g) + 8. └─plotly:::ggplotly.ggplot(g) + 9. └─plotly::gg2list(...) + + [ FAIL 58 | WARN 0 | SKIP 0 | PASS 193 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘heatmaply.Rmd’ + ... + + > library("heatmaply") + + > library("heatmaply") + + > heatmaply(mtcars) + + When sourcing ‘heatmaply.R’: + Error: subscript out of bounds + Execution halted + + ‘heatmaply.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘heatmaply.Rmd’ using rmarkdown + + Quitting from lines 109-111 [unnamed-chunk-5] (heatmaply.Rmd) + Error: processing vignette 'heatmaply.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘heatmaply.Rmd’ + + SUMMARY: processing the following file failed: + ‘heatmaply.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 5.1Mb + ``` + +# hermiter + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/MikeJaredS/hermiter +* Source code: https://github.com/cran/hermiter +* Date/Publication: 2024-03-06 23:50:02 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "hermiter")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hermiter.Rmd’ + ... + > p2 <- ggplot(df_pdf_cdf) + geom_tile(aes(X, Y, fill = pdf_est)) + + + scale_fill_continuous_sequential(palette = "Oslo", breaks = seq(0, + + .... [TRUNCATED] + + > p1 + ggtitle("Actual PDF") + theme(legend.title = element_blank()) + + + p2 + ggtitle("Estimated PDF") + theme(legend.title = element_blank()) + .... [TRUNCATED] + + When sourcing ‘hermiter.R’: + Error: object is not a unit + Execution halted + + ‘hermiter.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘hermiter.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + R 2.6Mb + doc 1.9Mb + libs 2.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# heumilkr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/lschneiderbauer/heumilkr +* Source code: https://github.com/cran/heumilkr +* Date/Publication: 2024-04-01 13:50:06 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "heumilkr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘clarke_wright_performance.Rmd’ + ... + + "F", "tai"), group_desc = c("Augerat A, 1995", "Augerat B, 1995", + + "Christofides and ..." ... [TRUNCATED] + + > ggMarginal(ggplot(merge(result, description, by = "group"), + + aes(x = n_site, y = clarke_wright_perf_xi, color = group_desc)) + + + geom_poi .... [TRUNCATED] + + When sourcing ‘clarke_wright_performance.R’: + Error: argument is of length zero + Execution halted + + ‘clarke_wright_performance.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘clarke_wright_performance.Rmd’ using rmarkdown + + Quitting from lines 69-97 [perf_scale_based_graph] (clarke_wright_performance.Rmd) + Error: processing vignette 'clarke_wright_performance.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘clarke_wright_performance.Rmd’ + + SUMMARY: processing the following file failed: + ‘clarke_wright_performance.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# hilldiv + +
+ +* Version: 1.5.1 +* GitHub: https://github.com/anttonalberdi/hilldiv +* Source code: https://github.com/cran/hilldiv +* Date/Publication: 2019-10-01 14:40:02 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "hilldiv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘hilldiv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: div_test_plot + > ### Title: Diversity test plotting + > ### Aliases: div_test_plot + > ### Keywords: chart comparison hill numbers + > + > ### ** Examples + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# hmclearn + +
+ +* Version: 0.0.5 +* GitHub: NA +* Source code: https://github.com/cran/hmclearn +* Date/Publication: 2020-10-05 06:40:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "hmclearn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘hmclearn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hmclearn-plots + > ### Title: Plotting for MCMC visualization and diagnostics provided by + > ### 'bayesplot' package + > ### Aliases: hmclearn-plots mcmc_intervals mcmc_intervals.hmclearn + > ### mcmc_areas mcmc_areas.hmclearn mcmc_hist mcmc_hist.hmclearn + > ### mcmc_hist_by_chain mcmc_hist_by_chain.hmclearn mcmc_dens + > ### mcmc_dens.hmclearn mcmc_scatter mcmc_scatter.hmclearn mcmc_hex + ... + + param = list(y=y, X=X), + + parallel=FALSE, chains=2) + > + > mcmc_trace(f, burnin=100) + > mcmc_hist(f, burnin=100) + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + > mcmc_intervals(f, burnin=100) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# HTLR + +
+ +* Version: 0.4-4 +* GitHub: https://github.com/longhaiSK/HTLR +* Source code: https://github.com/cran/HTLR +* Date/Publication: 2022-10-22 12:47:53 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "HTLR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘simu.Rmd’ + ... + [1] "median" + + > post.t <- as.matrix(fit.t2, k = 2) + + > mcmc_intervals(post.t, pars = c("Intercept", "V1", + + "V2", "V3", "V1000")) + + When sourcing ‘simu.R’: + Error: argument is of length zero + Execution halted + + ‘simu.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘simu.Rmd’ using rmarkdown + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + data 2.0Mb + doc 1.1Mb + libs 5.4Mb + ``` + +# HVT + +
+ +* Version: 24.5.2 +* GitHub: https://github.com/Mu-Sigma/HVT +* Source code: https://github.com/cran/HVT +* Date/Publication: 2024-05-15 08:50:21 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "HVT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘HVT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getTransitionProbability + > ### Title: Creating Transition Probabilities list + > ### Aliases: getTransitionProbability + > ### Keywords: Transition_or_Prediction + > + > ### ** Examples + > + ... + Ignoring unknown parameters: `check_overlap` + Scale for x is already present. + Adding another scale for x, which will replace the existing scale. + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Warning in geom_polygon(data = boundaryCoords2, aes(x = bp.x, y = bp.y, : + Ignoring unknown aesthetics: text + Error in pm[[2]] : subscript out of bounds + Calls: scoreHVT -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# hypsoLoop + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/hypsoLoop +* Date/Publication: 2022-02-08 09:00:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "hypsoLoop")` for more info + +
+ +## Newly broken + +* checking whether package ‘hypsoLoop’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::set_theme’ by ‘sjPlot::set_theme’ when loading ‘hypsoLoop’ + See ‘/tmp/workdir/hypsoLoop/new/hypsoLoop.Rcheck/00install.out’ for details. + ``` + +# ibdsim2 + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/magnusdv/ibdsim2 +* Source code: https://github.com/cran/ibdsim2 +* Date/Publication: 2024-09-08 07:40:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "ibdsim2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ibdsim2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotSegmentDistribution + > ### Title: Scatter plots of IBD segment distributions + > ### Aliases: plotSegmentDistribution + > + > ### ** Examples + > + > + ... + Skip recomb : - + Total time used: 0.00288 secs + > + > # By default, the IBD segments of the "leaves" are computed and plotted + > plotSegmentDistribution(simPat, simMat, type = "ibd1", ids = 4:5, + + labels = c("HSpat", "HSmat")) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# ICtest + +
+ +* Version: 0.3-5 +* GitHub: NA +* Source code: https://github.com/cran/ICtest +* Date/Publication: 2022-05-18 07:30:29 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "ICtest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ICtest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplot.ictest + > ### Title: Scatterplot Matrix for a ictest Object using ggplot2 + > ### Aliases: ggplot.ictest + > ### Keywords: hplot + > + > ### ** Examples + > + ... + > # The aesthetics variables + > mapvar <- data.frame(iris[, 5]) + > colnames(mapvar) <- "species" + > + > TestCov <- PCAasymp(X, k = 2) + > ggplot(TestCov) + > ggplot(TestCov, aes(color = species), mapvar = mapvar, which = "k") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + doc 2.5Mb + libs 2.9Mb + ``` + +# idiogramFISH + +
+ +* Version: 2.0.13 +* GitHub: NA +* Source code: https://github.com/cran/idiogramFISH +* Date/Publication: 2023-08-22 16:50:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "idiogramFISH")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 2.0Mb + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘index.Rmd’ + ... + > if (requireNamespace("RCurl", quietly = TRUE)) { + + v <- sub("Version: ", "", readLines("../DESCRIPTION")[3]) + + pkg <- "idiogramFISH" + + l .... [TRUNCATED] + Warning in file(con, "r") : + cannot open file '../DESCRIPTION': No such file or directory + + When sourcing ‘index.R’: + Error: cannot open the connection + Execution halted + + ‘AVignette.Rmd’ using ‘UTF-8’... OK + ‘index.Rmd’ using ‘UTF-8’... failed + ``` + +# IDMIR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/IDMIR +* Date/Publication: 2023-11-09 15:30:02 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "IDMIR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IDMIR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PlotSurvival + > ### Title: PlotSurvival + > ### Aliases: PlotSurvival + > + > ### ** Examples + > + > # Obtain the example data + ... + > GEP<-GetData_Mirna("GEP") + > survival<-GetData_Mirna("survival") + > MiRNAs<-c("hsa-miR-21-5p","hsa-miR-26a-5p","hsa-miR-369-5p","hsa-miR-1238-3p","hsa-miR-10b-5p") + > # Run the function + > SingleMiRNA_CRData<-SingleMiRNA_CRModel(GEP, + + "hsa-miR-21-5p",survival,cutoff.point=NULL) + > PlotSurvival(SingleMiRNA_CRData) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PlotSurvival ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘IDMIR.Rmd’ + ... + > survival <- GetData_Mirna("survival") + + > SingleMiRNA_CRData <- SingleMiRNA_CRModel(GEP, "hsa-miR-21-5p", + + cutoff.point = NULL, survival) + + > PlotSurvival(SingleMiRNA_CRData) + + When sourcing ‘IDMIR.R’: + Error: argument is of length zero + Execution halted + + ‘IDMIR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘IDMIR.Rmd’ using rmarkdown + + Quitting from lines 120-130 [unnamed-chunk-7] (IDMIR.Rmd) + Error: processing vignette 'IDMIR.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘IDMIR.Rmd’ + + SUMMARY: processing the following file failed: + ‘IDMIR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# idopNetwork + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/cxzdsa2332/idopNetwork +* Source code: https://github.com/cran/idopNetwork +* Date/Publication: 2023-04-18 06:50:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "idopNetwork")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘idopNetwork_vignette.Rmd’ + ... + + > qdODE_plot_base(ode.test) + + > ode.module = test_result$d1_module + + > qdODE_plot_all(ode.module) + + When sourcing ‘idopNetwork_vignette.R’: + Error: object is not a unit + Execution halted + + ‘idopNetwork_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘idopNetwork_vignette.Rmd’ using rmarkdown + ``` + +# ihclust + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ihclust +* Date/Publication: 2022-04-27 07:20:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "ihclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ihclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ihclust + > ### Title: Iterative Hierarchical Clustering (IHC) + > ### Aliases: ihclust + > + > ### ** Examples + > + > # This is an example not using the permutation approach + ... + 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# immunarch + +
+ +* Version: 0.9.1 +* GitHub: https://github.com/immunomind/immunarch +* Source code: https://github.com/cran/immunarch +* Date/Publication: 2024-03-18 19:10:06 UTC +* Number of recursive dependencies: 198 + +Run `revdepcheck::cloud_details(, "immunarch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘immunarch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geneUsageAnalysis + > ### Title: Post-analysis of V-gene and J-gene statistics: PCA, clustering, + > ### etc. + > ### Aliases: geneUsageAnalysis + > + > ### ** Examples + > + ... + 17. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 22. └─base::.handleSimpleError(...) + 23. └─purrr (local) h(simpleError(msg, call)) + 24. └─cli::cli_abort(...) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 5.5Mb + doc 1.6Mb + ``` + +# incidental + +
+ +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/incidental +* Date/Publication: 2020-09-16 09:50:03 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "incidental")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘incidental-tutorial.Rmd’ + ... + + > data_subset = do.call("rbind", model_df_list) + + > ggplot(data_subset, aes(x = Time, y = Reported)) + + + geom_point(color = "coral2", shape = 3) + geom_line(aes(x = Time, + + y = Ihat), color .... [TRUNCATED] + + When sourcing ‘incidental-tutorial.R’: + Error: `x` must be a vector, not a object. + Execution halted + + ‘incidental-tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘incidental-tutorial.Rmd’ using rmarkdown + ``` + +# infer + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/tidymodels/infer +* Source code: https://github.com/cran/infer +* Date/Publication: 2024-03-25 21:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "infer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘infer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: shade_confidence_interval + > ### Title: Add information about confidence interval + > ### Aliases: shade_confidence_interval shade_ci + > + > ### ** Examples + > + > # find the point estimate---mean number of hours worked per week + ... + + type = "se") + > + > + > # and plot it! + > boot_dist %>% + + visualize() + + + shade_confidence_interval(ci) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.list(object, p, objectname) + 21. │ ├─ggplot2::ggplot_add(o, plot, object_name) + 22. │ └─ggplot2:::ggplot_add.Layer(o, plot, object_name) + 23. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 24. └─base::.handleSimpleError(...) + 25. └─testthat (local) h(simpleError(msg, call)) + 26. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘anova.Rmd’ + ... + + generate(reps = 1000, type = "permute") %>% calculate( .... [TRUNCATED] + Dropping unused factor levels DK from the supplied explanatory variable + 'partyid'. + + > null_dist %>% visualize() + shade_p_value(observed_f_statistic, + + direction = "greater") + + ... + When sourcing ‘t_test.R’: + Error: argument is of length zero + Execution halted + + ‘anova.Rmd’ using ‘UTF-8’... failed + ‘chi_squared.Rmd’ using ‘UTF-8’... failed + ‘infer.Rmd’ using ‘UTF-8’... failed + ‘observed_stat_examples.Rmd’ using ‘UTF-8’... failed + ‘paired.Rmd’ using ‘UTF-8’... failed + ‘t_test.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘anova.Rmd’ using rmarkdown + ``` + +# injurytools + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/lzumeta/injurytools +* Source code: https://github.com/cran/injurytools +* Date/Publication: 2023-11-14 17:20:05 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "injurytools")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘model-injury-data-ii.Rmd’ + ... + n events median 0.95LCL 0.95UCL + seasonb=2017/2018 23 16 265 152 NA + seasonb=2018/2019 19 17 106 84 165 + + > ggsurvplot(fit, data = injd_sub, palette = c("#E7B800", + + "#2E9FDF")) + xlab("Time [calendar days]") + ylab(expression("Survival probability ( ..." ... [TRUNCATED] + + When sourcing ‘model-injury-data-ii.R’: + Error: argument is of length zero + Execution halted + + ‘estimate-epi-measures.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-i.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-ii.Rmd’ using ‘UTF-8’... failed + ‘prepare-injury-data.Rmd’ using ‘UTF-8’... OK + ‘visualize-injury-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘estimate-epi-measures.Rmd’ using rmarkdown + --- finished re-building ‘estimate-epi-measures.Rmd’ + + --- re-building ‘model-injury-data-i.Rmd’ using rmarkdown + ``` + +# inlabru + +
+ +* Version: 2.11.1 +* GitHub: https://github.com/inlabru-org/inlabru +* Source code: https://github.com/cran/inlabru +* Date/Publication: 2024-07-01 23:30:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "inlabru")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘inlabru-Ex.R’ failed + The error most likely occurred in: + + > ### Name: seals + > ### Title: Seal pups + > ### Aliases: seals seals_sp + > ### Keywords: datasets + > + > ### ** Examples + > + > if (require(ggplot2, quietly = TRUE)) { + + ggplot() + + + geom_fm(data = seals_sp$mesh) + + + gg(seals_sp$points) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (require(testthat, quietly = TRUE)) { + + test_check("inlabru") + + } + Loading required package: inlabru + Loading required package: fmesher + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] + ... + 9. │ └─INLA:::expand.inla.stack.responses(responses) + 10. │ └─base::lapply(...) + 11. │ └─INLA (local) FUN(X[[i]], ...) + 12. │ └─dplyr::bind_rows(...) + 13. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env()) + 14. └─rlang::abort(message = message) + + [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] + Error: Test failures + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘stars’ + ``` + +# insurancerating + +
+ +* Version: 0.7.4 +* GitHub: https://github.com/mharinga/insurancerating +* Source code: https://github.com/cran/insurancerating +* Date/Publication: 2024-05-20 11:30:03 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "insurancerating")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘insurancerating-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.univariate + > ### Title: Automatically create a ggplot for objects obtained from + > ### univariate() + > ### Aliases: autoplot.univariate + > + > ### ** Examples + > + ... + > xzip <- univariate(MTPL, x = bm, severity = amount, nclaims = nclaims, + + exposure = exposure, by = zip) + > autoplot(xzip, show_plots = 1:2) + Warning: Removed 16 rows containing missing values or values outside the scale range + (`geom_point()`). + Warning: Removed 5 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# inTextSummaryTable + +
+ +* Version: 3.3.3 +* GitHub: https://github.com/openanalytics/inTextSummaryTable +* Source code: https://github.com/cran/inTextSummaryTable +* Date/Publication: 2024-06-12 18:30:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(inTextSummaryTable) + > + > test_check("inTextSummaryTable") + [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 6. └─inTextSummaryTable::subjectProfileSummaryPlot(...) + 7. └─ggplot2:::`+.gg`(gg, do.call(geom_line, argsGeomLine)) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘inTextSummaryTable-aesthetics.Rmd’ + ... + + > summaryTable <- data.frame(visit = c(1, 2, 1, 2), + + TRT = c("A", "A", "B", "B"), statMean = rnorm(4)) + + > subjectProfileSummaryPlot(data = summaryTable, xVar = "visit", + + colorVar = "TRT") + + ... + Error: argument is of length zero + Execution halted + + ‘inTextSummaryTable-advanced.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-aesthetics.Rmd’ using ‘UTF-8’... failed + ‘inTextSummaryTable-createTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-exportTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-introduction.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-standardTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-visualization.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown + --- finished re-building ‘inTextSummaryTable-advanced.Rmd’ + + --- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown + + Quitting from lines 211-224 [aesthetics-defaultsVisualization] (inTextSummaryTable-aesthetics.Rmd) + Error: processing vignette 'inTextSummaryTable-aesthetics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘inTextSummaryTable-aesthetics.Rmd’ + ... + Error: processing vignette 'inTextSummaryTable-visualization.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘inTextSummaryTable-visualization.Rmd’ + + SUMMARY: processing the following files failed: + ‘inTextSummaryTable-aesthetics.Rmd’ + ‘inTextSummaryTable-visualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.3Mb + sub-directories of 1Mb or more: + doc 9.7Mb + ``` + +# inventorize + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "inventorize")` for more info + +
+ +## Newly broken + +* checking whether package ‘inventorize’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel -# actxps (thematic) - -# AeRobiology (unknown) - -``` -#
-# -# * Version: 2.0.1 -# * GitHub: NA -# * Source code: https://github.com/cran/AeRobiology -# * Date/Publication: 2019-06-03 06:20:03 UTC -# * Number of recursive dependencies: 98 -# -# Run `revdepcheck::cloud_details(, "AeRobiology")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘my-vignette.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘my-vignette.Rmd’ -# ... -# + export.plot = FALSE, export.result = FALSE, n.types = 3, -# + y.start = 2011, y.end = .... [TRUNCATED] -# -# > iplot_abundance(munich_pollen, interpolation = FALSE, -# + export.plot = FALSE, export.result = FALSE, n.types = 3, -# + y.start = 2011, y.end = .... [TRUNCATED] -# -# When sourcing ‘my-vignette.R’: -# Error: subscript out of bounds -# Execution halted -# -# ‘my-vignette.Rmd’ using ‘UTF-8’... failed -# ``` ``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in pm[[2]] : subscript out of bounds +Error: unable to load R code in package ‘inventorize’ +Execution halted +ERROR: lazy loading failed for package ‘inventorize’ +* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ -# agricolaeplotr (missing labels) - -# AnalysisLin (plotly) - -# animbook (plotly) - -# ANN2 (missing labels) - -# aplot (patchwork) - -# applicable (missing labels) - -# ASRgenomics (factoextra) - -# autoplotly (plotly) - -# autoReg (patchwork) - -# bartMan (ggnewscale) - -# bayesAB (missing labels) - -# BayesGrowth (ggdist) - -# BayesianReasoning (missing labels) - -# BayesMallows (missing labels) - -# bayesplot (missing labels) - -# bayestestR (patchwork) - -# beastt (ggdist) - -# besthr (patchwork) - -# biclustermd (xintercept/yintercept class) - -# biodosetools (missing labels) - -# boxly (plotly) - -# braidReports (annotation_logticks) - -# breathtestcore (plot slots) - -# brolgar (facet params: as.table) - -# cartograflow (plotly) - -# cartographr (unknown) ``` -#
-# -# * Version: 0.2.2 -# * GitHub: https://github.com/da-wi/cartographr -# * Source code: https://github.com/cran/cartographr -# * Date/Publication: 2024-06-28 14:50:09 UTC -# * Number of recursive dependencies: 99 -# -# Run `revdepcheck::cloud_details(, "cartographr")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > # This file is part of the standard setup for testthat. -# > # It is recommended that you do not modify it. -# > # -# > # Where should you do additional test configuration? -# > # Learn more about the roles of various files in: -# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview -# > # * https://testthat.r-lib.org/articles/special-files.html -# ... -# 21. │ └─base::stop(...) -# 22. └─base::.handleSimpleError(...) -# 23. └─rlang (local) h(simpleError(msg, call)) -# 24. └─handlers[[1L]](cnd) -# 25. └─cli::cli_abort(...) -# 26. └─rlang::abort(...) -# -# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ] -# Error: Test failures -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 5.3Mb -# sub-directories of 1Mb or more: -# data 3.5Mb -# ``` -``` - -# cats (plotly) - -# cheem (plotly) - -# chillR (patchwork) - -# chronicle (plotly) - -# circhelp (patchwork) - -# clifro (missing labels) - -# clinDataReview (plotly) - -# clinUtils (plotly) - -# CohortPlat (plotly) - -# CoreMicrobiomeR (plotly) - -# correlationfunnel (plotly) - -# corrViz (plotly) - -# countfitteR (missing labels) - -# covidcast (unknown) - -``` -#
-# -# * Version: 0.5.2 -# * GitHub: https://github.com/cmu-delphi/covidcast -# * Source code: https://github.com/cran/covidcast -# * Date/Publication: 2023-07-12 23:40:06 UTC -# * Number of recursive dependencies: 93 -# -# Run `revdepcheck::cloud_details(, "covidcast")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(covidcast) -# We encourage COVIDcast API users to register on our mailing list: -# https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api -# We'll send announcements about new data sources, package updates, -# server maintenance, and new features. -# > -# ... -# • plot/default-county-choropleth.svg -# • plot/default-hrr-choropleth-with-include.svg -# • plot/default-msa-choropleth-with-include.svg -# • plot/default-state-choropleth-with-include.svg -# • plot/default-state-choropleth-with-range.svg -# • plot/state-choropleth-with-no-metadata.svg -# • plot/state-line-graph-with-range.svg -# • plot/state-line-graph-with-stderrs.svg -# Error: Test failures -# Execution halted -# ``` -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘plotting-signals.Rmd’ -# ... -# > knitr::opts_chunk$set(fig.width = 6, fig.height = 4) -# -# > plot(dv) -# -# When sourcing ‘plotting-signals.R’: -# Error: Problem while setting up geom aesthetics. -# ℹ Error occurred in the 6th layer. -# Caused by error in `$<-.data.frame`: -# ! replacement has 1 row, data has 0 -# Execution halted -# -# ‘correlation-utils.Rmd’ using ‘UTF-8’... OK -# ‘covidcast.Rmd’ using ‘UTF-8’... OK -# ‘external-data.Rmd’ using ‘UTF-8’... OK -# ‘multi-signals.Rmd’ using ‘UTF-8’... OK -# ‘plotting-signals.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘correlation-utils.Rmd’ using rmarkdown -# --- finished re-building ‘correlation-utils.Rmd’ -# -# --- re-building ‘covidcast.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking data for non-ASCII characters ... NOTE -# ``` -# Note: found 20 marked UTF-8 strings -# ``` -``` - -# crosshap (plotly) - -# cubble (patchwork) - -# deeptime (ggnewscale) - -# distributional (ggdist) - -# dittoViz (plotly) - -# EGM (missing labels) - -# entropart (default access) - -# epiCleanr (ggdist) - -# esci (ggdist) - -# evalITR (unknown) - -``` -#
-# -# * Version: 1.0.0 -# * GitHub: https://github.com/MichaelLLi/evalITR -# * Source code: https://github.com/cran/evalITR -# * Date/Publication: 2023-08-25 23:10:06 UTC -# * Number of recursive dependencies: 167 -# -# Run `revdepcheck::cloud_details(, "evalITR")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘cv_multiple_alg.Rmd’ -# ... -# intersect, setdiff, setequal, union -# -# -# > load("../data/star.rda") -# Warning in readChar(con, 5L, useBytes = TRUE) : -# cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' -# -# ... -# Execution halted -# -# ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed -# ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed -# ‘install.Rmd’ using ‘UTF-8’... OK -# ‘paper_alg1.Rmd’ using ‘UTF-8’... OK -# ‘sample_split.Rmd’ using ‘UTF-8’... failed -# ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed -# ‘user_itr.Rmd’ using ‘UTF-8’... failed -# ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking dependencies in R code ... NOTE -# ``` -# Namespaces in Imports field not imported from: -# ‘forcats’ ‘rqPen’ ‘utils’ -# All declared Imports should be used. -# ``` -``` - -# eventstudyr (missing labels) - -# EvoPhylo (patchwork) - -# expirest (missing labels) - -# explainer (plotly) - -# ezEDA (missing labels) - -# ezplot (0-length width) - -# fable.prophet (ggdist) - -# fabletools (ggdist) +### CRAN -# factoextra (0-length width) - -# fairmodels (missing labels) - -# fddm (ggforce) - -# feasts (missing labels) - -# ffp (ggdist) - -# fido (ggdist) - -# flipr (unknown) - -``` -#
-# -# * Version: 0.3.3 -# * GitHub: https://github.com/LMJL-Alea/flipr -# * Source code: https://github.com/cran/flipr -# * Date/Publication: 2023-08-23 09:00:02 UTC -# * Number of recursive dependencies: 106 -# -# Run `revdepcheck::cloud_details(, "flipr")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘alternative.Rmd’ using rmarkdown -# --- finished re-building ‘alternative.Rmd’ -# -# --- re-building ‘exactness.Rmd’ using rmarkdown -# -# Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) -# Error: processing vignette 'exactness.Rmd' failed with diagnostics: -# subscript out of bounds -# --- failed re-building ‘exactness.Rmd’ -# -# --- re-building ‘flipr.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘exactness.Rmd’ -# ... -# -# > library(flipr) -# -# > load("../R/sysdata.rda") -# Warning in readChar(con, 5L, useBytes = TRUE) : -# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' -# -# ... -# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' -# -# When sourcing ‘plausibility.R’: -# Error: cannot open the connection -# Execution halted -# -# ‘alternative.Rmd’ using ‘UTF-8’... OK -# ‘exactness.Rmd’ using ‘UTF-8’... failed -# ‘flipr.Rmd’ using ‘UTF-8’... failed -# ‘plausibility.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking installed package size ... NOTE -# ``` -# installed size is 11.0Mb -# sub-directories of 1Mb or more: -# doc 9.1Mb -# libs 1.2Mb -# ``` -``` - -# foqat (ggnewscale) - -# forestly (patchwork) - -# frailtyEM (plotly) - -# funcharts (patchwork) - -# geomtextpath (default access) - -# GGally (missing labels) - -# gganimate (gganimate) - -# ggbrain (ggnewscale) - -# ggbreak (patchwork) - -# ggdark (default access) - -# ggdist (ggdist) - -# ggDoubleHeat (ggnewscale) - -# ggeasy (missing labels) - -# ggedit (saved to disk) - -# ggESDA (passing NULL aesthetic mapping) - -# ggfixest (visual differences) - -# ggforce (ggforce) - -Note: facet_zoom/facet_col/facet_row - -# ggformula (docs) - -# ggfortify (tests) - -# gggenomes (patchwork) - -# ggh4x (unknown) - -``` -#
-# -# * Version: 0.2.8 -# * GitHub: https://github.com/teunbrand/ggh4x -# * Source code: https://github.com/cran/ggh4x -# * Date/Publication: 2024-01-23 21:00:02 UTC -# * Number of recursive dependencies: 77 -# -# Run `revdepcheck::cloud_details(, "ggh4x")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggh4x-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: guide_stringlegend -# > ### Title: String legend -# > ### Aliases: guide_stringlegend -# > -# > ### ** Examples -# > -# > p <- ggplot(mpg, aes(displ, hwy)) + -# + geom_point(aes(colour = manufacturer)) -# > -# > # String legend can be set in the `guides()` function -# > p + guides(colour = guide_stringlegend(ncol = 2)) -# Error in (function (layer, df) : -# argument "theme" is missing, with no default -# Calls: ... use_defaults -> eval_from_theme -> %||% -> calc_element -# Execution halted -# ``` -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(ggh4x) -# Loading required package: ggplot2 -# > -# > test_check("ggh4x") -# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] -# -# ... -# 25. └─ggplot2 (local) compute_geom_2(..., self = self) -# 26. └─self$geom$use_defaults(...) -# 27. └─ggplot2 (local) use_defaults(..., self = self) -# 28. └─ggplot2:::eval_from_theme(default_aes, theme) -# 29. ├─calc_element("geom", theme) %||% .default_geom_element -# 30. └─ggplot2::calc_element("geom", theme) -# -# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] -# Error: Test failures -# Execution halted -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘Facets.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘Miscellaneous.Rmd’ -# ... -# -# > ggplot(diamonds, aes(price, carat, colour = clarity)) + -# + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", -# + guide = "stri ..." ... [TRUNCATED] -# Warning: The S3 guide system was deprecated in ggplot2 3.5.0. -# ℹ It has been replaced by a ggproto system that can be extended. -# -# ... -# ℹ Error occurred in the 1st layer. -# Caused by error in `setup_params()`: -# ! A discrete 'nbinom' distribution cannot be fitted to continuous data. -# Execution halted -# -# ‘Facets.Rmd’ using ‘UTF-8’... OK -# ‘Miscellaneous.Rmd’ using ‘UTF-8’... failed -# ‘PositionGuides.Rmd’ using ‘UTF-8’... OK -# ‘Statistics.Rmd’ using ‘UTF-8’... failed -# ‘ggh4x.Rmd’ using ‘UTF-8’... OK -# ``` -``` - -# gghighlight (default access) - -# ggHoriPlot (patchwork) - -# ggiraph (additional params) - -# ggiraphExtra (additional params) - -# ggmice (plotly) - -# ggmulti (custom use_defaults) - -# ggnewscale (ggnewscale) - -# ggparallel (unknown) - -``` -#
-# -# * Version: 0.4.0 -# * GitHub: https://github.com/heike/ggparallel -# * Source code: https://github.com/cran/ggparallel -# * Date/Publication: 2024-03-09 22:00:02 UTC -# * Number of recursive dependencies: 51 -# -# Run `revdepcheck::cloud_details(, "ggparallel")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > # This file is part of the standard setup for testthat. -# > # It is recommended that you do not modify it. -# > # -# > # Where should you do additional test configuration? -# > # Learn more about the roles of various files in: -# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview -# > # * https://testthat.r-lib.org/articles/special-files.html -# ... -# 12. └─self$get_layer_key(params, layers[include], data[include], theme) -# 13. └─ggplot2 (local) get_layer_key(...) -# 14. └─base::Map(...) -# 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) -# 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) -# 17. └─layer$compute_geom_2(key, single_params, theme) -# -# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] -# Error: Test failures -# Execution halted -# ``` -``` - -# ggpicrust2 (patchwork) - -# ggpie (ggnewscale) - -# ggplotlyExtra (plotly) - -# ggpol (default access) - -# ggpubr (update tests) - -# ggraph (guide theme passing) - -# ggredist (unknown) - -``` -#
-# -# * Version: 0.0.2 -# * GitHub: https://github.com/alarm-redist/ggredist -# * Source code: https://github.com/cran/ggredist -# * Date/Publication: 2022-11-23 11:20:02 UTC -# * Number of recursive dependencies: 67 -# -# Run `revdepcheck::cloud_details(, "ggredist")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggredist-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: geom_district_text -# > ### Title: Label Map Regions -# > ### Aliases: geom_district_text geom_district_label -# > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText -# > ### Keywords: datasets -# > -# > ### ** Examples -# ... -# 22. │ └─coord$transform(data, panel_params) -# 23. │ └─ggplot2 (local) transform(..., self = self) -# 24. │ └─ggplot2:::sf_rescale01(...) -# 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) -# 26. └─base::.handleSimpleError(...) -# 27. └─rlang (local) h(simpleError(msg, call)) -# 28. └─handlers[[1L]](cnd) -# 29. └─cli::cli_abort(...) -# 30. └─rlang::abort(...) -# Execution halted -# ``` -``` - -# ggRtsy (missing labels) - -# ggseqplot (length 0 width) - -# ggside (unknown) - -``` -#
-# -# * Version: 0.3.1 -# * GitHub: https://github.com/jtlandis/ggside -# * Source code: https://github.com/cran/ggside -# * Date/Publication: 2024-03-01 09:12:37 UTC -# * Number of recursive dependencies: 76 -# -# Run `revdepcheck::cloud_details(, "ggside")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(ggplot2) -# > library(ggside) -# Registered S3 method overwritten by 'ggside': -# method from -# +.gg ggplot2 -# > -# ... -# • ops_meaningful/alpha-0-5-from-function.svg -# • side_layers/boxplot2.svg -# • vdiff_irisScatter/collapsed-histo.svg -# • vdiff_irisScatter/facetgrid-collapsed-density.svg -# • vdiff_irisScatter/facetgrid-histo.svg -# • vdiff_irisScatter/facetgrid-side-density.svg -# • vdiff_irisScatter/stacked-side-density.svg -# • vdiff_irisScatter/yside-histo.svg -# Error: Test failures -# Execution halted -# ``` -# -# * checking for code/documentation mismatches ... WARNING -# ``` -# Codoc mismatches from documentation object 'geom_xsideabline': -# geom_xsidehline -# Code: function(mapping = NULL, data = NULL, position = "identity", -# ..., yintercept, na.rm = FALSE, show.legend = NA) -# Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = -# FALSE, show.legend = NA) -# Argument names in code not in docs: -# position -# Mismatches in argument names (first 3): -# Position: 3 Code: position Docs: ... -# ... -# Docs: function(mapping = NULL, data = NULL, stat = "identity", -# position = "identity", ..., lineend = "butt", linejoin -# = "round", linemitre = 10, arrow = NULL, na.rm = -# FALSE, show.legend = NA, inherit.aes = TRUE) -# Argument names in code not in docs: -# arrow.fill -# Mismatches in argument names: -# Position: 10 Code: arrow.fill Docs: na.rm -# Position: 11 Code: na.rm Docs: show.legend -# Position: 12 Code: show.legend Docs: inherit.aes -# ``` -``` - -# ggspatial (missing defaults) - -# ggtern (ggtern) - -# ggupset (unknown) - -``` -#
-# -# * Version: 0.4.0 -# * GitHub: https://github.com/const-ae/ggupset -# * Source code: https://github.com/cran/ggupset -# * Date/Publication: 2024-06-24 10:10:04 UTC -# * Number of recursive dependencies: 46 -# -# Run `revdepcheck::cloud_details(, "ggupset")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggupset-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: axis_combmatrix -# > ### Title: Convert delimited text labels into a combination matrix axis -# > ### Aliases: axis_combmatrix -# > -# > ### ** Examples -# > -# > library(ggplot2) -# ... -# Datsun 710 Cyl: 4_Gears: 4 -# Hornet 4 Drive Cyl: 6_Gears: 3 -# Hornet Sportabout Cyl: 8_Gears: 3 -# Valiant Cyl: 6_Gears: 3 -# > ggplot(mtcars, aes(x=combined)) + -# + geom_bar() + -# + axis_combmatrix(sep = "_") -# Error in as.unit(e2) : object is not coercible to a unit -# Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit -# Execution halted -# ``` ``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Warning in qgamma(service_level, alpha, beta) : NaNs produced +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (inventorize) -# ggVennDiagram (plotly) - -# greatR (patchwork) - -# Greymodels (plotly) - -# gtExtras (unknown) ``` -#
-# -# * Version: 0.5.0 -# * GitHub: https://github.com/jthomasmock/gtExtras -# * Source code: https://github.com/cran/gtExtras -# * Date/Publication: 2023-09-15 22:32:06 UTC -# * Number of recursive dependencies: 105 -# -# Run `revdepcheck::cloud_details(, "gtExtras")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(gtExtras) -# Loading required package: gt -# -# Attaching package: 'gt' -# -# The following object is masked from 'package:testthat': -# ... -# ══ Failed tests ════════════════════════════════════════════════════════════════ -# ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── -# `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). -# -# `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" -# `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" -# -# [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] -# Error: Test failures -# Execution halted -# ``` -``` - -# HaploCatcher (patchwork) - -# healthyR (plotly) - -# healthyR.ts (plotly) - -# heatmaply (plotly) - -# hermiter (patchwork) - -# hesim (missing labels) - -# hidecan (ggnewscale) - -# HVT (plotly) - -# hypsoLoop (namespace conflict) - -# ICvectorfields (ggnewscale) - -# idopNetwork (patchwork) - -# inferCSN (plotly) - -# insurancerating (patchwork) +# IPV + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/NilsPetras/IPV +* Source code: https://github.com/cran/IPV +* Date/Publication: 2022-09-30 15:00:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "IPV")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IPV-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nested_chart + > ### Title: Nested Chart + > ### Aliases: nested_chart + > + > ### ** Examples + > + > # as simple as that + ... + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 8. └─vctrs::vec_as_names(names, repair = "check_unique") + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_cannot_be_empty(names, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ipv-vignette.Rmd’ + ... + Facet circle radius set to 0.211 based on the data. + cor_spacing set to 0.193 based on the data. + Relative scaling set to 3.78 based on the data. + Axis tick set to 0.1 based on the data. + dist_construct_label set to 0.5 based on the data. + + When sourcing ‘ipv-vignette.R’: + Error: Names can't be empty. + ✖ Empty name found at location 4. + Execution halted + + ‘ipv-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ipv-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + data 7.0Mb + ``` + +# IRon + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/nunompmoniz/IRon +* Source code: https://github.com/cran/IRon +* Date/Publication: 2023-01-20 07:20:06 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "IRon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IRon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sera + > ### Title: Squared Error-Relevance Area (SERA) + > ### Aliases: sera + > + > ### ** Examples + > + > library(IRon) + ... + 16. │ └─self$stat$setup_params(data, self$stat_params) + 17. │ └─ggplot2 (local) setup_params(...) + 18. │ └─base::match.fun(method) + 19. │ └─base::get(as.character(FUN), mode = "function", envir = envir) + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.7Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +# irt + +
+ +* Version: 0.2.9 +* GitHub: https://github.com/egonulates/irt +* Source code: https://github.com/cran/irt +* Date/Publication: 2024-02-20 20:40:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "irt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘irt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_distractor_icc + > ### Title: Plot Empirical Item or Test characteristic curve + > ### Aliases: plot_distractor_icc + > + > ### ** Examples + > + > n_item <- 10 # sample(8:12, 1) + ... + > raw_resp <- matrix(sample(LETTERS[1:4], n_item * n_theta, replace = TRUE), + + nrow = n_theta, ncol = n_item, + + dimnames = list(paste0("Examinee-", 1:n_theta), + + paste0("Item_", 1:n_item))) + > key <- sample(LETTERS[1:4], n_item, replace = TRUE) + > plot_distractor_icc(raw_resp, 3, key) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plot_distractor_icc ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 20.3Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 18.0Mb + ``` + +# isoorbi + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/isoverse/isoorbi +* Source code: https://github.com/cran/isoorbi +* Date/Publication: 2024-08-27 05:10:03 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "isoorbi")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dual_inlet.Rmd’ + ... + |20230518_05_USGS32_vs_USGS34 | 16| 7|reference |changeover | NA| 10695| 11020| 65.019| 66.994| + |20230518_05_USGS32_vs_USGS34 | 17| 7|reference |data | NA| 11025| 12335| 67.025| 74.985| + + > orbi_plot_raw_data(df_w_blocks, isotopocules = "15N", + + y = ions.incremental) + + When sourcing ‘dual_inlet.R’: + ... + + When sourcing ‘shot_noise.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘dual_inlet.Rmd’ using ‘UTF-8’... failed + ‘flow_injection.Rmd’ using ‘UTF-8’... OK + ‘isoxl_demo.Rmd’ using ‘UTF-8’... OK + ‘quick_start.Rmd’ using ‘UTF-8’... OK + ‘shot_noise.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dual_inlet.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + doc 2.0Mb + extdata 3.3Mb + ``` + +# ivDiag + +
+ +* Version: 1.0.6 +* GitHub: NA +* Source code: https://github.com/cran/ivDiag +* Date/Publication: 2023-09-17 06:00:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "ivDiag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ivDiag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ltz + > ### Title: Local-to-Zero Test + > ### Aliases: ltz + > + > ### ** Examples + > + > data(ivDiag) + > controls <- c('altitudine', 'escursione', 'costal', 'nearsea', 'population', + + 'pop2', 'gini_land', 'gini_income') + > ltz_out <- ltz(data = gsz, Y = "totassoc_p", D = "libero_comune_allnord", + + Z = "bishopcity", controls = controls, weights = "population", + + prior = c(0.178, 0.137)) + > plot_ltz(ltz_out) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_ltz ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ivreg + +
+ +* Version: 0.6-3 +* GitHub: https://github.com/zeileis/ivreg +* Source code: https://github.com/cran/ivreg +* Date/Publication: 2024-04-20 15:22:35 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ivreg")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ivreg.Rmd’ + ... + | F | 204.932 | | + +----------------------+-----------+---------+ + | RMSE | 0.37 | 0.40 | + +----------------------+-----------+---------+ + + > modelplot(m_list, coef_omit = "Intercept|experience") + + When sourcing ‘ivreg.R’: + Error: argument is of length zero + Execution halted + + ‘Diagnostics-for-2SLS-Regression.Rmd’ using ‘UTF-8’... OK + ‘ivreg.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Diagnostics-for-2SLS-Regression.Rmd’ using rmarkdown + ``` + +# jarbes + +
+ +* Version: 2.2.1 +* GitHub: NA +* Source code: https://github.com/cran/jarbes +* Date/Publication: 2024-06-07 09:20:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "jarbes")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hmr.Rmd’ + ... + Warning: Contour data has duplicated x, y coordinates. + ℹ 15940 duplicated rows have been dropped. + Warning: Removed 161 rows containing non-finite outside the scale range + (`stat_contour()`). + Warning: Removed 92 rows containing missing values or values outside the scale range + (`geom_point()`). + + When sourcing ‘hmr.R’: + Error: argument is of length zero + Execution halted + + ‘bmeta.Rmd’ using ‘UTF-8’... OK + ‘hmr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘bmeta.Rmd’ using rmarkdown + ``` + +# karel + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/mpru/karel +* Source code: https://github.com/cran/karel +* Date/Publication: 2022-03-26 21:50:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "karel")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘karel-Ex.R’ failed + The error most likely occurred in: + + > ### Name: acciones + > ### Title: Acciones que Karel puede realizar + > ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso + > ### girar_derecha darse_vuelta + > + > ### ** Examples + > + ... + 1. └─karel::ejecutar_acciones() + 2. ├─base::suppressWarnings(...) + 3. │ └─base::withCallingHandlers(...) + 4. ├─gganimate::animate(...) + 5. └─gganimate:::animate.gganim(...) + 6. └─args$renderer(frames_vars$frame_source, args$fps) + 7. └─gganimate:::png_dim(frames[1]) + 8. └─cli::cli_abort("Provided file ({file}) does not exist") + 9. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(karel) + > + > test_check("karel") + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 5. ├─gganimate::animate(...) + 6. └─gganimate:::animate.gganim(...) + 7. └─args$renderer(frames_vars$frame_source, args$fps) + 8. └─gganimate:::png_dim(frames[1]) + 9. └─cli::cli_abort("Provided file ({file}) does not exist") + 10. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘gifski’ + All declared Imports should be used. + ``` + +# kDGLM + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/silvaneojunior/kDGLM +* Source code: https://github.com/cran/kDGLM +* Date/Publication: 2024-05-25 09:50:03 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "kDGLM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘kDGLM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: forecast.fitted_dlm + > ### Title: Auxiliary function for forecasting + > ### Aliases: forecast.fitted_dlm + > + > ### ** Examples + > + > + ... + > forecast(fitted.data, 24, + + chickenPox = list(Total = rep(175, 24)), # Optional + + Vaccine.1.Covariate = rep(TRUE, 24), + + Vaccine.2.Covariate = rep(TRUE, 24) + + ) + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Error in pm[[2]] : subscript out of bounds + Calls: forecast ... lapply -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘fitting.Rmd’ + ... + > outcome <- Multinom(p = c("p.1", "p.2"), data = chickenPox[, + + c(2, 3, 5)]) + + > fitted.model <- fit_model(structure * 2, chickenPox = outcome) + + > forecast(fitted.model, t = 24, plot = "base") + + When sourcing ‘fitting.R’: + Error: Error: Missing extra argument: Vaccine.1.Covariate + Execution halted + + ‘example1.Rmd’ using ‘UTF-8’... OK + ‘fitting.Rmd’ using ‘UTF-8’... failed + ‘intro.Rmd’ using ‘UTF-8’... OK + ‘outcomes.Rmd’ using ‘UTF-8’... OK + ‘structures.Rmd’ using ‘UTF-8’... OK + ``` + +# KMEANS.KNN + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/KMEANS.KNN +* Date/Publication: 2024-05-17 09:20:12 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "KMEANS.KNN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘KMEANS.KNN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: KMEANS_FUNCTION + > ### Title: KMEANS_FUNCTION + > ### Aliases: KMEANS_FUNCTION + > + > ### ** Examples + > + > data(iris) + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +# latentcor + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/latentcor +* Date/Publication: 2022-09-05 20:50:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "latentcor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘latentcor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: latentcor + > ### Title: Estimate latent correlation for mixed types. + > ### Aliases: latentcor + > + > ### ** Examples + > + > # Example 1 - truncated data type, same type for all variables + ... + > R_approx = latentcor(X = X, types = "tru", method = "approx")$R + > proc.time() - start_time + user system elapsed + 0.027 0.000 0.027 + > # Heatmap for latent correlation matrix. + > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx", + + showplot = TRUE)$plotR + Error in pm[[2]] : subscript out of bounds + Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# lcars + +
+ +* Version: 0.3.8 +* GitHub: https://github.com/leonawicz/lcars +* Source code: https://github.com/cran/lcars +* Date/Publication: 2023-09-10 04:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "lcars")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lcars-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lcars_border + > ### Title: LCARS border plot + > ### Aliases: lcars_border + > + > ### ** Examples + > + > lcars_border() + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + invalid font type + Calls: lcars_border ... drawDetails -> drawDetails.text -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘lcars.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + + When sourcing ‘lcars.R’: + Error: invalid font type + Execution halted + + ‘lcars.Rmd’ using ‘UTF-8’... failed + ``` + +# lemon + +
+ +* Version: 0.4.9 +* GitHub: https://github.com/stefanedwards/lemon +* Source code: https://github.com/cran/lemon +* Date/Publication: 2024-02-08 08:00:08 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "lemon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lemon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate_y_axis + > ### Title: Annotations on the axis + > ### Aliases: annotate_y_axis annotate_x_axis + > + > ### ** Examples + > + > library(ggplot2) + > + > p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point() + > + > l <- p + annotate_y_axis('mark at', y=200, tick=TRUE) + > l + Error in identicalUnits(x) : object is not a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(lemon) + > + > + > if (TRUE) { + + test_check("lemon") + + } #else { + ... + 17. ├─grid::unit.c(unit(1, "npc"), unit(1, "npc") - tick.length) + 18. └─grid:::Ops.unit(unit(1, "npc"), tick.length) + 19. └─grid:::as.unit(e2) + + [ FAIL 1 | WARN 0 | SKIP 3 | PASS 138 ] + Deleting unused snapshots: + • facet/facet-rep-wrap-spacing.svg + • facet_aux/facet-rep-wrap.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘capped-axes.Rmd’ + ... + > p + coord_capped_cart(bottom = "right") + + > p + coord_capped_cart(bottom = "right", left = "none") + + > ggplot(dat1, aes(gp, y)) + geom_point(position = position_jitter(width = 0.2, + + height = 0)) + coord_capped_cart(left = "none", bottom = bracke .... [TRUNCATED] + + ... + When sourcing ‘legends.R’: + Error: Could not find panel named `panel-1-5`. + Execution halted + + ‘capped-axes.Rmd’ using ‘UTF-8’... failed + ‘facet-rep-labels.Rmd’ using ‘UTF-8’... failed + ‘geoms.Rmd’ using ‘UTF-8’... OK + ‘gtable_show_lemonade.Rmd’ using ‘UTF-8’... OK + ‘legends.Rmd’ using ‘UTF-8’... failed + ‘lemon_print.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘capped-axes.Rmd’ using rmarkdown + ``` + +# lfproQC + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/lfproQC +* Date/Publication: 2024-09-06 13:00:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "lfproQC")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lfproQC-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Boxplot_data + > ### Title: Creating Boxplot for a dataset + > ### Aliases: Boxplot_data + > + > ### ** Examples + > + > Boxplot_data(yeast_data) + Using Majority protein IDs as id variables + Warning: Removed 269 rows containing non-finite outside the scale range + (`stat_boxplot()`). + Error in pm[[2]] : subscript out of bounds + Calls: Boxplot_data -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘user_guide.Rmd’ + ... + > yeast$`Best combinations` + PCV_best_combination PEV_best_combination PMAD_best_combination + 1 knn_rlr lls_vsn lls_rlr + + > Boxplot_data(yeast$knn_rlr_data) + Using Majority protein IDs as id variables + + When sourcing ‘user_guide.R’: + Error: subscript out of bounds + Execution halted + + ‘user_guide.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘user_guide.Rmd’ using rmarkdown + + Quitting from lines 53-54 [unnamed-chunk-8] (user_guide.Rmd) + Error: processing vignette 'user_guide.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘user_guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘user_guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 5.8Mb + ``` + +# lgpr + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/jtimonen/lgpr +* Source code: https://github.com/cran/lgpr +* Date/Publication: 2023-09-24 06:50:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "lgpr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # Short tests + > # - focus on testing that everything runs + > # - should take less than minute + > library(testthat) + > library(lgpr) + Attached lgpr 1.2.4, using rstan 2.32.6. Type ?lgpr to get started. + > + ... + 3. └─bayesplot::mcmc_areas(sf, regex_pars = regex_pars, ...) + 4. └─ggplot2:::`+.gg`(...) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 3 | WARN 1 | SKIP 0 | PASS 434 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 156.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 155.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# LightLogR + +
+ +* Version: 0.3.8 +* GitHub: https://github.com/tscnlab/LightLogR +* Source code: https://github.com/cran/LightLogR +* Date/Publication: 2024-07-04 17:00:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "LightLogR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘LightLogR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: aggregate_Date + > ### Title: Aggregate dates to a single day + > ### Aliases: aggregate_Date + > + > ### ** Examples + > + > library(ggplot2) + > #gg_days without aggregation + > sample.data.environment %>% + + gg_days() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# LMoFit + +
+ +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/LMoFit +* Date/Publication: 2024-05-14 07:33:23 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "LMoFit")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LMoFit.Rmd’ + ... + + > lspace_BrIII + + When sourcing ‘LMoFit.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, + Execution halted + + ‘LMoFit.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘LMoFit.Rmd’ using rmarkdown + + Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd) + Error: processing vignette 'LMoFit.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + ... + NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 11, list("white", NA, NULL, NULL, TRUE), list(), 5.5, NULL, NULL, list("grey92", NULL, NULL, NULL, FALSE, TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, + 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, c(5.5, 5.5, 5.5, 5.5), list("white", "black", 2, NULL, TRUE), NULL, NULL, "inherit", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, + NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75, list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5))) + --- failed re-building ‘LMoFit.Rmd’ + + SUMMARY: processing the following file failed: + ‘LMoFit.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +# lnmixsurv + +
+ +* Version: 3.1.6 +* GitHub: NA +* Source code: https://github.com/cran/lnmixsurv +* Date/Publication: 2024-09-03 15:20:08 UTC +* Number of recursive dependencies: 196 + +Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + Error in `pm[[2]]`: subscript out of bounds + Backtrace: + ▆ + 1. └─testthat::expect_snapshot(plot(mod1)) at test-survival_ln_mixture_em-methods.R:25:3 + 2. └─rlang::cnd_signal(state$error) + + [ FAIL 1 | WARN 0 | SKIP 7 | PASS 50 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘expectation_maximization.Rmd’ + ... + + x, data = data, iter = 200, starting_seed = 20, number_em_search = 0) + + > gg <- plot_fit_on_data(model_em, data)$ggplot + + > plot(model_em) + Loading required namespace: plotly + + When sourcing ‘expectation_maximization.R’: + Error: subscript out of bounds + Execution halted + + ‘compare.Rmd’ using ‘UTF-8’... OK + ‘expectation_maximization.Rmd’ using ‘UTF-8’... failed + ‘intercept_only.Rmd’ using ‘UTF-8’... OK + ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK + ‘parallel_computation.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘compare.Rmd’ using rmarkdown + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + ... + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.0Mb + sub-directories of 1Mb or more: + doc 4.0Mb + libs 5.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘purrr’ ‘readr’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘rstanarm’ + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# LocalControl + +
+ +* Version: 1.1.4 +* GitHub: https://github.com/OHDSI/LocalControl +* Source code: https://github.com/cran/LocalControl +* Date/Publication: 2024-09-04 22:30:18 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "LocalControl")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LocalControl-jss-2020.Rnw’ + ... + Warning: A numeric `legend.position` argument in `theme()` was deprecated in + ggplot2 3.5.0. + ℹ Please use the `legend.position.inside` argument of `theme()` + instead. + + > grid.arrange(plotz$rad_1, plotz$rad_11, ncol = 1) + + When sourcing 'LocalControl-jss-2020.R': + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LocalControl-jss-2020.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 2.0Mb + libs 2.7Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LocalControl-jss-2020.Rnw’ using Sweave + Loading required package: data.table + Loading required package: colorspace + Loading required package: RColorBrewer + Loading required package: gridExtra + Loading required package: ggplot2 + Loading required package: rpart + Loading required package: rpart.plot + Loading required package: LocalControl + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building 'LocalControl-jss-2020.Rnw' + + SUMMARY: processing the following file failed: + 'LocalControl-jss-2020.Rnw' + + Error: Vignette re-building failed. + Execution halted + ``` + +# LocalCop + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/mlysy/LocalCop +* Source code: https://github.com/cran/LocalCop +* Date/Publication: 2024-03-21 14:50:06 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "LocalCop")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LocalCop-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LocalCop-vignette.Rmd’ + ... + > tibble(x = x0, True = BiCopEta2Tau(family, eta = eta_fun(x0)), + + Fitted = BiCopEta2Tau(fitseq$eta, family = family)) %>% pivot_longer(True:Fitt .... [TRUNCATED] + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_line()`). + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_point()`). + + When sourcing ‘LocalCop-vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LocalCop-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 55.7Mb + sub-directories of 1Mb or more: + libs 55.3Mb + ``` + +# LongDat + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/CCY-dev/LongDat +* Source code: https://github.com/cran/LongDat +* Date/Publication: 2023-07-17 05:40:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "LongDat")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LongDat_cont_tutorial.Rmd’ + ... + + > test_plot <- cuneiform_plot(result_table = test_cont[[1]], + + title_size = 15) + [1] "Finished plotting successfully!" + + > test_plot + + ... + [1] "Finished plotting successfully!" + + > test_plot + + When sourcing ‘LongDat_disc_tutorial.R’: + Error: object is not coercible to a unit + Execution halted + + ‘LongDat_cont_tutorial.Rmd’ using ‘UTF-8’... failed + ‘LongDat_disc_tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LongDat_cont_tutorial.Rmd’ using rmarkdown + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + + ... + Quitting from lines 181-182 [unnamed-chunk-11] (LongDat_disc_tutorial.Rmd) + Error: processing vignette 'LongDat_disc_tutorial.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘LongDat_disc_tutorial.Rmd’ + + SUMMARY: processing the following files failed: + ‘LongDat_cont_tutorial.Rmd’ ‘LongDat_disc_tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# longreadvqs + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/NakarinP/longreadvqs +* Source code: https://github.com/cran/longreadvqs +* Date/Publication: 2024-08-26 19:30:05 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "longreadvqs")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘longreadvqs-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vqscompare + > ### Title: Comparing viral quasispecies profile and operational taxonomic + > ### unit (OTU) classified by k-means clustering between samples + > ### Aliases: vqscompare + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘longreadvqs-vignette.Rmd’ + ... + + > comp <- vqscompare(samplelist = list(s1, s2, s3, s4_fix), + + lab_name = "Sample", kmeans.n = 10) + + When sourcing ‘longreadvqs-vignette.R’: + Error: ℹ In index: 1. + ℹ With name: Dim.2. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘longreadvqs-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘longreadvqs-vignette.Rmd’ using rmarkdown + ``` + +# lpdensity + +
+ +* Version: 2.4 +* GitHub: NA +* Source code: https://github.com/cran/lpdensity +* Date/Publication: 2023-01-21 23:50:02 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "lpdensity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lpdensity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lpdensity + > ### Title: Local Polynomial Density Estimation and Inference + > ### Aliases: lpdensity + > + > ### ** Examples + > + > # Generate a random sample + ... + 18 1.2878 0.6298 457 0.1749 0.0097 0.1222 , 0.2179 + 19 1.5768 0.6298 299 0.1221 0.0086 0.0863 , 0.1719 + ============================================================================= + > + > # Plot the estimates and confidence intervals + > plot(est1, legendTitle="My Plot", legendGroups=c("X")) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# lspartition + +
+ +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/lspartition +* Date/Publication: 2019-08-08 22:40:06 UTC +* Number of recursive dependencies: 34 + +Run `revdepcheck::cloud_details(, "lspartition")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lspartition-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lsprobust.plot + > ### Title: Graphic Presentation of Results for 'lspartition' Package + > ### Aliases: lsprobust.plot + > + > ### ** Examples + > + > x <- runif(500) + > y <- sin(4*x)+rnorm(500) + > est <- lsprobust(y, x) + > lsprobust.plot(est) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# LSTbook + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/dtkaplan/LSTbook +* Source code: https://github.com/cran/LSTbook +* Date/Publication: 2024-02-23 19:20:15 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "LSTbook")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 73 ] + Deleting unused snapshots: + • model_plot/four-facets.png + • pointplot/1-var-plot.png + • pointplot/bird-logistic-plot.png + • pointplot/color-and-facet-na.png + • pointplot/logistic-fun-plot.png + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘DAGs.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘DAGs.Rmd’ + ... + 3 -1.35 -11.9 + 4 0.429 0.171 + 5 0.622 5.85 + 6 2.35 16.5 + + > Wrong_way <- datasim_make(x = rnorm(n, mean = 0, sd = 2)) + + ... + + > model_plot(height_model) + + When sourcing ‘modeling.R’: + Error: argument is of length zero + Execution halted + + ‘DAGs.Rmd’ using ‘UTF-8’... failed + ‘LSTbook.Rmd’ using ‘UTF-8’... OK + ‘modeling.Rmd’ using ‘UTF-8’... failed + ``` + +* checking loading without being on the library search path ... WARNING + ``` + Error: package or namespace load failed for ‘LSTbook’: + .onLoad failed in loadNamespace() for 'LSTbook', details: + call: loadNamespace(name) + error: there is no package called ‘mosaicData’ + Execution halted + + It looks like this package has a loading problem when not on .libPaths: + see the messages for details. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 20 marked UTF-8 strings + ``` + +# manydata + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/globalgov/manydata +* Source code: https://github.com/cran/manydata +* Date/Publication: 2024-05-06 19:00:02 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "manydata")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(manydata) + manydata 0.9.3 + Please see manydata.ch for more information. + Type 'citation("manydata")' for citing this R package in publications. + > + > test_check("manydata") + ... + ── Failure ('test_compare.R:8:3'): plot for compare_categories returns the correct output format ── + Names of `db` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' + ── Failure ('test_compare.R:74:3'): compare_missing() and plot_missing() returns the correct output format ── + `pl` has length 11, not length 10. + ── Failure ('test_compare.R:76:3'): compare_missing() and plot_missing() returns the correct output format ── + Names of `pl` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' + + [ FAIL 4 | WARN 0 | SKIP 3 | PASS 121 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 3 marked UTF-8 strings + ``` + +# manymome + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/sfcheung/manymome +* Source code: https://github.com/cran/manymome +* Date/Publication: 2024-06-05 23:30:03 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "manymome")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘manymome-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_effect_vs_w + > ### Title: Plot an Effect Against a Moderator + > ### Aliases: plot_effect_vs_w + > + > ### ** Examples + > + > + ... + + y = "y", + + m = "m", + + fit = fit_lm, + + sd_from_mean = seq(-2, 2, length.out = 10), + + boot_ci = TRUE, + + boot_out = boot_out_lm) + > p <- plot_effect_vs_w(out_lm) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_effect_vs_w ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# mapbayr + +
+ +* Version: 0.10.0 +* GitHub: https://github.com/FelicienLL/mapbayr +* Source code: https://github.com/cran/mapbayr +* Date/Publication: 2023-07-17 08:20:02 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "mapbayr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mapbayr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mapbayr_plot + > ### Title: Make mapbayr plot + > ### Aliases: mapbayr_plot + > + > ### ** Examples + > + > aug <- data.frame( + ... + > obs <- data.frame( + + ID = 1, time = c(6, 20), evid = 0, + + mdv = c(0,1), DV = c(0.5, 5), cmt = 2 + + ) + > + > mapbayr_plot(aug, obs) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# MBNMAdose + +
+ +* Version: 0.4.3 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAdose +* Date/Publication: 2024-04-18 12:42:47 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "MBNMAdose")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘outputs-4.Rmd’ + ... + + > plot(trip.emax) + + When sourcing ‘outputs-4.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + Execution halted + + ‘consistencychecking-3.Rmd’ using ‘UTF-8’... OK + ‘dataexploration-1.Rmd’ using ‘UTF-8’... OK + ‘mbnmadose-overview.Rmd’ using ‘UTF-8’... OK + ‘metaregression-6.Rmd’ using ‘UTF-8’... OK + ‘nma_in_mbnmadose.Rmd’ using ‘UTF-8’... OK + ‘outputs-4.Rmd’ using ‘UTF-8’... failed + ‘predictions-5.Rmd’ using ‘UTF-8’... OK + ‘runmbnmadose-2.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6 marked Latin-1 strings + ``` + +# MBNMAtime + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAtime +* Date/Publication: 2023-10-14 15:20:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "MBNMAtime")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown + + Quitting from lines 141-146 [unnamed-chunk-8] (consistencychecking-3.Rmd) + Error: processing vignette 'consistencychecking-3.Rmd' failed with diagnostics: + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, + NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.2, 0, 2.2), NULL, TRUE), list("grey20", NULL, NULL, NULL, FALSE, "grey20", TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, + NULL, NULL, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), NULL, 2, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list(), list(NULL, "grey20", NULL, NULL, TRUE), NULL, NULL, + NULL, list("grey92", NULL, NULL, NULL, FALSE, "grey92", TRUE), list("grey95", NULL, NULL, NULL, FALSE, "grey95", FALSE), list("grey95", 0.5, NULL, NULL, FALSE, "grey95", FALSE), NULL, NULL, NULL, NULL, FALSE, list("white", NA, NULL, NULL, FALSE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list( + NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list("lightsteelblue1", "black", NULL, NULL, FALSE), NULL, NULL, "on", "inside", list(NULL, NULL, "black", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, FALSE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘consistencychecking-3.Rmd’ + + --- re-building ‘dataexploration-1.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘consistencychecking-3.Rmd’ + ... + |-> direct | | 0.228| -0.213| 0.684| + |-> indirect | | -0.515| -0.891| -0.137| + | | | | | | + + > plot(nodesplit, plot.type = "forest") + + When sourcing ‘consistencychecking-3.R’: + ... + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘consistencychecking-3.Rmd’ using ‘UTF-8’... failed + ‘dataexploration-1.Rmd’ using ‘UTF-8’... failed + ‘mbnmatime-overview.Rmd’ using ‘UTF-8’... OK + ‘outputs-4.Rmd’ using ‘UTF-8’... failed + ‘predictions-5.Rmd’ using ‘UTF-8’... OK + ‘runmbnmatime-2.Rmd’ using ‘UTF-8’... OK + ``` + +# mecoturn + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/ChiLiubio/mecoturn +* Source code: https://github.com/cran/mecoturn +* Date/Publication: 2023-09-10 13:40:02 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "mecoturn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mecoturn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: betaturn + > ### Title: Analyze the 'turnover' of microbial communities. + > ### Aliases: betaturn + > + > ### ** Examples + > + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +# MetaNet + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/Asa12138/MetaNet +* Source code: https://github.com/cran/MetaNet +* Date/Publication: 2024-03-25 20:40:07 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "MetaNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MetaNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.ggig + > ### Title: Transfer an igraph object to a ggig + > ### Aliases: as.ggig + > + > ### ** Examples + > + > as.ggig(co_net, coors = c_net_layout(co_net)) -> ggig + > plot(ggig) + Warning: Removed 446 rows containing missing values or values outside the scale range + (`geom_text()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +# metR + +
+ +* Version: 0.15.0 +* GitHub: https://github.com/eliocamp/metR +* Source code: https://github.com/cran/metR +* Date/Publication: 2024-02-09 00:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "metR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘metR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_contour_tanaka + > ### Title: Illuminated contours + > ### Aliases: geom_contour_tanaka GeomContourTanaka + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 20. │ └─self$draw_panel(...) + 21. │ └─metR (local) draw_panel(...) + 22. │ └─metR:::stopf(...) + 23. │ └─base::stop(e) + 24. └─rlang (local) ``(``) + 25. └─handlers[[1L]](cnd) + 26. └─cli::cli_abort(...) + 27. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(metR) + > # library(vdiffr) + > + > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false"))) + > if (on_cran) data.table::setDTthreads(2) + > + ... + • vis-streamline/streamline-ywrapped.svg + • vis-text-contour/labels-text.svg + • vis-text-contour/minsize.svg + • vis-text-contour/placement-fraction.svg + • vis-text-contour/placement-minmax-horizontal.svg + • vis-text-contour/placement-minmax-vertical.svg + • vis-text-contour/placement-n.svg + • vis-text-contour/text-contour-norotate.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Visualization-tools.Rmd’ + ... + + > ggplot(temperature[lev == 300], aes(lon, lat, z = air.z)) + + + geom_contour_fill() + geom_contour_tanaka() + scale_fill_divergent() + + When sourcing ‘Visualization-tools.R’: + Error: Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + Execution halted + + ‘Visualization-tools.Rmd’ using ‘UTF-8’... failed + ‘Working-with-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Visualization-tools.Rmd’ using knitr + + Quitting from lines 241-245 [unnamed-chunk-16] (Visualization-tools.Rmd) + Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics: + Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + ... + --- failed re-building ‘Visualization-tools.Rmd’ + + --- re-building ‘Working-with-data.Rmd’ using knitr + --- finished re-building ‘Working-with-data.Rmd’ + + SUMMARY: processing the following file failed: + ‘Visualization-tools.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.0Mb + doc 1.8Mb + ``` + +# metrica + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/adriancorrendo/metrica +* Source code: https://github.com/cran/metrica +* Date/Publication: 2024-06-30 14:20:02 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "metrica")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘regression_case.Rmd’ + ... + + mutate(Year = seq(2001, 2020, by = 1)) + + > wheat_time %>% ggplot2::ggplot(aes(x = Year)) + geom_point(aes(y = pred, + + fill = "Predicted", shape = "Predicted")) + geom_point(aes(y = obs, .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + ... + Execution halted + + ‘Cheatsheet.Rmd’ using ‘UTF-8’... OK + ‘JOSS_publication.Rmd’ using ‘UTF-8’... OK + ‘Shinyapp.Rmd’ using ‘UTF-8’... OK + ‘apsim_open.Rmd’ using ‘UTF-8’... OK + ‘available_metrics_classification.Rmd’ using ‘UTF-8’... OK + ‘available_metrics_regression.Rmd’ using ‘UTF-8’... OK + ‘classification_case.Rmd’ using ‘UTF-8’... OK + ‘regression_case.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Cheatsheet.Rmd’ using rmarkdown + --- finished re-building ‘Cheatsheet.Rmd’ + + --- re-building ‘JOSS_publication.Rmd’ using rmarkdown + --- finished re-building ‘JOSS_publication.Rmd’ + + --- re-building ‘Shinyapp.Rmd’ using rmarkdown + --- finished re-building ‘Shinyapp.Rmd’ + + ... + --- re-building ‘apsim_open.Rmd’ using rmarkdown + --- finished re-building ‘apsim_open.Rmd’ + + --- re-building ‘available_metrics_classification.Rmd’ using rmarkdown + --- finished re-building ‘available_metrics_classification.Rmd’ + + --- re-building ‘available_metrics_regression.Rmd’ using rmarkdown + --- finished re-building ‘available_metrics_regression.Rmd’ + + --- re-building ‘classification_case.Rmd’ using rmarkdown + ``` + +# miceRanger + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/FarrellDay/miceRanger +* Source code: https://github.com/cran/miceRanger +* Date/Publication: 2021-09-06 15:20:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "miceRanger")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘usingMiceRanger.Rmd’ + ... + > plotList <- lapply(plotVars, function(x) { + + missIndx <- is.na(ampIris[, get(x)]) + + impVsAmp <- data.table(originalData = iris[missIndx, x], .... [TRUNCATED] + + When sourcing ‘usingMiceRanger.R’: + Error: ℹ In index: 1. + ℹ With name: imputedData. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘diagnosticPlotting.Rmd’ using ‘UTF-8’... OK + ‘miceAlgorithm.Rmd’ using ‘UTF-8’... OK + ‘usingMiceRanger.Rmd’ using ‘UTF-8’... failed + ``` + +# microbial + +
+ +* Version: 0.0.21 +* GitHub: NA +* Source code: https://github.com/cran/microbial +* Date/Publication: 2024-05-15 18:20:02 UTC +* Number of recursive dependencies: 179 + +Run `revdepcheck::cloud_details(, "microbial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘microbial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotalpha + > ### Title: plot alpha diversity + > ### Aliases: plotalpha + > + > ### ** Examples + > + > { + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘microbial.Rmd’ + ... + > plotbar(phy, level = "Phylum") + + > plotalpha(physeq, group = "group") + + When sourcing ‘microbial.R’: + Error: ℹ In index: 1. + ℹ With name: val. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘microbial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘microbial.Rmd’ using knitr + ``` + +# MicrobiomeSurv + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/N-T-Huyen/MicrobiomeSurv +* Source code: https://github.com/cran/MicrobiomeSurv +* Date/Publication: 2023-10-12 06:20:02 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "MicrobiomeSurv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MicrobiomeSurv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EstimateHR + > ### Title: Classification, Survival Estimation and Visualization + > ### Aliases: EstimateHR + > + > ### ** Examples + > + > # Prepare data + ... + + Mean = TRUE) + > + > # Using the function + > est_HR_fam_shan_w3 = EstimateHR(Risk.Scores = lasso_fam_shan_w3$Risk.Scores, + + Data.Survival = lasso_fam_shan_w3$Data.Survival, + + Prognostic = prog_fam_shan_w3, Plots = TRUE, + + Mean = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: EstimateHR ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# migraph + +
+ +* Version: 1.4.2 +* GitHub: https://github.com/stocnet/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2024-09-04 12:00:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "migraph")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(manynet) + > library(migraph) + > + > test_check("migraph") + Starting 2 test processes + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] + ... + `expected` is a character vector ('Statistic') + ── Failure ('test-model_tests.R:73:3'): qap plot works ───────────────────────── + qapplot$labels$x (`actual`) not identical to "Statistic" (`expected`). + + `actual` is NULL + `expected` is a character vector ('Statistic') + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +# mikropml + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2023-08-21 15:10:05 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "mikropml")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mikropml) + > test_check("mikropml") + Fraction of data in the training set: 0.778 + Groups in the training set: A C D + Groups in the testing set: B + Fraction of data in the training set: 0.778 + ... + `names(expected)` is absent + ── Failure ('test-plot.R:140:3'): plot_mean_prc uses geom ribbon, line, and hline ── + ... %>% unlist() (`actual`) not equal to c(...) (`expected`). + + `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...) + `names(expected)` is absent + + [ FAIL 2 | WARN 19 | SKIP 12 | PASS 314 ] + Error: Test failures + Execution halted + ``` + +# MiMIR + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/MiMIR +* Date/Publication: 2024-02-01 08:50:02 UTC +* Number of recursive dependencies: 191 + +Run `revdepcheck::cloud_details(, "MiMIR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MiMIR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: LOBOV_accuracies + > ### Title: LOBOV_accuracies + > ### Aliases: LOBOV_accuracies + > + > ### ** Examples + > + > require(pROC) + ... + 56 metabolites x 500 samples + | Pruning samples on5SD: + 56 metabolites x 500 samples + | Performing scaling ... DONE! + | Imputation ... DONE! + > p_avail<-colnames(b_p)[c(1:5)] + > LOBOV_accuracies(sur$surrogates, b_p, p_avail, MiMIR::acc_LOBOV) + Error in pm[[2]] : subscript out of bounds + Calls: LOBOV_accuracies -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# miRetrieve + +
+ +* Version: 1.3.4 +* GitHub: NA +* Source code: https://github.com/cran/miRetrieve +* Date/Publication: 2021-09-18 17:30:02 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "miRetrieve")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(miRetrieve) + > + > test_check("miRetrieve") + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + Backtrace: + ▆ + 1. └─miRetrieve::compare_mir_terms_scatter(df_merged, "miR-21", title = "Test_title") at test-comparemirterms.R:56:1 + 2. ├─plotly::ggplotly(plot) + 3. └─plotly:::ggplotly.ggplot(plot) + 4. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] + Error: Test failures + Execution halted + ``` + +# MiscMetabar + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/adrientaudiere/MiscMetabar +* Source code: https://github.com/cran/MiscMetabar +* Date/Publication: 2024-09-09 09:20:01 UTC +* Number of recursive dependencies: 420 + +Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MiscMetabar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggscatt_pq + > ### Title: Scatterplot with marginal distributions and statistical results + > ### against Hill diversity of phyloseq object + > ### Aliases: ggscatt_pq + > + > ### ** Examples + > + ... + + ) + + } + Loading required namespace: ggstatsplot + Taxa are now in columns. + Cleaning suppress 0 taxa and 0 samples. + Taxa are now in rows. + Joining with `by = join_by(Sample)` + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggscatt_pq ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(MiscMetabar) + Loading required package: phyloseq + Loading required package: ggplot2 + Loading required package: dada2 + Loading required package: Rcpp + Loading required package: dplyr + ... + 14. └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. ├─ggplot2::ggplot_add(object, p, objectname) + 16. └─ggplot2:::ggplot_add.list(object, p, objectname) + 17. ├─ggplot2::ggplot_add(o, plot, object_name) + 18. └─ggplot2:::ggplot_add.Layer(o, plot, object_name) + 19. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 76 | PASS 82 ] + Error: Test failures + Execution halted + ``` + +# misspi + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/misspi +* Date/Publication: 2023-10-17 09:50:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "misspi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘misspi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: evaliq + > ### Title: Evaluate the Imputation Quality + > ### Aliases: evaliq + > + > ### ** Examples + > + > # A very quick example + ... + > # Default plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx]) + `geom_smooth()` using formula = 'y ~ x' + > + > # Interactive plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx], interactive = TRUE) + `geom_smooth()` using formula = 'y ~ x' + Error in pm[[2]] : subscript out of bounds + Calls: evaliq -> print -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# mixpoissonreg + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/vpnsctl/mixpoissonreg +* Source code: https://github.com/cran/mixpoissonreg +* Date/Publication: 2021-03-10 19:50:06 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "mixpoissonreg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mixpoissonreg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.mixpoissonreg + > ### Title: Autoplot Method for 'mixpoissonreg' Objects + > ### Aliases: autoplot.mixpoissonreg autoplot + > + > ### ** Examples + > + > daysabs_prog <- mixpoissonregML(daysabs ~ prog, data = Attendance) + > autoplot(daysabs_prog) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mixpoissonreg) + > + > test_check("mixpoissonreg") + + Negative Binomial Regression - Expectation-Maximization Algorithm + + ... + 2. └─mixpoissonreg:::autoplot.mixpoissonreg(fit_ml1, nrow = 2) + 3. └─ggplot2:::`+.gg`(...) + 4. └─ggplot2:::add_ggplot(e1, e2, e2name) + 5. ├─ggplot2::ggplot_add(object, p, objectname) + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 28 | SKIP 0 | PASS 35 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘influence-mixpoissonreg.Rmd’ + ... + 5 2.747544 -0.2460342 -0.006644830 -0.4252217 -1.269154 + 6 2.746786 -0.2443429 -0.006641383 -0.4268347 -1.269387 + + > plot(fit, which = c(3, 4, 5)) + + > autoplot(fit, which = c(3, 4, 5)) + + ... + + When sourcing ‘tutorial-mixpoissonreg.R’: + Error: argument is of length zero + Execution halted + + ‘influence-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘intervals-mixpoissonreg.Rmd’ using ‘UTF-8’... OK + ‘ml-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘tidyverse-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘tutorial-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘influence-mixpoissonreg.Rmd’ using rmarkdown + ``` + +# mizer + +
+ +* Version: 2.5.1 +* GitHub: https://github.com/sizespectrum/mizer +* Source code: https://github.com/cran/mizer +* Date/Publication: 2024-03-08 23:10:02 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "mizer")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mizer) + > + > test_check("mizer") + [ FAIL 10 | WARN 0 | SKIP 5 | PASS 1251 ] + + ... + • plots/plot-spectra.svg + • plots/plot-yield-by-gear.svg + • plots/plot-yield.svg + • plots/plotfishing-mortality.svg + • plots/plotfmort-truncated.svg + • plots/plotpredation-mortality.svg + • plots/plotpredmort-truncated.new.svg + • plots/plotpredmort-truncated.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 1.5Mb + help 1.8Mb + ``` + +# mlr3spatiotempcv + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/mlr-org/mlr3spatiotempcv +* Source code: https://github.com/cran/mlr3spatiotempcv +* Date/Publication: 2024-04-17 12:10:05 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "mlr3spatiotempcv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mlr3spatiotempcv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.ResamplingCustomCV + > ### Title: Visualization Functions for Non-Spatial CV Methods. + > ### Aliases: autoplot.ResamplingCustomCV plot.ResamplingCustomCV + > + > ### ** Examples + > + > if (mlr3misc::require_namespaces(c("sf", "patchwork"), quietly = TRUE)) { + ... + + + + autoplot(resampling, task) + + + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) + + autoplot(resampling, task, fold_id = 1) + + autoplot(resampling, task, fold_id = c(1, 2)) * + + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) + + } + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘spatiotemp-viz.Rmd’ + ... + + > knitr::opts_chunk$set(collapse = TRUE, comment = "#>") + + > knitr::include_graphics("../man/figures/sptcv_cstf_multiplot.png") + + When sourcing ‘spatiotemp-viz.R’: + Error: Cannot find the file(s): "../man/figures/sptcv_cstf_multiplot.png" + Execution halted + + ‘mlr3spatiotempcv.Rmd’ using ‘UTF-8’... OK + ‘spatiotemp-viz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + data 3.5Mb + ``` + +# mlr3viz + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/mlr-org/mlr3viz +* Source code: https://github.com/cran/mlr3viz +* Date/Publication: 2024-07-01 12:30:02 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "mlr3viz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mlr3viz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.OptimInstanceBatchSingleCrit + > ### Title: Plots for Optimization Instances + > ### Aliases: autoplot.OptimInstanceBatchSingleCrit + > + > ### ** Examples + > + > if (requireNamespace("mlr3") && requireNamespace("bbotk") && requireNamespace("patchwork")) { + ... + INFO [09:22:56.650] [bbotk] 5.884797 2.2371095 -32.51896 + INFO [09:22:56.650] [bbotk] -7.841127 -0.8872557 -91.31148 + INFO [09:22:56.668] [bbotk] Finished optimizing after 20 evaluation(s) + INFO [09:22:56.669] [bbotk] Result: + INFO [09:22:56.670] [bbotk] x1 x2 x_domain y + INFO [09:22:56.670] [bbotk] + INFO [09:22:56.670] [bbotk] 2.582281 -2.940254 9.657379 + Error in identicalUnits(x) : object is not a unit + Calls: print ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (requireNamespace("testthat", quietly = TRUE)) { + + library("testthat") + + library("mlr3viz") + + test_check("mlr3viz") + + } + Starting 2 test processes + [ FAIL 4 | WARN 1 | SKIP 24 | PASS 84 ] + ... + • TuningInstanceSingleCrit/tisc-surface-grid-50.svg + • TuningInstanceSingleCrit/tisc-surface-regr-lm.svg + • TuningInstanceSingleCrit/tisc-surface.svg + • plot_learner_prediction/learner-prediction-1d-se.svg + • plot_learner_prediction/learner-prediction-binary-prob.svg + • plot_learner_prediction/learner-prediction-binary-response.svg + • plot_learner_prediction/learner-prediction-categorical.svg + • plot_learner_prediction/learner-prediction-prob.svg + Error: Test failures + Execution halted + ``` + +# modeltime.resample + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/business-science/modeltime.resample +* Source code: https://github.com/cran/modeltime.resample +* Date/Publication: 2023-04-12 15:50:02 UTC +* Number of recursive dependencies: 227 + +Run `revdepcheck::cloud_details(, "modeltime.resample")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > # Machine Learning + > library(tidymodels) + ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ── + ✔ broom 1.0.6 ✔ recipes 1.1.0 + ✔ dials 1.3.0 ✔ rsample 1.2.1 + ... + ▆ + 1. ├─m750_models_resample %>% ... at test-modeltime_fit_resamples.R:116:5 + 2. └─modeltime.resample::plot_modeltime_resamples(., .interactive = TRUE) + 3. ├─plotly::ggplotly(g) + 4. └─plotly:::ggplotly.ggplot(g) + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 16 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’ + All declared Imports should be used. + ``` + +# moreparty + +
+ +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/moreparty +* Date/Publication: 2023-11-22 14:30:02 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "moreparty")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Titanic_example.Rmd’ + ... + 24 Age 57 0.3187270 + 25 Embarked Cherbourg 0.4603041 + [ reached 'max' / getOption("max.print") -- omitted 2 rows ] + + > ggForestEffects(pdep, vline = mean(pred_foret), xlab = "Probability of survival") + + + xlim(c(0, 1)) + + When sourcing ‘Titanic_example.R’: + Error: `x` must be a vector, not a object. + Execution halted + + ‘Titanic_example.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Titanic_example.Rmd’ using rmarkdown + ``` + +# mosaicCalc + +
+ +* Version: 0.6.4 +* GitHub: https://github.com/ProjectMOSAIC/mosaicCalc +* Source code: https://github.com/cran/mosaicCalc +* Date/Publication: 2024-07-26 15:50:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "mosaicCalc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mosaicCalc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box_set + > ### Title: Evenly spaced samples across a one- or two-dim domain + > ### Aliases: box_set + > + > ### ** Examples + > + > box_set(x*y ~ x & y, domain(x=0:1, y=0:1), n = 4) + ... + [1] 0 + > # a polygon + > poly <- tibble(x = c(1:9, 8:1), y = c(1, 2*(5:3), 2, -1, 17, 9, 8, 2:9)) + > boxes <- box_set(1 ~ x & y, poly, dx = 1) + > gf_polygon(y ~ x, data = poly, color="blue", fill="blue", alpha=0.2) %>% + + gf_rect((y - dy/3) + (y + dy/3) ~ (x - dx/3) + (x + dx/3), + + data = boxes) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Calculus_with_R.Rmd’ + ... + + > soln <- integrateODE(SIR, bounds(t = 0:20)) + Solution containing functions S(t), I(t). + + > traj_plot(S(t) ~ I(t), soln, color = "blue") %>% vectorfield_plot(SIR, + + bounds(I = 0:75, S = 60:400), transform = I, npts = 20, alpha = 0.6) + + ... + + > gf_point(flipper_length_mm ~ body_mass_g, data = palmerpenguins::penguins) + + When sourcing ‘quick-reference.R’: + Error: argument is of length zero + Execution halted + + ‘Calculus_with_R.Rmd’ using ‘UTF-8’... failed + ‘Instructors.Rmd’ using ‘UTF-8’... failed + ‘quick-reference.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Calculus_with_R.Rmd’ using rmarkdown + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 56 marked UTF-8 strings + ``` + +# mosaicData + +
+ +* Version: 0.20.4 +* GitHub: https://github.com/ProjectMOSAIC/mosaicData +* Source code: https://github.com/cran/mosaicData +* Date/Publication: 2023-11-05 05:50:02 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "mosaicData")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mosaicData-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Birthdays + > ### Title: US Births in 1969 - 1988 + > ### Aliases: Birthdays + > + > ### ** Examples + > + > data(Birthdays) + ... + IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test, + quantile, sd, t.test, var + + The following objects are masked from ‘package:base’: + + max, mean, min, prod, range, sample, sum + + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7 marked UTF-8 strings + ``` + +# mosaicModel + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/mosaicModel +* Date/Publication: 2017-09-22 16:21:41 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "mosaicModel")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Basics.Rmd’ + ... + + out.width = "45%") + + > mtcars <- mtcars %>% mutate(transmission = ifelse(am, + + "manual", "automatic")) + + > gf_point(mpg ~ hp, color = ~transmission, data = mtcars) + + When sourcing ‘Basics.R’: + Error: argument is of length zero + Execution halted + + ‘Basics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Basics.Rmd’ using rmarkdown + + Quitting from lines 66-68 [fuel_intro] (Basics.Rmd) + Error: processing vignette 'Basics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Basics.Rmd’ + + SUMMARY: processing the following file failed: + ‘Basics.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’ + All declared Imports should be used. + ``` + +# mppR + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/vincentgarin/mppR +* Source code: https://github.com/cran/mppR +* Date/Publication: 2024-02-22 17:20:02 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "mppR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MPP_ME_QTL_detect.Rmd’ + ... + F2 -2.9970560 0.18508863 -0.00806081 0.1266095 + F283 10.2417600 1.78749082 -0.04223259 2.0862106 + DK105 0.1792433 0.03829626 NA NA + + > plot_QxEC(Qeff, EC = EC, env_id = c("CIAM", "TUM", + + "INRA", "KWS"), QTL = 2, EC_id = "cum rain", trait_id = "DMY") + + When sourcing ‘MPP_ME_QTL_detect.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘MPP_ME_QTL_detect.Rmd’ using ‘UTF-8’... failed + ‘mppR_gen_vignette.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown + ``` + +# MSCMT + +
+ +* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/MSCMT +* Date/Publication: 2024-03-19 10:20:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "MSCMT")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘WorkingWithMSCMT.Rmd’ + ... + (Predictor weights V are standardized by sum(V)=1) + + + > library(ggplot2) + + > ggplot(res, type = "comparison") + + When sourcing ‘WorkingWithMSCMT.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘CheckingSynth.Rmd’ using ‘UTF-8’... OK + ‘UsingTimeSeries.Rmd’ using ‘UTF-8’... OK + ‘WorkingWithMSCMT.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CheckingSynth.Rmd’ using rmarkdown + --- finished re-building ‘CheckingSynth.Rmd’ + + --- re-building ‘UsingTimeSeries.Rmd’ using rmarkdown + --- finished re-building ‘UsingTimeSeries.Rmd’ + + --- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown + + ... + Quitting from lines 156-158 [unnamed-chunk-8] (WorkingWithMSCMT.Rmd) + Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘WorkingWithMSCMT.Rmd’ + + SUMMARY: processing the following file failed: + ‘WorkingWithMSCMT.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mstate + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/hputter/mstate +* Source code: https://github.com/cran/mstate +* Date/Publication: 2024-07-11 21:30:06 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "mstate")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mstate-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.Cuminc + > ### Title: Plot method for Cuminc objects + > ### Aliases: plot.Cuminc + > + > ### ** Examples + > + > library(ggplot2) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘visuals_demo.Rmd’ + ... + + > msf.WW <- msfit(object = c1, newdata = WW, trans = tmat) + + > plot(msf.WW) + + > plot(msf.WW, use.ggplot = TRUE) + + When sourcing ‘visuals_demo.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘visuals_demo.Rmd’ using ‘UTF-8’... failed + ‘Tutorial.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘visuals_demo.Rmd’ using rmarkdown + ``` + +# mtb + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/yh202109/mtb +* Source code: https://github.com/cran/mtb +* Date/Publication: 2022-10-20 17:22:35 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "mtb")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mtb) + > + > test_check("mtb") + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + - "yend" [6] + - "xmin" [7] + - "xmax" [8] + - "ymin" [9] + - "ymax" [10] + ... ... ... and 3 more ... + + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] + Error: Test failures + Execution halted + ``` + +# mulgar + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/dicook/mulgar +* Source code: https://github.com/cran/mulgar +* Date/Publication: 2023-08-25 22:00:02 UTC +* Number of recursive dependencies: 43 + +Run `revdepcheck::cloud_details(, "mulgar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mulgar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggmcbic + > ### Title: Produces an mclust summary plot with ggplot + > ### Aliases: ggmcbic + > + > ### ** Examples + > + > require(mclust) + ... + Type 'citation("mclust")' for citing this R package in publications. + > data(clusters) + > clusters_BIC <- mclustBIC(clusters[,1:5], G=2:6) + > ggmcbic(clusters_BIC) + Warning: Removed 5 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + data 8.5Mb + ``` + +# MultivariateAnalysis + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/MultivariateAnalysis +* Date/Publication: 2024-04-08 18:40:03 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "MultivariateAnalysis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MultivariateAnalysis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ContribuicaoRelativa + > ### Title: Contribuicao das variaveis independentes para o agrupamento + > ### Aliases: ContribuicaoRelativa + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# mxfda + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/julia-wrobel/mxfda +* Source code: https://github.com/cran/mxfda +* Date/Publication: 2024-05-08 11:00:02 UTC +* Number of recursive dependencies: 221 + +Run `revdepcheck::cloud_details(, "mxfda")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + data 4.0Mb + ``` + +# neatmaps + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/PhilBoileau/neatmaps +* Source code: https://github.com/cran/neatmaps +* Date/Publication: 2019-05-12 19:10:03 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "neatmaps")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neatmaps-Ex.R’ failed + The error most likely occurred in: + + > ### Name: consClustResTable + > ### Title: Consensus Cluster Results in a Table + > ### Aliases: consClustResTable + > + > ### ** Examples + > + > # create the data frame using the network, node and edge attributes + ... + > df <- netsDataFrame(network_attr_df, + + node_attr_df, + + edge_df) + > + > # run the neatmap code on df + > neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, + + xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1) + Error in pm[[2]] : subscript out of bounds + Calls: neatmap ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + ``` + +# neatStats + +
+ +* Version: 1.13.3 +* GitHub: https://github.com/gasparl/neatstats +* Source code: https://github.com/cran/neatStats +* Date/Publication: 2022-12-07 20:50:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "neatStats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neatStats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: peek_neat + > ### Title: Cursory Summaries and Plots per Group + > ### Aliases: peek_neat + > + > ### ** Examples + > + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# netcom + +
+ +* Version: 2.1.7 +* GitHub: https://github.com/langendorfr/netcom +* Source code: https://github.com/cran/netcom +* Date/Publication: 2024-06-04 17:50:05 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "netcom")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tutorial.Rmd’ + ... + > networks <- c(networks_undisturbed, networks_disturbed) + + > comparisons <- netcom::compare(networks, method = "align") + + > stats::prcomp(comparisons) %>% ggplot2::autoplot(data = tibble(Kind = c(rep("Undisturbed", + + num_networks), rep("Disturbed", num_networks))), c .... [TRUNCATED] + + When sourcing ‘tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘tutorial.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’ + All declared Imports should be used. + ``` + +# NetFACS + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/NetFACS +* Date/Publication: 2022-12-06 17:32:35 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "NetFACS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetFACS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network_conditional + > ### Title: Create a network based on conditional probabilities of dyads of + > ### elements + > ### Aliases: network_conditional + > + > ### ** Examples + > + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + invalid font type + Calls: ... drawDetails -> drawDetails.text -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘netfacs_tutorial.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + When sourcing ‘netfacs_tutorial.R’: + Error: invalid font type + Execution halted + + ‘netfacs_tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +# neuroUp + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/eduardklap/neuroUp +* Source code: https://github.com/cran/neuroUp +* Date/Publication: 2024-08-28 08:20:05 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "neuroUp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neuroUp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estim_corr + > ### Title: Estimate correlations + > ### Aliases: estim_corr + > + > ### ** Examples + > + > data_gambling <- gambling + ... + 8 100 -0.0787 -0.271 0.120 2 NA + 9 140 -0.0555 -0.219 0.111 2 NA + 10 221 -0.0405 -0.172 0.0920 2 NA + # ℹ 45 more rows + + $fig_corr + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ] + Deleting unused snapshots: + • estim_corr/create-fig-corr-nozero.svg + • estim_diff/create-fig-cohen-s-d.svg + • estim_diff/create-fig-d-nozero.svg + • estim_diff/create-fig-nozero.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘neuroUp.Rmd’ + ... + > set.seed(1234) + + > feedback_estim <- estim_diff(feedback_data, c("mfg_learning", + + "mfg_application"), 20:271, 20, "Feedback middle frontal gyrus") + + > feedback_estim$fig_diff + + When sourcing ‘neuroUp.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘neuroUp.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘neuroUp.Rmd’ using rmarkdown + + Quitting from lines 92-93 [unnamed-chunk-5] (neuroUp.Rmd) + Error: processing vignette 'neuroUp.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘neuroUp.Rmd’ + + SUMMARY: processing the following file failed: + ‘neuroUp.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# NHSRplotthedots + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/NHSRplotthedots +* Date/Publication: 2021-11-03 20:20:10 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "NHSRplotthedots")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(NHSRplotthedots) + > + > test_check("NHSRplotthedots") + [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + + ... + + `actual$type` is absent + `expected$type` is a character vector ('type') + + `actual$text` is absent + `expected$text` is a character vector ('text') + + [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘NHSRdatasets’ ‘grid’ ‘utils’ + All declared Imports should be used. + ``` + +# nichetools + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/benjaminhlina/nichetools +* Source code: https://github.com/cran/nichetools +* Date/Publication: 2024-09-06 17:00:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "nichetools")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘using-nichetools-with-the-package-SIBER.Rmd’ + ... + + option = "A", alpha = 0.75) + + > ggplot() + stat_pointinterval(data = bays_95_overlap, + + aes(x = group_1, y = prop_overlap, point_fill = group_2), + + interval_colour = "gre ..." ... [TRUNCATED] + + When sourcing ‘using-nichetools-with-the-package-SIBER.R’: + Error: unused argument (theme = list(list("black", 0.681818181818182, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.681818181818182, 1, TRUE), list("", "plain", "black", 15, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.681818181818182, 0.681818181818182, 1, 1, "", 5.27189705271897, 2.04545454545455, 19, TRUE), 7.5, c(7.5, 7.5, 7.5, 7.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + Execution halted + + ‘using-nichetools-with-the-package-SIBER.Rmd’ using ‘UTF-8’... failed + ‘using-nichetools-with-the-package-nicheROVER.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘using-nichetools-with-the-package-SIBER.Rmd’ using rmarkdown + ``` + +# NIMAA + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/jafarilab/NIMAA +* Source code: https://github.com/cran/NIMAA +* Date/Publication: 2022-04-11 14:12:45 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "NIMAA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NIMAA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: extractSubMatrix + > ### Title: Extract the non-missing submatrices from a given matrix. + > ### Aliases: extractSubMatrix + > + > ### ** Examples + > + > # load part of the beatAML data + ... + + row.vars = "inhibitor") + binmatnest.temperature + 13.21221 + Size of Square: 66 rows x 66 columns + Size of Rectangular_row: 6 rows x 105 columns + Size of Rectangular_col: 99 rows x 2 columns + Size of Rectangular_element_max: 59 rows x 79 columns + Error in pm[[2]] : subscript out of bounds + Calls: extractSubMatrix ... plotSubmatrix -> print -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(NIMAA) + Warning message: + In check_dep_version() : ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original 'Matrix' package + ... + 1. └─NIMAA::extractSubMatrix(...) at test-extract-nonmissing-submatrix.R:5:3 + 2. └─NIMAA:::plotSubmatrix(...) + 3. ├─base::print(plotly::ggplotly(p)) + 4. ├─plotly::ggplotly(p) + 5. └─plotly:::ggplotly.ggplot(p) + 6. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 7 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘NIMAA-vignette.Rmd’ + ... + + > beatAML_incidence_matrix <- plotIncMatrix(x = beatAML_data, + + index_nominal = c(2, 1), index_numeric = 3, print_skim = FALSE, + + plot_weigh .... [TRUNCATED] + + Na/missing values Proportion: 0.2603 + + When sourcing ‘NIMAA-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘NIMAA-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown + + Quitting from lines 49-57 [plotIncMatrix function] (NIMAA-vignette.Rmd) + Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘NIMAA-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘NIMAA-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + data 2.0Mb + doc 4.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 24 marked UTF-8 strings + ``` + +# nonmem2R + +
+ +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/nonmem2R +* Date/Publication: 2024-03-11 17:30:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "nonmem2R")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nonmem2R-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vpcfig2 + > ### Title: Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) + > ### generated VPC files (ggplot2-version). + > ### Aliases: vpcfig2 + > + > ### ** Examples + > + ... + VPC based on files: + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat + and + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv + Facetting was set using: + facet_wrap(~strata) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘VPCvignette.Rmd’ + ... + VPC based on files: + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat + and + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv + Facetting was set using: + facet_wrap(~strata) + + When sourcing ‘VPCvignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘GOFvignette.Rmd’ using ‘UTF-8’... OK + ‘VPCvignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘GOFvignette.Rmd’ using rmarkdown + ``` + +# nphRCT + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/nphRCT +* Date/Publication: 2024-06-27 12:30:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "nphRCT")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘explanation.Rmd’ + ... + + > km <- survfit(Surv(time, event) ~ arm, data = dat) + + > p_km <- survminer::ggsurvplot(km, data = dat, risk.table = TRUE, + + break.x.by = 6, legend.title = "", xlab = "Time (months)", + + ylab = "Ov ..." ... [TRUNCATED] + + When sourcing ‘explanation.R’: + Error: argument is of length zero + Execution halted + + ‘explanation.Rmd’ using ‘UTF-8’... failed + ‘weighted_log_rank_tests.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘explanation.Rmd’ using rmarkdown + + Quitting from lines 44-73 [unnamed-chunk-1] (explanation.Rmd) + Error: processing vignette 'explanation.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘explanation.Rmd’ + + --- re-building ‘weighted_log_rank_tests.Rmd’ using rmarkdown + ``` + +# nprobust + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/nprobust +* Date/Publication: 2020-08-26 10:40:02 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "nprobust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nprobust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nprobust.plot + > ### Title: Graphical Presentation of Results from 'nprobust' Package. + > ### Aliases: nprobust.plot + > + > ### ** Examples + > + > x <- runif(500) + > y <- sin(4*x) + rnorm(500) + > est <- lprobust(y,x) + > nprobust.plot(est) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# nzelect + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/nzelect +* Date/Publication: 2017-10-02 20:35:23 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "nzelect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nzelect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: polls + > ### Title: New Zealand Opinion Polls + > ### Aliases: polls + > ### Keywords: datasets + > + > ### ** Examples + > + ... + ℹ This can happen when ggplot fails to infer the correct grouping structure in + the data. + ℹ Did you forget to specify a `group` aesthetic or to convert a numerical + variable into a factor? + Warning: Removed 159 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘README.Rmd’ + ... + > proportions <- nzge %>% filter(election_year == 2014) %>% + + group_by(voting_place, voting_type) %>% summarise(`proportion Labour` = sum(votes[p .... [TRUNCATED] + `summarise()` has grouped output by 'voting_place'. You can override using the + `.groups` argument. + + > ggpairs(proportions, aes(colour = voting_type), columns = 3:5) + + When sourcing ‘README.R’: + Error: argument is of length zero + Execution halted + + ‘README.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘README.Rmd’ using rmarkdown + + Quitting from lines 64-82 [unnamed-chunk-3] (README.Rmd) + Error: processing vignette 'README.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘README.Rmd’ + + SUMMARY: processing the following file failed: + ‘README.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + data 5.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6409 marked UTF-8 strings + ``` + +# OBIC + +
+ +* Version: 3.0.3 +* GitHub: https://github.com/AgroCares/Open-Bodem-Index-Calculator +* Source code: https://github.com/cran/OBIC +* Date/Publication: 2024-09-09 08:30:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "OBIC")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘obic_workability.Rmd’ + ... + > gg2 <- ggplot(data = dt, aes(x = field, fill = field)) + + + geom_col(aes(y = I_P_WO)) + theme_bw() + theme(axis.text = element_text(size = 10, + .... [TRUNCATED] + + > (gg | gg2) + plot_layout(guides = "collect") + plot_annotation(caption = "Baseline workability scores.", + + theme = theme(plot.caption = element .... [TRUNCATED] + + When sourcing ‘obic_workability.R’: + Error: object is not a unit + Execution halted + + ‘description-of-the-columns.Rmd’ using ‘UTF-8’... OK + ‘obic_introduction.Rmd’ using ‘UTF-8’... OK + ‘obic_score_aggregation.Rmd’ using ‘UTF-8’... OK + ‘obic_water_functions.Rmd’ using ‘UTF-8’... OK + ‘obic_workability.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘description-of-the-columns.Rmd’ using rmarkdown + --- finished re-building ‘description-of-the-columns.Rmd’ + + --- re-building ‘obic_introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.0Mb + sub-directories of 1Mb or more: + data 4.0Mb + doc 1.4Mb + ``` + +# oceanic + +
+ +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/oceanic +* Date/Publication: 2024-06-11 03:40:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "oceanic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘oceanic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dotplot + > ### Title: dotplot + > ### Aliases: dotplot + > + > ### ** Examples + > + > dotplot(141,23) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 8.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1242 marked UTF-8 strings + ``` + +# oddsratio + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/pat-s/oddsratio +* Source code: https://github.com/cran/oddsratio +* Date/Publication: 2020-05-24 22:00:02 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "oddsratio")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘oddsratio-Ex.R’ failed + The error most likely occurred in: + + > ### Name: insert_or + > ### Title: Insert odds ratios of GAM(M)s into smoothing function + > ### Aliases: insert_or + > + > ### ** Examples + > + > library(oddsratio) + ... + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 7. └─vctrs::vec_as_names(names, repair = "check_unique") + 8. └─vctrs (local) ``() + 9. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 10. └─vctrs:::stop_names_cannot_be_empty(names, call = call) + 11. └─vctrs:::stop_names(...) + 12. └─vctrs:::stop_vctrs(...) + 13. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘oddsratio.Rmd’ + ... + + pred = "x2", values = c(0.4, 0.6)) + + > insert_or(plot, or_object2, or_yloc = 2.1, values_yloc = 2, + + line_col = "green4", text_col = "black", rect_col = "green4", + + rect_alpha = .... [TRUNCATED] + + When sourcing ‘oddsratio.R’: + Error: Names can't be empty. + ✖ Empty name found at location 1. + Execution halted + + ‘oddsratio.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘oddsratio.Rmd’ using rmarkdown + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘gam’ + ``` + +# ofpetrial + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/DIFM-Brain/ofpetrial +* Source code: https://github.com/cran/ofpetrial +* Date/Publication: 2024-05-15 08:50:03 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "ofpetrial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ofpetrial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: check_ortho_with_chars + > ### Title: Check the orthogonality with field/topographic characteristics + > ### Aliases: check_ortho_with_chars + > + > ### ** Examples + > + > data(td_single_input) + ... + 33. │ └─ggplot2:::`+.gg`(init, x[[i]]) + 34. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 35. │ ├─ggplot2::ggplot_add(object, p, objectname) + 36. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 37. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 38. └─base::.handleSimpleError(...) + 39. └─purrr (local) h(simpleError(msg, call)) + 40. └─cli::cli_abort(...) + 41. └─rlang::abort(...) + Execution halted + ``` + +# OmicNavigator + +
+ +* Version: 1.13.13 +* GitHub: https://github.com/abbvie-external/OmicNavigator +* Source code: https://github.com/cran/OmicNavigator +* Date/Publication: 2023-08-25 20:40:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "OmicNavigator")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > # Test files in inst/tinytest/ + > if (requireNamespace("tinytest", quietly = TRUE)) { + + suppressMessages(tinytest::test_package("OmicNavigator")) + + } + + testAdd.R..................... 0 tests + testAdd.R..................... 0 tests + ... + testPlot.R.................... 140 tests OK + testPlot.R.................... 140 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 142 tests OK + testPlot.R.................... 142 tests OK + testPlot.R.................... 143 tests OK Error in pm[[2]] : subscript out of bounds + Calls: suppressMessages ... plotStudy -> f -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave + OmicNavigator R package version: 1.13.13 + The app is not installed. Install it with installApp() + Installing study "ABC" in /tmp/RtmpFyTBK9/file1d2273c45a46 + Exporting study "ABC" as an R package + Note: No maintainer email was specified. Using the placeholder: Unknown + Calculating pairwise overlaps. This may take a while... + Exported study to /tmp/RtmpFyTBK9/ONstudyABC + Success! + ... + l.14 ^^M + + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘OmicNavigatorUsersGuide.Rnw’ + + SUMMARY: processing the following files failed: + ‘OmicNavigatorAPI.Rnw’ ‘OmicNavigatorUsersGuide.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# omu + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/connor-reid-tiffany/Omu +* Source code: https://github.com/cran/omu +* Date/Publication: 2024-03-06 23:40:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "omu")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘omu-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PCA_plot + > ### Title: Create a PCA plot + > ### Aliases: PCA_plot + > + > ### ** Examples + > + > PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata, + + variable = "Treatment", color = "Treatment", response_variable = "Metabolite") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PCA_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Omu_vignette.Rmd’ using rmarkdown + + Quitting from lines 97-104 [unnamed-chunk-4] (Omu_vignette.Rmd) + Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Omu_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Omu_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Omu_vignette.Rmd’ + ... + + > library(knitr) + + > load("../data/c57_nos2KO_mouse_countDF.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../data/c57_nos2KO_mouse_countDF.rda', probable reason 'No such file or directory' + + When sourcing ‘Omu_vignette.R’: + Error: cannot open the connection + Execution halted + + ‘Omu_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# OncoBayes2 + +
+ +* Version: 0.8-9 +* GitHub: NA +* Source code: https://github.com/cran/OncoBayes2 +* Date/Publication: 2023-07-20 18:40:05 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "OncoBayes2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OncoBayes2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_blrm + > ### Title: Plot a fitted model + > ### Aliases: plot_blrm plot_toxicity_curve plot_toxicity_intervals + > ### plot_toxicity_intervals_stacked plot_toxicity_curve.blrmfit + > ### plot_toxicity_curve.blrm_trial plot_toxicity_intervals.blrmfit + > ### plot_toxicity_intervals.blrm_trial + > ### plot_toxicity_intervals_stacked.blrmfit + ... + > # Plot the dose-toxicity curve + > plot_toxicity_curve(blrmfit, + + x = "drug_A", + + group = ~ group_id * drug_B, + + newdata = subset(dose_info_combo2, group_id == "trial_AB"), + + facet_args = list(ncol = 4)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 76.7Mb + sub-directories of 1Mb or more: + libs 74.7Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# oncomsm + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/Boehringer-Ingelheim/oncomsm +* Source code: https://github.com/cran/oncomsm +* Date/Publication: 2023-04-17 07:00:02 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "oncomsm")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(dplyr) + + Attaching package: 'dplyr' + + The following objects are masked from 'package:stats': + + filter, lag + ... + 10. └─grid::unit.c(legend.box.margin[4], widths, legend.box.margin[2]) + 11. └─grid:::identicalUnits(x) + + [ FAIL 1 | WARN 0 | SKIP 2 | PASS 59 ] + Deleting unused snapshots: + • plots/plot-mstate-srp-model-2.svg + • plots/plot-mstate-srp-model-3.svg + • plots/plot-srp-model-2.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘avoiding-bias.Rmd’ + ... + + > mdl <- create_srpmodel(A = define_srp_prior(median_t_q05 = c(1, + + 4, 12), median_t_q95 = c(6, 8, 36), shape_q05 = c(0.99, 0.99, + + 0.99), s .... [TRUNCATED] + + > plot(mdl, confidence = 0.9) + + ... + + > plot(mdl, parameter_sample = smpl_prior, confidence = 0.75) + + When sourcing ‘oncomsm.R’: + Error: object is not a unit + Execution halted + + ‘avoiding-bias.Rmd’ using ‘UTF-8’... failed + ‘oncomsm.Rmd’ using ‘UTF-8’... failed + ‘prior-choice.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘avoiding-bias.Rmd’ using rmarkdown + + Quitting from lines 35-46 [unnamed-chunk-2] (avoiding-bias.Rmd) + Error: processing vignette 'avoiding-bias.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘avoiding-bias.Rmd’ + + --- re-building ‘oncomsm.Rmd’ using rmarkdown + + Quitting from lines 211-215 [plotting-the-prior] (oncomsm.Rmd) + Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘oncomsm.Rmd’ + + --- re-building ‘prior-choice.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 59.2Mb + sub-directories of 1Mb or more: + doc 1.1Mb + libs 57.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# OneSampleLogRankTest + +
+ +* Version: 0.9.2 +* GitHub: NA +* Source code: https://github.com/cran/OneSampleLogRankTest +* Date/Publication: 2024-02-03 12:30:15 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "OneSampleLogRankTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OneSampleLogRankTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotKM + > ### Title: Plot Kaplan-Meier Curve against Population + > ### Aliases: plotKM + > + > ### ** Examples + > + > # load data + > data(dataSurv_small) + > data(dataPop_2018_2021) + > + > plotKM(dataSurv_small, dataPop_2018_2021, type = "exact") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘oneSampleLogRankTest.Rmd’ + ... + $estimate + std_mort_ratio_est lwr upr + 1 1.531173 0.8302562 2.823816 + + + > plotKM(dataSurv, dataPop_2018_2021_race_sex_eth, type = "approximate") + + When sourcing ‘oneSampleLogRankTest.R’: + Error: argument is of length zero + Execution halted + + ‘oneSampleLogRankTest.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘oneSampleLogRankTest.Rmd’ using rmarkdown + + Quitting from lines 74-77 [unnamed-chunk-3] (oneSampleLogRankTest.Rmd) + Error: processing vignette 'oneSampleLogRankTest.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘oneSampleLogRankTest.Rmd’ + + SUMMARY: processing the following file failed: + ‘oneSampleLogRankTest.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# onpoint + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/r-spatialecology/onpoint +* Source code: https://github.com/cran/onpoint +* Date/Publication: 2024-01-10 14:03:06 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "onpoint")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘onpoint-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.env_summarized + > ### Title: plot.env_summarized + > ### Aliases: plot.env_summarized + > + > ### ** Examples + > + > set.seed(42) + ... + 39. + + Done. + > + > x <- summarize_envelope(cluster_env) + > plot(x) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# ordbetareg + +
+ +* Version: 0.7.2 +* GitHub: https://github.com/saudiwin/ordbetareg_pack +* Source code: https://github.com/cran/ordbetareg +* Date/Publication: 2023-08-10 07:30:02 UTC +* Number of recursive dependencies: 174 + +Run `revdepcheck::cloud_details(, "ordbetareg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ordbetareg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pp_check_ordbeta + > ### Title: Accurate Posterior Predictive Plots for Ordbetareg Models + > ### Aliases: pp_check_ordbeta + > + > ### ** Examples + > + > + ... + 16. │ └─ggplot2 (local) setup_params(...) + 17. │ └─ggplot2:::make_summary_fun(...) + 18. │ └─rlang::as_function(fun.data) + 19. │ └─base::get(x, envir = env, mode = "function") + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 36 marked UTF-8 strings + ``` + +# packcircles + +
+ +* Version: 0.3.6 +* GitHub: https://github.com/mbedward/packcircles +* Source code: https://github.com/cran/packcircles +* Date/Publication: 2023-09-08 06:30:02 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "packcircles")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘progressive_packing.Rmd’ + ... + + scale_fill_man .... [TRUNCATED] + + > if (requireNamespace("ggiraph")) { + + gg <- ggplot(data = dat.gg) + ggiraph::geom_polygon_interactive(aes(x, + + y, group = id, fill = fac .... [TRUNCATED] + Loading required namespace: ggiraph + + When sourcing ‘progressive_packing.R’: + Error: argument is of length zero + Execution halted + + ‘graph_packing.Rmd’ using ‘UTF-8’... OK + ‘intro.Rmd’ using ‘UTF-8’... OK + ‘progressive_packing.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘graph_packing.Rmd’ using rmarkdown + --- finished re-building ‘graph_packing.Rmd’ + + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +# pafr + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/dwinter/pafr +* Source code: https://github.com/cran/pafr +* Date/Publication: 2020-12-08 10:20:12 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "pafr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pafr) + Loading required package: ggplot2 + > + > test_check("pafr") + [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] + + ... + ── Failure ('test_plot.r:11:5'): dotplot works produces a plot ───────────────── + unname(labs["xintercept"]) not equal to "xintercept". + target is NULL, current is character + ── Failure ('test_plot.r:12:5'): dotplot works produces a plot ───────────────── + unname(labs["yintercept"]) not equal to "yintercept". + target is NULL, current is character + + [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# patchwork + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/thomasp85/patchwork +* Source code: https://github.com/cran/patchwork +* Date/Publication: 2024-01-08 14:40:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "patchwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘patchwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: free + > ### Title: Free a plot from alignment + > ### Aliases: free + > + > ### ** Examples + > + > # Sometimes you have a plot that defies good composition alginment, e.g. due + ... + > p1 / p2 + > + > # We can fix this be using free + > free(p1) / p2 + > + > # We can still collect guides like before + > free(p1) / p2 + plot_layout(guides = "collect") + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# pathviewr + +
+ +* Version: 1.1.7 +* GitHub: https://github.com/ropensci/pathviewr +* Source code: https://github.com/cran/pathviewr +* Date/Publication: 2023-03-08 08:10:05 UTC +* Number of recursive dependencies: 182 + +Run `revdepcheck::cloud_details(, "pathviewr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pathviewr) + > #library(vdiffr) + > + > test_check("pathviewr") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] + + ... + ── Error ('test-plot_by_subject.R:168:3'): elev views wrangled correctly via tidyverse ── + Error in `expect_match(elev_all_plots[[3]][[4]][["labels"]][["x"]], "position_height")`: is.character(act$val) is not TRUE + Backtrace: + ▆ + 1. └─testthat::expect_match(...) at test-plot_by_subject.R:168:3 + 2. └─base::stopifnot(is.character(act$val)) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] + Error: Test failures + Execution halted + ``` + +# patientProfilesVis + +
+ +* Version: 2.0.9 +* GitHub: https://github.com/openanalytics/patientProfilesVis +* Source code: https://github.com/cran/patientProfilesVis +* Date/Publication: 2024-06-18 09:00:02 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "patientProfilesVis")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘patientProfiles-template-SDTM.Rmd’ + ... + > patientProfilesPlots <- c(patientProfilesPlots, list(MH = mhPlots)) + + > cmPlots <- subjectProfileIntervalPlot(data = dataAll$CM, + + paramVar = c("CMTRT", "CMDOSE", "CMDOSU", "CMROUTE", "CMDOSFRQ"), + + timeStartVa .... [TRUNCATED] + 171 record(s) with missing Study Day of Start of Medication and 208 record(s) with missing Study Day of End of Medication are imputed with minimal imputation. + + ... + + paramVar = "AETERM", timeStartVar = "AESTDY", timeEndVar = "AEENDY", + + colorVar = " ..." ... [TRUNCATED] + 3 record(s) with missing Study Day of Start of Adverse Event and 19 record(s) with missing Study Day of End of Adverse Event are imputed with minimal imputation. + + When sourcing ‘patientProfilesVis-introduction.R’: + Error: argument is of length zero + Execution halted + + ‘patientProfiles-template-SDTM.Rmd’ using ‘UTF-8’... failed + ‘patientProfilesVis-introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘patientProfiles-template-SDTM.Rmd’ using rmarkdown + + Quitting from lines 129-153 [patientProfiles-concomitantMedications] (patientProfiles-template-SDTM.Rmd) + Error: processing vignette 'patientProfiles-template-SDTM.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘patientProfiles-template-SDTM.Rmd’ + + --- re-building ‘patientProfilesVis-introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(patientProfilesVis) + > + > test_check("patientProfilesVis") + [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] + + ══ Skipped tests (20) ══════════════════════════════════════════════════════════ + ... + 11. └─patientProfilesVis (local) .fun(piece, ...) + 12. └─ggplot2:::`+.gg`(...) + 13. └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. ├─ggplot2::ggplot_add(object, p, objectname) + 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] + Error: Test failures + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + doc 5.2Mb + ``` + +# PCADSC + +
+ +* Version: 0.8.0 +* GitHub: https://github.com/annepetersen1/PCADSC +* Source code: https://github.com/cran/PCADSC +* Date/Publication: 2017-04-19 10:07:43 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "PCADSC")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PCADSC-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CEPlot + > ### Title: Cumulative eigenvalue plot + > ### Aliases: CEPlot + > + > ### ** Examples + > + > #load iris data + ... + > CEPlot(irisPCADSC_fast) + Warning: The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in + ggplot2 3.3.4. + ℹ Please use "none" instead. + ℹ The deprecated feature was likely used in the PCADSC package. + Please report the issue at . + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Matrix’ ‘pander’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘data.table’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# pcutils + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/Asa12138/pcutils +* Source code: https://github.com/cran/pcutils +* Date/Publication: 2024-06-25 21:20:05 UTC +* Number of recursive dependencies: 281 + +Run `revdepcheck::cloud_details(, "pcutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pcutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gghist + > ### Title: gg histogram + > ### Aliases: gghist + > + > ### ** Examples + > + > if (requireNamespace("ggpubr")) { + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# pdxTrees + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/mcconvil/pdxTrees +* Source code: https://github.com/cran/pdxTrees +* Date/Publication: 2020-08-17 14:00:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "pdxTrees")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘pdxTrees-vignette.Rmd’ + ... + + y = Pollution_Removal_value, color = Mature_Size)) + geom_point(size = 2, + + .... [TRUNCATED] + + > berkeley_graph + transition_states(states = Mature_Size, + + transition_length = 10, state_length = 8) + enter_grow() + + + exit_shrink() + + When sourcing ‘pdxTrees-vignette.R’: + Error: argument "theme" is missing, with no default + Execution halted + + ‘pdxTrees-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# personalized + +
+ +* Version: 0.2.7 +* GitHub: https://github.com/jaredhuling/personalized +* Source code: https://github.com/cran/personalized +* Date/Publication: 2022-06-27 20:20:03 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "personalized")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > Sys.setenv("R_TESTS" = "") + > library(testthat) + > library(personalized) + Loading required package: glmnet + Loading required package: Matrix + Loaded glmnet 4.1-8 + Loading required package: mgcv + ... + 4. └─personalized:::plot.subgroup_validated(subgrp.val, type = "stability") + 5. ├─plotly::subplot(...) + 6. │ └─plotly:::dots2plots(...) + 7. ├─plotly::ggplotly(p.primary, tooltip = paste0("tooltip", 1:4)) + 8. └─plotly:::ggplotly.ggplot(...) + 9. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 215 ] + Error: Test failures + Execution halted + ``` + +# phyloseqGraphTest + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/jfukuyama/phyloseqGraphTest +* Source code: https://github.com/cran/phyloseqGraphTest +* Date/Publication: 2024-02-05 19:00:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phyloseqGraphTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_test_network + > ### Title: Plots the graph used for testing + > ### Aliases: plot_test_network + > + > ### ** Examples + > + > library(phyloseq) + ... + > plot_test_network(gt) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • layout = layout + ℹ Did you misspell an argument name? + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gt_vignette.Rmd’ + ... + > plot_test_network(gt) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • layout = layout + ℹ Did you misspell an argument name? + + When sourcing ‘gt_vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘gt_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘gt_vignette.Rmd’ using rmarkdown + + Quitting from lines 175-176 [unnamed-chunk-5] (gt_vignette.Rmd) + Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘gt_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘gt_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# PieGlyph + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/rishvish/PieGlyph +* Source code: https://github.com/cran/PieGlyph +* Date/Publication: 2024-06-28 12:00:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PieGlyph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PieGlyph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_pie_interactive + > ### Title: Scatter plots with interactive pie-chart glyphs + > ### Aliases: geom_pie_interactive + > + > ### ** Examples + > + > #' ## Load libraries + ... + > # One of the interactive aesthetics is tooltip. It is set that by default + > # it shows the value and percentage of each slice in the pie-chart. + > # Hover over any pie-chart in the plot to see this + > plot_obj1 <- ggplot(data = plot_data, aes(x = system, y = response)) + + + geom_pie_interactive(slices = c("A", "B", "C", "D"), + + data = plot_data)+ + + theme_classic() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + ... + • geom_pie_interactive/custom-tooltip.svg + • geom_pie_interactive/data-id.svg + • geom_pie_interactive/long-form-data-works.svg + • geom_pie_interactive/multiple-interactive-parameters.svg + • geom_pie_interactive/only-one-attribute.svg + • pie-grob/pie-grob-with-multiple-values-no-fill-works.svg + • pie-grob/pie-grob-with-single-non-zero-value-no-fill-works.svg + • pie-grob/pie-grob-with-single-non-zero-value-works.svg + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PieGlyph.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PieGlyph.Rmd’ + ... + + geom_pie_glyph(slices = "Attributes", values = "values") + + + theme_cla .... [TRUNCATED] + + > plot_obj <- ggplot(data = plot_data) + geom_pie_interactive(aes(x = system, + + y = response, data_id = system), slices = c("A", "B", "C", + + .... [TRUNCATED] + + ... + before plotting. + Execution halted + + ‘PieGlyph.Rmd’ using ‘UTF-8’... failed + ‘interactive-pie-glyphs.Rmd’ using ‘UTF-8’... failed + ‘multinomial-classification-example.Rmd’ using ‘UTF-8’... OK + ‘pie-lollipop-example.Rmd’ using ‘UTF-8’... OK + ‘spatial-example.Rmd’ using ‘UTF-8’... OK + ‘time-series-example.Rmd’ using ‘UTF-8’... failed + ‘unusual-situations.Rmd’ using ‘UTF-8’... failed + ``` + +# Plasmidprofiler + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/Plasmidprofiler +* Date/Publication: 2017-01-06 01:10:47 +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "Plasmidprofiler")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Plasmidprofiler-Ex.R’ failed + The error most likely occurred in: + + > ### Name: main + > ### Title: Main: Run everything + > ### Aliases: main + > + > ### ** Examples + > + > main(blastdata, + ... + Saving 12 x 7 in image + Warning: Vectorized input to `element_text()` is not officially supported. + ℹ Results may be unexpected or may change in future versions of ggplot2. + Warning in geom_tile(aes(x = Plasmid, y = Sample, label = AMR_gene, fill = Inc_group, : + Ignoring unknown aesthetics: label and text + Warning: Use of `report$Sureness` is discouraged. + ℹ Use `Sureness` instead. + Error in pm[[2]] : subscript out of bounds + Calls: main ... -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# platetools + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/swarchal/platetools +* Source code: https://github.com/cran/platetools +* Date/Publication: 2024-03-07 16:50:02 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "platetools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(platetools) + > + > test_check("platetools") + [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] + + ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ + ... + length(out96) not equal to length(ggplot()). + 1/1 mismatches + [1] 11 - 10 == 1 + ── Failure ('test-plot_wrapper.R:34:5'): returns expected ggplot object ──────── + names(out96) not equal to names(ggplot()). + Lengths differ: 11 is not 10 + + [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] + Error: Test failures + Execution halted + ``` + +# PLNmodels + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/pln-team/PLNmodels +* Source code: https://github.com/cran/PLNmodels +* Date/Publication: 2024-03-05 15:50:03 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "PLNmodels")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PLNPCA.Rmd’ + ... + 3 "$contrib" "contributions of the individuals" + + > factoextra::fviz_pca_biplot(myPCA_ICL) + + When sourcing ‘PLNPCA.R’: + Error: ℹ In index: 1. + ℹ With name: y. + ... + ! argument is of length zero + Execution halted + + ‘Import_data.Rmd’ using ‘UTF-8’... OK + ‘PLN.Rmd’ using ‘UTF-8’... OK + ‘PLNLDA.Rmd’ using ‘UTF-8’... OK + ‘PLNPCA.Rmd’ using ‘UTF-8’... failed + ‘PLNmixture.Rmd’ using ‘UTF-8’... failed + ‘PLNnetwork.Rmd’ using ‘UTF-8’... OK + ‘Trichoptera.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Import_data.Rmd’ using rmarkdown + --- finished re-building ‘Import_data.Rmd’ + + --- re-building ‘PLN.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 26.0Mb + sub-directories of 1Mb or more: + R 1.0Mb + data 3.5Mb + doc 2.1Mb + libs 18.6Mb + ``` + +# plotBart + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/priism-center/plotBart +* Source code: https://github.com/cran/plotBart +* Date/Publication: 2022-05-27 07:50:06 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "plotBart")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(vdiffr) + > library(plotBart) + Loading required package: bartCause + Loading required package: ggplot2 + > + > test_check("plotBart") # run tests + ... + • plots/mod-search.svg + • plots/overlappscoresdensity.svg + • plots/overlapvarsdensity.svg + • plots/pate.svg + • plots/sate.svg + • plots/supportchi.svg + • plots/supportsd.svg + • plots/waterfall2.svg + Error: Test failures + Execution halted + ``` + +# plotDK + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/plotDK +* Date/Publication: 2021-10-01 08:00:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "plotDK")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(plotDK) + > + > test_check("plotDK") + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + Error in `expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), + names(labels))`: `object` and `expected` must both be vectors + Backtrace: + ▆ + 1. └─testthat::expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), names(labels)) at test-plotDK.R:67:5 + 2. └─rlang::abort("`object` and `expected` must both be vectors") + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘mapproj’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 12992 marked UTF-8 strings + ``` + +# plotly + +
+ +* Version: 4.10.4 +* GitHub: https://github.com/plotly/plotly.R +* Source code: https://github.com/cran/plotly +* Date/Publication: 2024-01-13 22:40:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "plotly")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘plotly-Ex.R’ failed + The error most likely occurred in: + + > ### Name: style + > ### Title: Modify trace(s) + > ### Aliases: style + > + > ### ** Examples + > + > ## Don't show: + ... + + # this clobbers the previously supplied marker.line.color + + style(p, marker.line = list(width = 2.5), marker.size = 10) + + ## Don't show: + + }) # examplesIf + > (p <- ggplotly(qplot(data = mtcars, wt, mpg, geom = c("point", "smooth")))) + Warning: `qplot()` was deprecated in ggplot2 3.4.0. + `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + Error in pm[[2]] : subscript out of bounds + Calls: ... eval -> eval -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library("testthat") + > library("plotly") + Loading required package: ggplot2 + + Attaching package: 'plotly' + + The following object is masked from 'package:ggplot2': + ... + • plotly-subplot/subplot-bump-axis-annotation.svg + • plotly-subplot/subplot-bump-axis-image.svg + • plotly-subplot/subplot-bump-axis-shape-shared.svg + • plotly-subplot/subplot-bump-axis-shape.svg + • plotly-subplot/subplot-reposition-annotation.svg + • plotly-subplot/subplot-reposition-image.svg + • plotly-subplot/subplot-reposition-shape-fixed.svg + • plotly-subplot/subplot-reposition-shape.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + R 1.0Mb + htmlwidgets 4.0Mb + ``` + +# pmartR + +
+ +* Version: 2.4.5 +* GitHub: https://github.com/pmartR/pmartR +* Source code: https://github.com/cran/pmartR +* Date/Publication: 2024-05-21 15:50:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "pmartR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pmartR) + > + > test_check("pmartR") + [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] + + ══ Skipped tests (11) ══════════════════════════════════════════════════════════ + ... + • plots/plot-spansres-color-high-color-low.svg + • plots/plot-spansres.svg + • plots/plot-statres-anova-volcano.svg + • plots/plot-statres-anova.svg + • plots/plot-statres-combined-volcano.svg + • plots/plot-statres-combined.svg + • plots/plot-statres-gtest.svg + • plots/plot-totalcountfilt.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + help 1.5Mb + libs 6.7Mb + ``` + +# pmxTools + +
+ +* Version: 1.3 +* GitHub: https://github.com/kestrel99/pmxTools +* Source code: https://github.com/cran/pmxTools +* Date/Publication: 2023-02-21 16:00:08 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "pmxTools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pmxTools) + Loading required package: patchwork + > + > test_check("pmxTools") + [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ] + + ... + 24. └─handlers[[1L]](cnd) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + + [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ] + Deleting unused snapshots: + • plot/conditioned-distplot.svg + • plot/perc.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘DiagrammeR’ + ``` + +# posterior + +
+ +* Version: 1.6.0 +* GitHub: https://github.com/stan-dev/posterior +* Source code: https://github.com/cran/posterior +* Date/Publication: 2024-07-03 23:00:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "posterior")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘pareto_diagnostics.Rmd’ using rmarkdown + --- finished re-building ‘pareto_diagnostics.Rmd’ + + --- re-building ‘posterior.Rmd’ using rmarkdown + --- finished re-building ‘posterior.Rmd’ + + --- re-building ‘rvar.Rmd’ using rmarkdown + + Quitting from lines 530-533 [mixture] (rvar.Rmd) + ... + NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("grey92", NA, NULL, NULL, TRUE), list(), NULL, NULL, NULL, list("white", NULL, NULL, NULL, FALSE, + "white", TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list("grey85", + NA, NULL, NULL, TRUE), NULL, NULL, "on", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘rvar.Rmd’ + + SUMMARY: processing the following file failed: + ‘rvar.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘rvar.Rmd’ + ... + > y + rvar<4000>[3] mean ± sd: + [1] 3.00 ± 1.00 2.02 ± 0.99 0.96 ± 0.99 + + > X + y + + When sourcing ‘rvar.R’: + Error: Cannot broadcast array of shape [4000,3,1] to array of shape [4000,4,3]: + All dimensions must be 1 or equal. + Execution halted + + ‘pareto_diagnostics.Rmd’ using ‘UTF-8’... OK + ‘posterior.Rmd’ using ‘UTF-8’... OK + ‘rvar.Rmd’ using ‘UTF-8’... failed + ``` + +# PPQplan + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/allenzhuaz/PPQplan +* Source code: https://github.com/cran/PPQplan +* Date/Publication: 2020-10-08 04:30:06 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "PPQplan")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPQnote.Rmd’ using rmarkdown + --- finished re-building ‘PPQnote.Rmd’ + + --- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPQplan-vignette.Rmd’ + ... + + > devtools::load_all() + + When sourcing ‘PPQplan-vignette.R’: + Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in + '/tmp/RtmpeoIsxA/file11156538c652/vignettes'. + ℹ Are you in your project directory and does your project have a 'DESCRIPTION' + file? + Execution halted + + ‘PPQnote.Rmd’ using ‘UTF-8’... OK + ‘PPQplan-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 12.1Mb + sub-directories of 1Mb or more: + doc 12.0Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ppseq + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/zabore/ppseq +* Source code: https://github.com/cran/ppseq +* Date/Publication: 2024-09-04 22:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "ppseq")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘one_sample_expansion.Rmd’ + ... + + + + + > ptest <- plot(one_sample_cal_tbl, type1_range = c(0.05, + + 0.1), minimum_power = 0.7, plotly = TRUE) + + ... + + > ptest <- plot(two_sample_cal_tbl, type1_range = c(0.05, + + 0.1), minimum_power = 0.7, plotly = TRUE) + + When sourcing ‘two_sample_randomized.R’: + Error: subscript out of bounds + Execution halted + + ‘one_sample_expansion.Rmd’ using ‘UTF-8’... failed + ‘two_sample_randomized.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘one_sample_expansion.Rmd’ using rmarkdown + + Quitting from lines 183-188 [unnamed-chunk-13] (one_sample_expansion.Rmd) + Error: processing vignette 'one_sample_expansion.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘one_sample_expansion.Rmd’ + + --- re-building ‘two_sample_randomized.Rmd’ using rmarkdown + ... + Quitting from lines 179-184 [unnamed-chunk-13] (two_sample_randomized.Rmd) + Error: processing vignette 'two_sample_randomized.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘two_sample_randomized.Rmd’ + + SUMMARY: processing the following files failed: + ‘one_sample_expansion.Rmd’ ‘two_sample_randomized.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.0Mb + sub-directories of 1Mb or more: + doc 10.5Mb + ``` + +# PPtreeregViz + +
+ +* Version: 2.0.5 +* GitHub: https://github.com/sunsmiling/PPtreeregViz +* Source code: https://github.com/cran/PPtreeregViz +* Date/Publication: 2022-12-23 19:20:05 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "PPtreeregViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PPtreeregViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PPregNodeViz + > ### Title: Node visualization + > ### Aliases: PPregNodeViz + > ### Keywords: tree + > + > ### ** Examples + > + > data(dataXY) + > Model <- PPTreereg(Y~., data = dataXY, DEPTH = 2) + > PPregNodeViz(Model,node.id=1) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PPregNodeViz ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPtreeregViz.Rmd’ + ... + + > plot(Tree.Imp) + + > plot(Tree.Imp, marginal = TRUE, num_var = 5) + + > PPregNodeViz(Model, node.id = 1) + + When sourcing ‘PPtreeregViz.R’: + Error: argument is of length zero + Execution halted + + ‘PPtreeregViz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPtreeregViz.Rmd’ using rmarkdown + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# precintcon + +
+ +* Version: 2.3.0 +* GitHub: https://github.com/lucasvenez/precintcon +* Source code: https://github.com/cran/precintcon +* Date/Publication: 2016-07-17 13:49:19 +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "precintcon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘precintcon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pplot.deciles + > ### Title: Plot deciles + > ### Aliases: pplot.deciles precintcon.plot.deciles + > ### Keywords: deciles precipitation + > + > ### ** Examples + > + ... + 9. │ └─layout$setup(data, plot$data, plot$plot_env) + 10. │ └─ggplot2 (local) setup(..., self = self) + 11. │ └─base::lapply(...) + 12. │ └─ggplot2 (local) FUN(X[[i]], ...) + 13. │ └─ggplot2::map_data(...) + 14. │ └─vctrs::vec_slice(data, facet_vals$.index) + 15. └─vctrs:::stop_scalar_type(``(``), "x", ``) + 16. └─vctrs:::stop_vctrs(...) + 17. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +# precrec + +
+ +* Version: 0.14.4 +* GitHub: https://github.com/evalclass/precrec +* Source code: https://github.com/cran/precrec +* Date/Publication: 2023-10-11 22:10:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "precrec")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + > autoplot(mscurves) + Warning in ggplot2::fortify(object, raw_curves = raw_curves, reduce_points = reduce_points) : + Arguments in `...` must be used. + ✖ Problematic argument: + • raw_curves = raw_curves + ℹ Did you misspell an argument name? + + When sourcing ‘introduction.R’: + Error: object is not a unit + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 4.3Mb + ``` + +# priorsense + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/priorsense +* Date/Publication: 2024-07-16 10:30:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "priorsense")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘priorsense-Ex.R’ failed + The error most likely occurred in: + + > ### Name: powerscale_plots + > ### Title: Diagnostic plots for power-scaling sensitivity + > ### Aliases: powerscale_plots powerscale_plot_dens powerscale_plot_ecdf + > ### powerscale_plot_ecdf.powerscaled_sequence powerscale_plot_quantities + > ### powerscale_plot_quantities.powerscaled_sequence + > + > ### ** Examples + > + > ex <- example_powerscale_model() + > + > powerscale_plot_dens(ex$draws) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘powerscaling.Rmd’ + ... + + 1 mu 0.435 0.644 prior-data conflict + 2 sigma 0.361 0.677 prior-data conflict + + > powerscale_plot_dens(fit, variable = "mu", facet_rows = "variable") + + When sourcing ‘powerscaling.R’: + Error: unused argument (theme = list(list("black", 0.545454545454545, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.545454545454545, 1, TRUE), list("sans", "plain", "black", 12, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.545454545454545, 0.545454545454545, 1, 1, "sans", 4.21751764217518, 1.63636363636364, 19, TRUE), 6, c(6, 6, 6, 6), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NU + Execution halted + + ‘powerscaling.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘powerscaling.Rmd’ using rmarkdown + + Quitting from lines 124-125 [unnamed-chunk-7] (powerscaling.Rmd) + Error: processing vignette 'powerscaling.Rmd' failed with diagnostics: + unused argument (theme = list(list("black", 0.545454545454545, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.545454545454545, 1, TRUE), list("sans", "plain", "black", 12, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.545454545454545, 0.545454545454545, 1, 1, "sans", 4.21751764217518, 1.63636363636364, 19, TRUE), 6, c(6, 6, 6, 6), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.4, 0), + NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.4), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.4, 0, 2.4), NULL, TRUE), list("grey20", 0.3, NULL, NULL, FALSE, "grey20", FALSE), NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(NULL, 0.4, NULL, NULL, FALSE, NULL, FALSE), + NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, list(), NULL, 2, NULL, NULL, list(), 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 13, 0, NULL, NULL, NULL, NULL, NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list(), list(), 1.5, NULL, NULL, list(), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, + NULL, NULL, FALSE, list(), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 6, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 6, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(6, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list(), NULL, NULL, "on", "outside", list(NULL, NULL, "grey10", 0.9, NULL, NULL, NULL, NULL, c(4.8, 4.8, 4.8, 4.8), NULL, FALSE), NULL, NULL, + NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 3, 3, list(), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, 0.5, 0.5, 0, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), 0.666666666666667, 0.333333333333333)) + --- failed re-building ‘powerscaling.Rmd’ + + SUMMARY: processing the following file failed: + ‘powerscaling.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# probably + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/tidymodels/probably +* Source code: https://github.com/cran/probably +* Date/Publication: 2024-02-23 03:20:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "probably")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + `actual$ymin` is absent + `expected$ymin` is a character vector ('lower') + + `actual$ymax` is absent + `expected$ymax` is a character vector ('upper') + + [ FAIL 2 | WARN 0 | SKIP 46 | PASS 466 ] + Error: Test failures + Execution halted + ``` + +# processmapR + +
+ +* Version: 0.5.5 +* GitHub: https://github.com/bupaverse/processmapr +* Source code: https://github.com/cran/processmapR +* Date/Publication: 2024-08-30 13:10:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "processmapR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(processmapR) + + Attaching package: 'processmapR' + + The following object is masked from 'package:stats': + + ... + 10. └─processmapR:::return_plotly(p, plotly) + 11. ├─plotly::ggplotly(p) + 12. └─plotly:::ggplotly.ggplot(p) + 13. └─plotly::gg2list(...) + ── Failure ('test_trace_explorer.R:240:3'): test trace_explorer on eventlog with param `plotly` ── + `chart` inherits from 'gg'/'ggplot' not 'plotly'. + + [ FAIL 6 | WARN 0 | SKIP 10 | PASS 107 ] + Error: Test failures + Execution halted + ``` + +# projpred + +
+ +* Version: 2.8.0 +* GitHub: https://github.com/stan-dev/projpred +* Source code: https://github.com/cran/projpred +* Date/Publication: 2023-12-15 00:00:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "projpred")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘projpred-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.matrix.projection + > ### Title: Extract projected parameter draws and coerce to matrix + > ### Aliases: as.matrix.projection + > + > ### ** Examples + > + > ## Don't show: + ... + 2 X1 1.70 0.155 1.40 1.97 + 3 X3 0.924 0.266 0.560 1.45 + 4 X5 -1.21 0.111 -1.53 -0.602 + 5 sigma 2.01 0.183 1.83 2.35 + > if (requireNamespace("bayesplot", quietly = TRUE)) { + + print(bayesplot::mcmc_intervals(prj_mat)) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘projpred.Rmd’ + ... + + + > bayesplot_theme_set(ggplot2::theme_bw()) + + > mcmc_intervals(prj_mat) + ggplot2::coord_cartesian(xlim = c(-1.5, + + 1.6)) + + When sourcing ‘projpred.R’: + Error: argument is of length zero + Execution halted + + ‘latent.Rmd’ using ‘UTF-8’... OK + ‘projpred.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(projpred) + This is projpred version 2.8.0. NOTE: In projpred 2.7.0, the default search method was set to "forward" (for all kinds of models). + > + > test_check("projpred") + Warning in check_dep_version() : + ABI version mismatch: + ... + 41. │ └─methods (local) ``(...) + 42. │ └─methods::new(def, ...) + 43. │ ├─methods::initialize(value, ...) + 44. │ └─methods::initialize(value, ...) + 45. │ └─.Object$initialize(...) + 46. │ └─lme4 (local) initializePtr() + 47. └─base::.handleSimpleError(...) + 48. └─testthat (local) h(simpleError(msg, call)) + 49. └─rlang::abort(...) + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 1.4Mb + libs 3.1Mb + ``` + +# psborrow + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/psborrow +* Date/Publication: 2023-03-03 10:30:07 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "psborrow")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(psborrow) + > + > test_check("psborrow") + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 142 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + `expected` is a character vector ('ref') + ── Failure ('test-plots.R:126:5'): Ensure output is producing a ggplot2 object with appropriate parameters ── + p1$labels$yintercept (`actual`) not equal to "ref" (`expected`). + + `actual` is NULL + `expected` is a character vector ('ref') + + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 142 ] + Error: Test failures + Execution halted + ``` + +# pubh + +
+ +* Version: 1.3.7 +* GitHub: https://github.com/josie-athens/pubh +* Source code: https://github.com/cran/pubh +* Date/Publication: 2024-08-17 02:20:02 UTC +* Number of recursive dependencies: 187 + +Run `revdepcheck::cloud_details(, "pubh")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + ─────────────────────────────────────────────────────────────── + R2 = 0.123 + + Column names: Parameter, Coefficient, Pr(>|t|) + + > multiple(model_bwt, ~race)$df + + ... + > gf_labs(gf_facet_wrap(gf_errorbar(gf_point(estimate_means(model_norm, + + c("race", "smoke")), Mean ~ race), CI_low + CI_high ~ race, + + widt .... [TRUNCATED] + + When sourcing ‘regression.R’: + Error: argument is of length zero + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ‘regression.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘pubh-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Kirkwood + > ### Title: Body weight and plasma volume. + > ### Aliases: Kirkwood + > ### Keywords: datasets + > + > ### ** Examples + > + > data(Kirkwood) + > + > Kirkwood |> + + gf_point(volume ~ weight) |> + + gf_lm(col = "indianred3", interval = "confidence", fill = "indianred3") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_lm ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# PUPMSI + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/PUPMSI +* Date/Publication: 2022-05-31 10:50:04 UTC +* Number of recursive dependencies: 32 + +Run `revdepcheck::cloud_details(, "PUPMSI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PUPMSI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BradleyMSI + > ### Title: Bradley Moisture Sorption Isotherm + > ### Aliases: BradleyMSI + > + > ### ** Examples + > + > WaterAct <- c(0.1145,0.2274,0.3265,0.4291,0.6342,0.7385,0.8274,0.9573) + ... + Adsorption 0.002148893 0.001891231 4.617743e-06 0.04298251 7.517135e-18 + Desorption 0.004371350 0.003905913 1.910870e-05 0.10015162 3.122502e-17 + Constants of Bradley Sorption Model + Isotherm k1 k2 + Adsorption 1.752876e-10 3.525154 + Desorption 3.920525e-12 8.480898 + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: BradleyMSI -> BradleyMSIPlot + Execution halted + ``` + +# qacBase + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/rkabacoff/qacBase +* Source code: https://github.com/cran/qacBase +* Date/Publication: 2022-02-09 22:20:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "qacBase")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qacBase-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatter + > ### Title: Scatterplot + > ### Aliases: scatter + > + > ### ** Examples + > + > scatter(cars74, hp, mpg) + > scatter(cars74, wt, hp) + > p <- scatter(ggplot2::mpg, displ, hwy, + + margin="histogram", + + title="Engine Displacement vs. Highway Mileage") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatter ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# qPCRhelper + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/qPCRhelper +* Date/Publication: 2023-02-23 14:00:08 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "qPCRhelper")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qPCRhelper-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qPCRhelper + > ### Title: qPCRhelper + > ### Aliases: qPCRhelper + > + > ### ** Examples + > + > ## Create sample table with expected 'Sample', 'Group', and gene Ct columns + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘qPCRhelper.Rmd’ + ... + + ref.gene = "GAPDH", ref.group = "Control") + Warning in (function (mapping = NULL, data = NULL, geom = "boxplot", position = "dodge2", : + Ignoring unknown aesthetics: fill + + When sourcing ‘qPCRhelper.R’: + Error: ℹ In index: 1. + ℹ With name: log2RelExp. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘qPCRhelper.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘qPCRhelper.Rmd’ using rmarkdown + + Quitting from lines 18-29 [setup] (qPCRhelper.Rmd) + Error: processing vignette 'qPCRhelper.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: log2RelExp. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘qPCRhelper.Rmd’ + + SUMMARY: processing the following file failed: + ‘qPCRhelper.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# r2dii.plot + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/RMI-PACTA/r2dii.plot +* Source code: https://github.com/cran/r2dii.plot +* Date/Publication: 2024-02-29 16:40:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "r2dii.plot")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(r2dii.plot) + > + > test_check("r2dii.plot") + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + ... + `expected` is a character vector ('year') + ── Failure ('test-plot_trajectory.R:41:3'): outputs default axis labels ──────── + p$labels$y (`actual`) not equal to "value" (`expected`). + + `actual` is NULL + `expected` is a character vector ('value') + + [ FAIL 2 | WARN 2 | SKIP 40 | PASS 122 ] + Error: Test failures + Execution halted + ``` + +# r2spss + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/aalfons/r2spss +* Source code: https://github.com/cran/r2spss +* Date/Publication: 2022-05-25 11:00:08 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "r2spss")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘r2spss-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ANOVA + > ### Title: One-way and Two-way ANOVA + > ### Aliases: ANOVA to_SPSS.ANOVA_SPSS print.ANOVA_SPSS plot.ANOVA_SPSS + > ### Keywords: htest + > + > ### ** Examples + > + ... + \arrayrulecolor{darkgraySPSS}\hline + Total & 495.474 & 416 & & & \\ + \arrayrulecolor{black}\hline + \noalign{\smallskip} + \end{NiceTabular} + + > plot(oneway) # create profile plot + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘r2spss-intro.Rnw’ + ... + Valid N (listwise) & 417 & & & & \\ + \hline + \noalign{\smallskip} + \end{tabular} + + > histogram(Eredivisie, "logMarketValue") + + When sourcing 'r2spss-intro.R': + Error: argument is of length zero + Execution halted + + ‘r2spss-intro.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘r2spss-intro.Rnw’ using knitr + + Quitting from lines 327-328 [unnamed-chunk-8] (r2spss-intro.Rnw) + Error: processing vignette 'r2spss-intro.Rnw' failed with diagnostics: + argument is of length zero + --- failed re-building ‘r2spss-intro.Rnw’ + + SUMMARY: processing the following file failed: + ‘r2spss-intro.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# radiant.basics + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.basics +* Source code: https://github.com/cran/radiant.basics +* Date/Publication: 2024-05-15 04:30:07 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "radiant.basics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.basics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.clt + > ### Title: Plot method for the Central Limit Theorem simulation + > ### Aliases: plot.clt + > + > ### ** Examples + > + > clt("Uniform", 100, 100, unif_min = 10, unif_max = 20) %>% plot() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# radiant.data + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.data +* Source code: https://github.com/cran/radiant.data +* Date/Publication: 2024-05-14 23:30:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "radiant.data")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.data-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visualize + > ### Title: Visualize data using ggplot2 + > ### Aliases: visualize + > + > ### ** Examples + > + > visualize(diamonds, "price:cut", type = "dist", fillcol = "red") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: visualize ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# radiant.model + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.model +* Source code: https://github.com/cran/radiant.model +* Date/Publication: 2024-05-15 09:10:08 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "radiant.model")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.model-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.simulater + > ### Title: Plot method for the simulater function + > ### Aliases: plot.simulater + > + > ### ** Examples + > + > simdat <- simulater( + ... + + const = "cost 3", + + norm = "demand 2000 1000", + + discrete = "price 5 8 .3 .7", + + form = "profit = demand * (price - cost)", + + seed = 1234 + + ) + > plot(simdat, bins = 25) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# Radviz + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/yannabraham/Radviz +* Source code: https://github.com/cran/Radviz +* Date/Publication: 2022-03-25 18:10:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "Radviz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Radviz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Radviz + > ### Title: Radviz Projection of Multidimensional Data + > ### Aliases: Radviz + > + > ### ** Examples + > + > data(iris) + > das <- c('Sepal.Length','Sepal.Width','Petal.Length','Petal.Width') + > S <- make.S(das) + > rv <- do.radviz(iris,S) + > plot(rv,anchors.only=FALSE) + Error in plot.radviz(rv, anchors.only = FALSE) : + 'language' object cannot be coerced to type 'double' + Calls: plot -> plot.radviz + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘multivariate_analysis.Rmd’ + ... + + > classic.S <- make.S(get.optim(classic.optim)) + + > btcells.rv <- do.radviz(btcells.df, classic.S) + + > plot(btcells.rv) + geom_point(aes(color = Treatment)) + + ... + [1] 15792 18 + + > ct.rv + + When sourcing ‘single_cell_projections.R’: + Error: 'language' object cannot be coerced to type 'double' + Execution halted + + ‘multivariate_analysis.Rmd’ using ‘UTF-8’... failed + ‘single_cell_projections.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘multivariate_analysis.Rmd’ using rmarkdown + ``` + +# randomForestExplainer + +
+ +* Version: 0.10.1 +* GitHub: https://github.com/ModelOriented/randomForestExplainer +* Source code: https://github.com/cran/randomForestExplainer +* Date/Publication: 2020-07-11 20:30:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "randomForestExplainer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘randomForestExplainer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_min_depth_interactions + > ### Title: Plot the top mean conditional minimal depth + > ### Aliases: plot_min_depth_interactions + > + > ### ** Examples + > + > forest <- randomForest::randomForest(Species ~ ., data = iris, ntree = 100) + ... + The first warning was: + ℹ In argument: `Petal.Width = min(Petal.Width, na.rm = TRUE)`. + ℹ In group 1: `tree = 1` and `split var = "Petal.Length"`. + Caused by warning in `min()`: + ! no non-missing arguments to min; returning Inf + ℹ Run `dplyr::last_dplyr_warnings()` to see the 203 remaining warnings. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(randomForestExplainer) + > + > test_check("randomForestExplainer") + [ FAIL 6 | WARN 70 | SKIP 0 | PASS 55 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 24. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 25. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 26. └─grid:::drawGrob(x) + 27. ├─grid::drawDetails(x, recording = FALSE) + 28. └─grid:::drawDetails.segments(x, recording = FALSE) + 29. └─grid:::grid.Call.graphics(...) + + [ FAIL 6 | WARN 70 | SKIP 0 | PASS 55 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘randomForestExplainer.Rmd’ + ... + 3 3.308 + 23 2.600 + 33 1.288 + 8 3.512 + + > plot_min_depth_interactions(interactions_frame) + + When sourcing ‘randomForestExplainer.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘randomForestExplainer.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘randomForestExplainer.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# rassta + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/bafuentes/rassta +* Source code: https://github.com/cran/rassta +* Date/Publication: 2024-08-19 06:20:13 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "rassta")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rassta-Ex.R’ failed + The error most likely occurred in: + + > ### Name: select_functions + > ### Title: Select Constrained Univariate Distribution Functions + > ### Aliases: select_functions + > + > ### ** Examples + > + > require(terra) + ... + > tvars <- terra::rast(tf) + > # Single-layer SpatRaster of topographic classification units + > ## 5 classification units + > tcf <- list.files(path = p, pattern = "topography.tif", full.names = TRUE) + > tcu <- terra::rast(tcf) + > # Automatic selection of distribution functions + > tdif <- select_functions(cu.rast = tcu, var.rast = tvars, fun = mean) + Error in pm[[2]] : subscript out of bounds + Calls: select_functions -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("rassta") + + } + + Attaching package: 'rassta' + + ... + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests Error in pm[[2]] : subscript out of bounds + Calls: ... select_functions -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘signature.Rmd’ + ... + > clim.var <- rast(vardir) + + > clim.cu <- rast(paste(d, "/climate.tif", sep = "")) + + > clim.difun <- select_functions(cu.rast = clim.cu, + + var.rast = clim.var, mode = "auto") + + ... + When sourcing ‘signature.R’: + Error: subscript out of bounds + Execution halted + + ‘classunits.Rmd’ using ‘UTF-8’... OK + ‘modeling.Rmd’ using ‘UTF-8’... OK + ‘sampling.Rmd’ using ‘UTF-8’... OK + ‘signature.Rmd’ using ‘UTF-8’... failed + ‘similarity.Rmd’ using ‘UTF-8’... OK + ‘stratunits.Rmd’ using ‘UTF-8’... OK + ``` + +# rater + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/jeffreypullin/rater +* Source code: https://github.com/cran/rater +* Date/Publication: 2023-09-11 17:40:02 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "rater")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(rater) + * The rater package uses `Stan` to fit bayesian models. + * If you are working on a local, multicore CPU with excess RAM please call: + * options(mc.cores = parallel::detectCores()) + * This will allow Stan to run inference on multiple cores in parallel. + > + ... + ── Failure ('test_plotting.R:65:3'): plot_theta_points output has correct type ── + get_geoms(ds_plot) (`actual`) not equal to c("GeomPoint", "GeomErrorbar") (`expected`). + + `names(actual)` is a character vector ('geom_point', 'geom_errorbar') + `names(expected)` is absent + + [ FAIL 4 | WARN 0 | SKIP 6 | PASS 375 ] + Error: Test failures + In addition: There were 14 warnings (use warnings() to see them) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 128.0Mb + sub-directories of 1Mb or more: + libs 127.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# RBesT + +
+ +* Version: 1.7-3 +* GitHub: https://github.com/Novartis/RBesT +* Source code: https://github.com/cran/RBesT +* Date/Publication: 2024-01-08 15:20:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "RBesT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RBesT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: forest_plot + > ### Title: Forest Plot + > ### Aliases: forest_plot + > + > ### ** Examples + > + > # we consider the example AS MAP analysis + ... + Please consider increasing the MCMC simulation size. + + AS> ## Recover user set sampling defaults + AS> options(.user_mc_options) + > + > # default forest plot for a gMAP analysis + > forest_plot(map_AS) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: forest_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + + MAP Prior MCMC sample + mean sd 2.5% 50% 97.5% + 0.2580 0.0842 0.1120 0.2510 0.4590 + + > pl <- plot(map_mcmc) + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘introduction.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + + Quitting from lines 104-126 [unnamed-chunk-4] (introduction.Rmd) + Error: processing vignette 'introduction.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 97.6Mb + sub-directories of 1Mb or more: + libs 95.7Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# rddensity + +
+ +* Version: 2.5 +* GitHub: NA +* Source code: https://github.com/cran/rddensity +* Date/Publication: 2024-01-22 21:10:07 UTC +* Number of recursive dependencies: 29 + +Run `revdepcheck::cloud_details(, "rddensity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rddensity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rddensity + > ### Title: Manipulation Testing Using Local Polynomial Density Estimation + > ### Aliases: rddensity + > + > ### ** Examples + > + > ### Continuous Density + ... + sum densities 0.6532 3.9572 0.0042 + + > + > ### Plotting using rdplotdensity() + > # 1. From -2 to 2 with 25 evaluation points at each side + > plot1 <- rdplotdensity(rdd, x, plotRange = c(-2, 2), plotN = 25) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: rdplotdensity ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# RecordTest + +
+ +* Version: 2.2.0 +* GitHub: https://github.com/JorgeCastilloMateo/RecordTest +* Source code: https://github.com/cran/RecordTest +* Date/Publication: 2023-08-07 20:20:08 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "RecordTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RecordTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: N.plot + > ### Title: Number of Records Plot + > ### Aliases: N.plot + > + > ### ** Examples + > + > # Plot at Zaragoza, with linear weights and error bar as RIs aesthetic + > N.plot(ZaragozaSeries, weights = function(t) t-1, conf.aes = "errorbar") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘RecordTest.Rmd’ + ... + + R_lower = Olympic_records_200m$value, Trows = 27) + + > records(or200m, type = "points", alpha = c(1, 0, 1, + + 0)) + ggplot2::ylab("seconds") + + > N.plot(or200m, record = c(0, 1, 0, 0)) + + When sourcing ‘RecordTest.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘RecordTest.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘RecordTest.Rmd’ using rmarkdown + ``` + +# reda + +
+ +* Version: 0.5.4 +* GitHub: https://github.com/wenjie2wang/reda +* Source code: https://github.com/cran/reda +* Date/Publication: 2022-07-08 21:50:02 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "reda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mcf + > ### Title: Mean Cumulative Function (MCF) + > ### Aliases: mcf mcf,formula-method mcf,rateReg-method + > + > ### ** Examples + > + > library(reda) + ... + > + > ## Example 2. the simulated data + > simuMcf <- mcf(Recur(time, ID, event) ~ group + gender, + + data = simuDat, ID %in% 1 : 50) + > plot(simuMcf, conf.int = TRUE, lty = 1 : 4, + + legendName = "Treatment & Gender") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘reda-intro.Rmd’ + ... + + data = simuDat, subset = ID %in% seq_len(50)) + + > plot(valveMcf0, conf.int = TRUE, mark.time = TRUE, + + addOrigin = TRUE, col = 2) + ggplot2::xlab("Days") + ggplot2::theme_bw() + + > plot(simuMcf, conf.int = TRUE, lty = 1:4, legendName = "Treatment & Gender") + + When sourcing ‘reda-intro.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘reda-Recur.Rmd’ using ‘UTF-8’... OK + ‘reda-intro.Rmd’ using ‘UTF-8’... failed + ‘reda-simulate.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘reda-Recur.Rmd’ using rmarkdown + --- finished re-building ‘reda-Recur.Rmd’ + + --- re-building ‘reda-intro.Rmd’ using rmarkdown + + Quitting from lines 123-129 [plot-sampleMcf] (reda-intro.Rmd) + Error: processing vignette 'reda-intro.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + ... + --- failed re-building ‘reda-intro.Rmd’ + + --- re-building ‘reda-simulate.Rmd’ using rmarkdown + --- finished re-building ‘reda-simulate.Rmd’ + + SUMMARY: processing the following file failed: + ‘reda-intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + doc 3.3Mb + libs 4.1Mb + ``` + +# redist + +
+ +* Version: 4.2.0 +* GitHub: https://github.com/alarm-redist/redist +* Source code: https://github.com/cran/redist +* Date/Publication: 2024-01-13 13:20:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "redist")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘redist.Rmd’ + ... + # ℹ 991 more rows + + > library(patchwork) + + > hist(plan_sum, max_dev) + hist(iowa_plans, comp) + + + plot_layout(guides = "collect") + + When sourcing ‘redist.R’: + Error: object is not a unit + Execution halted + + ‘common_args.Rmd’ using ‘UTF-8’... OK + ‘flip.Rmd’ using ‘UTF-8’... OK + ‘map-preproc.Rmd’ using ‘UTF-8’... OK + ‘redist.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘common_args.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 29.5Mb + sub-directories of 1Mb or more: + data 1.2Mb + libs 25.5Mb + ``` + +# registr + +
+ +* Version: 2.1.0 +* GitHub: NA +* Source code: https://github.com/cran/registr +* Date/Publication: 2022-10-02 21:40:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "registr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘incomplete_curves.Rmd’ + ... + + ggplot(reg4_joint$Y, aes(x = t_hat, y = value, group = id)) + + + geom_line(alpha = 0.3) + xlab("t [registered]") + .... [TRUNCATED] + + > if (have_ggplot2) { + + plot(reg4_joint$fpca_obj) + + } + + ... + > if (have_ggplot2 && requireNamespace("cowplot", quietly = TRUE)) { + + registr:::plot.fpca(bfpca_object) + + } + + When sourcing ‘registr.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘incomplete_curves.Rmd’ using ‘UTF-8’... failed + ‘registr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘incomplete_curves.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘registr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fpca_gauss + > ### Title: Functional principal components analysis via variational EM + > ### Aliases: fpca_gauss + > + > ### ** Examples + > + > data(growth_incomplete) + ... + > + > # estimate 2 FPCs + > fpca_obj = fpca_gauss(Y = growth_incomplete, npc = 2) + Warning in (function (npc, npc_varExplained = NULL, Kt, maxiter, print.iter, : + fpca_gauss convergence not reached. Try increasing maxiter. + > plot(fpca_obj) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(registr) + Warning message: + In check_dep_version() : ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original 'Matrix' package + ... + 12. └─methods (local) ``(...) + 13. └─methods::new(def, ...) + 14. ├─methods::initialize(value, ...) + 15. └─methods::initialize(value, ...) + 16. └─.Object$initialize(...) + 17. └─lme4 (local) initializePtr() + + [ FAIL 13 | WARN 6 | SKIP 6 | PASS 166 ] + Error: Test failures + Execution halted + ``` + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + doc 1.8Mb + libs 3.1Mb + ``` + +# reliabilitydiag + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/aijordan/reliabilitydiag +* Source code: https://github.com/cran/reliabilitydiag +* Date/Publication: 2022-06-29 00:20:06 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "reliabilitydiag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reliabilitydiag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: c.reliabilitydiag + > ### Title: Combining reliability diagram objects + > ### Aliases: c.reliabilitydiag + > + > ### ** Examples + > + > data("precip_Niamey_2016", package = "reliabilitydiag") + > + > X <- precip_Niamey_2016[c("EMOS", "ENS")] + > Y <- precip_Niamey_2016$obs + > r0 <- reliabilitydiag0(Y) + > r1 <- c(r0, X, EPC = precip_Niamey_2016$EPC, region.level = NA) + > r1 + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# relliptical + +
+ +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/relliptical +* Date/Publication: 2024-02-07 12:50:02 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "relliptical")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘relliptical-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rtelliptical + > ### Title: Sampling Random Numbers from Truncated Multivariate Elliptical + > ### Distributions + > ### Aliases: rtelliptical + > + > ### ** Examples + > + ... + > Sigma = matrix(c(1,-0.5,-0.5,1), 2, 2) + > lower = c(-2, -2) + > upper = c(3, 2) + > sample4 = rtelliptical(2000, mu, Sigma, lower, upper, gFun=function(t){t^(-1/2)*exp(-2*t^(1/4))}) + > f1 = ggplot(data.frame(sample4), aes(x=X1,y=X2)) + geom_point(size=0.50) + + + labs(x=expression(X[1]), y=expression(X[2]), subtitle="Kotz(2,1/4,1/2)") + theme_bw() + > ggMarginal(f1, type="histogram", fill="grey") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggMarginal ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 6.5Mb + ``` + +# reportRmd + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/reportRmd +* Date/Publication: 2023-11-16 17:00:03 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "reportRmd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reportRmd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotuv + > ### Title: Plot multiple bivariate relationships in a single plot + > ### Aliases: plotuv + > ### Keywords: plot + > + > ### ** Examples + > + ... + > plotuv(data=pembrolizumab, response='cbr', + + covs=c('age','sex','l_size','baseline_ctdna'),showN=TRUE) + Warning: `stat(count)` was deprecated in ggplot2 3.4.0. + ℹ Please use `after_stat(count)` instead. + ℹ The deprecated feature was likely used in the reportRmd package. + Please report the issue to the authors. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘reportRmd.Rmd’ + ... + > ctDNA <- clear_labels(ctDNA) + + > plotuv(data = pembrolizumab, response = "orr", covs = c("age", + + "cohort", "pdl1", "change_ctdna_group")) + Boxplots not shown for categories with fewer than 20 observations. + Boxplots not shown for categories with fewer than 20 observations. + + When sourcing ‘reportRmd.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘reportRmd.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘reportRmd.Rmd’ using rmarkdown + + Quitting from lines 380-383 [unnamed-chunk-30] (reportRmd.Rmd) + Error: processing vignette 'reportRmd.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘reportRmd.Rmd’ + + SUMMARY: processing the following file failed: + ‘reportRmd.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# reservr + +
+ +* Version: 0.0.3 +* GitHub: https://github.com/AshesITR/reservr +* Source code: https://github.com/cran/reservr +* Date/Publication: 2024-06-24 16:40:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "reservr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reservr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: blended_transition + > ### Title: Transition functions for blended distributions + > ### Aliases: blended_transition blended_transition_inv + > + > ### ** Examples + > + > library(ggplot2) + ... + + theme_bw() %+% + + theme( + + legend.position = "bottom", legend.box = "horizontal" + + ) %+% + + guides(color = guide_legend(direction = "horizontal", title = ""), linetype = guide_none()) %+% + + scale_linetype_manual(values = c("TRUE" = 1, "FALSE" = 3)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘distributions.Rmd’ using rmarkdown + + Quitting from lines 170-227 [unnamed-chunk-10] (distributions.Rmd) + Error: processing vignette 'distributions.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘distributions.Rmd’ + + --- re-building ‘jss_paper.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘distributions.Rmd’ + ... + + > attr(trunc_fit$logLik, "nobs") + [1] 62 + + > plot_distributions(true = norm, fit1 = norm, fit2 = norm2, + + fit3 = dist_normal(3), .x = seq(-2, 7, 0.01), with_params = list(true = list(mean .... [TRUNCATED] + + ... + + > dist$sample(1) + + When sourcing ‘jss_paper.R’: + Error: invalid arguments + Execution halted + + ‘distributions.Rmd’ using ‘UTF-8’... failed + ‘jss_paper.Rmd’ using ‘UTF-8’... failed + ‘tensorflow.Rmd’ using ‘UTF-8’... OK + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.2Mb + libs 12.8Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# RestoreNet + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/RestoreNet +* Date/Publication: 2024-02-15 11:00:02 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "RestoreNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RestoreNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get.scatterpie + > ### Title: Clonal pie-chart + > ### Aliases: get.scatterpie + > + > ### ** Examples + > + > rcts <- c("A->1", "B->1", "C->1", "D->1", + ... + computing A^-1... + computing rho... + computing Chi2... + computing KLdiv... + computing BhattDist... + > + > get.scatterpie(re.res, txt = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: get.scatterpie ... ggplot_add.layer_scatterpie -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘RestoreNet.ltx’ using tex + Error: processing vignette 'RestoreNet.ltx' failed with diagnostics: + Running 'texi2dvi' on 'RestoreNet.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `realboxes.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.12 \usepackage + {amssymb}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘RestoreNet.ltx’ + + SUMMARY: processing the following file failed: + ‘RestoreNet.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rfPermute + +
+ +* Version: 2.5.2 +* GitHub: https://github.com/EricArcher/rfPermute +* Source code: https://github.com/cran/rfPermute +* Date/Publication: 2023-08-23 17:40:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "rfPermute")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rfPermute-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotTrace + > ### Title: Plot Trace + > ### Aliases: plotTrace + > + > ### ** Examples + > + > library(randomForest) + ... + randomForest 4.7-1.1 + Type rfNews() to see new features/changes/bug fixes. + > data(mtcars) + > + > rf <- randomForest(factor(am) ~ ., mtcars) + > plotTrace(rf) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotTrace ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# RKorAPClient + +
+ +* Version: 0.8.1 +* GitHub: https://github.com/KorAP/RKorAPClient +* Source code: https://github.com/cran/RKorAPClient +* Date/Publication: 2024-05-02 11:42:54 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "RKorAPClient")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library("testthat") + > library("RKorAPClient") + > + > test_check("RKorAPClient") + + apiUrl: https://korap.ids-mannheim.de/api/v1.0/ + [ FAIL 1 | WARN 0 | SKIP 30 | PASS 25 ] + ... + 'test-demos.R:129:3', 'test-textMetadata.R:2:3', 'test-textMetadata.R:9:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-misc.R:224:5'): geom_freq_by_year_ci works correctly ───────── + gpt[["labels"]][["url"]] not equal to "webUIRequestUrl". + target is NULL, current is character + + [ FAIL 1 | WARN 0 | SKIP 30 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +# roahd + +
+ +* Version: 1.4.3 +* GitHub: https://github.com/astamm/roahd +* Source code: https://github.com/cran/roahd +* Date/Publication: 2021-11-04 00:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "roahd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roahd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.depthgram + > ### Title: Specialized method to plot 'depthgram' objects + > ### Aliases: plot.depthgram + > + > ### ** Examples + > + > N <- 50 + ... + + N, + + centerline = sin(2 * pi * grid), + + Cov = Cov + + ) + > names <- paste0("id_", 1:nrow(Data[[1]])) + > DG <- depthgram(Data, marginal_outliers = TRUE, ids = names) + > plot(DG) + Error in pm[[2]] : subscript out of bounds + Calls: plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + data 5.0Mb + doc 1.7Mb + ``` + +# robCompositions + +
+ +* Version: 2.4.1 +* GitHub: NA +* Source code: https://github.com/cran/robCompositions +* Date/Publication: 2023-08-25 15:30:06 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "robCompositions")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘robCompositions-Ex.R’ failed + The error most likely occurred in: + + > ### Name: biplot.pcaCoDa + > ### Title: Biplot method + > ### Aliases: biplot.pcaCoDa + > ### Keywords: aplot + > + > ### ** Examples + > + ... + > ## with labels for the scores: + > data(arcticLake) + > rownames(arcticLake) <- paste(sample(letters[1:26], nrow(arcticLake), replace=TRUE), + + 1:nrow(arcticLake), sep="") + > pc <- pcaCoDa(arcticLake, method="classical") + > plot(pc, xlabs=rownames(arcticLake), which = 2) + > plot(pc, xlabs=rownames(arcticLake), which = 3) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 24.6Mb + sub-directories of 1Mb or more: + data 2.0Mb + libs 21.3Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘imputation.Rnw’ using knitr + Error: processing vignette 'imputation.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'imputation.tex' failed. + LaTeX errors: + ! LaTeX Error: File `scrartcl.cls' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: cls) + + ... + l.3 \usepackage + [pdftex]{hyperref}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘robCompositions-overview.Rnw’ + + SUMMARY: processing the following files failed: + ‘imputation.Rnw’ ‘robCompositions-overview.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# romic + +
+ +* Version: 1.1.3 +* GitHub: NA +* Source code: https://github.com/cran/romic +* Date/Publication: 2023-09-21 05:40:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "romic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘romic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_bivariate + > ### Title: Bivariate Plot + > ### Aliases: plot_bivariate + > + > ### ** Examples + > + > library(dplyr) + ... + > brauer_augmented <- brauer_2008_tidy %>% + + add_pcs(npcs = 5) %>% + + tomic_to("triple_omic") + 40 features dropped due to missing values + > + > tomic_table <- brauer_augmented$samples + > plot_bivariate(tomic_table, "PC1", "PC2", "nutrient", "nutrient", 0.5, 10) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_bivariate ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 1. └─romic::plot_bivariate(...) at test-module_ggbiv.R:8:3 + 2. └─ggplot2:::`+.gg`(ggplot(tomic_table, running_aes), plot_call) + 3. └─ggplot2:::add_ggplot(e1, e2, e2name) + 4. ├─ggplot2::ggplot_add(object, p, objectname) + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 7 | PASS 64 ] + Error: Test failures + Execution halted + ``` + +# roptions + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/roptions +* Date/Publication: 2020-05-11 11:10:06 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "roptions")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roptions-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box.spread + > ### Title: Box Spread Strategy Function + > ### Aliases: box.spread + > + > ### ** Examples + > + > box.spread(100, 105, 95, 110, 3.2, 2.6, 1.1, 2.4) + ... + 35 5.7 + 36 5.7 + 37 5.7 + 38 5.7 + 39 5.7 + 40 5.7 + 41 5.7 + Error in pm[[2]] : subscript out of bounds + Calls: box.spread -> print -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# rSAFE + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/ModelOriented/rSAFE +* Source code: https://github.com/cran/rSAFE +* Date/Publication: 2022-08-13 13:20:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "rSAFE")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(rSAFE) + Welcome to rSAFE (version: 0.1.4). + > + > test_check("rSAFE") + Single variables processing... + ... + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 10 | SKIP 0 | PASS 56 ] + Deleting unused snapshots: + • extraction/plot-continuous-variable.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example_apartments.Rmd’ + ... + + > plot(safe_extractor, variable = "district") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the rSAFE package. + Please report the issue at . + + ... + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the rSAFE package. + Please report the issue at . + + When sourcing ‘example_hr.R’: + Error: argument is of length zero + Execution halted + + ‘example_apartments.Rmd’ using ‘UTF-8’... failed + ‘example_hr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘example_apartments.Rmd’ using rmarkdown + ``` + +# santaR + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/adwolfer/santaR +* Source code: https://github.com/cran/santaR +* Date/Publication: 2024-03-07 00:30:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "santaR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(santaR) + + This is santaR version 1.2.4 + + > + > test_check("santaR") + ... + 1/1 mismatches + [1] 11 - 10 == 1 + ── Failure ('test_dfSearch-plot_nbTP_histogram.R:69:3'): change dfCuttOff ────── + length(result_nbTPHisto) not equal to length(ggplot2::ggplot()). + 1/1 mismatches + [1] 11 - 10 == 1 + + [ FAIL 8 | WARN 4 | SKIP 0 | PASS 681 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started.Rmd’ + ... + + > knitr::include_graphics("../man/figures/santaR-approach.jpg") + + When sourcing ‘getting-started.R’: + Error: Cannot find the file(s): "../man/figures/santaR-approach.jpg" + Execution halted + when running code in ‘selecting-optimal-df.Rmd’ + ... + Execution halted + + ‘advanced-command-line-functions.Rmd’ using ‘UTF-8’... OK + ‘automated-command-line.Rmd’ using ‘UTF-8’... OK + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘plotting-options.Rmd’ using ‘UTF-8’... OK + ‘prepare-input-data.Rmd’ using ‘UTF-8’... OK + ‘selecting-optimal-df.Rmd’ using ‘UTF-8’... failed + ‘theoretical-background.Rmd’ using ‘UTF-8’... OK + ‘santaR-GUI.pdf.asis’ using ‘UTF-8’... OK + ``` + +# saros + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/NIFU-NO/saros +* Source code: https://github.com/cran/saros +* Date/Publication: 2024-09-03 07:40:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "saros")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘saros-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fig_height_h_barchart2 + > ### Title: Estimate figure height for a horizontal bar chart + > ### Aliases: fig_height_h_barchart2 + > + > ### ** Examples + > + > fig_height_h_barchart2(makeme(data=ex_survey, dep=b_1:b_3, indep=x1_sex)) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • cumulative = TRUE + ℹ Did you misspell an argument name? + Error in if (new_name %in% existing) { : argument is of length zero + Calls: fig_height_h_barchart2 ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(saros) + > + > testthat::test_check("saros") + Starting 2 test processes + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 194 ] + ... + 9. └─saros:::make_content.cat_plot_html(...) + 10. └─ggplot2:::`+.gg`(...) + 11. └─ggplot2:::add_ggplot(e1, e2, e2name) + 12. ├─ggplot2::ggplot_add(object, p, objectname) + 13. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 194 ] + Error: Test failures + Execution halted + ``` + +# scatterpie + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/scatterpie +* Date/Publication: 2024-08-28 17:20:02 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "scatterpie")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘scatterpie-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_scatterpie + > ### Title: geom_scatterpie + > ### Aliases: geom_scatterpie geom_scatterpie2 + > + > ### ** Examples + > + > library(ggplot2) + ... + > d$C <- abs(rnorm(5, sd=3)) + > + > ggplot() + + + geom_scatterpie( + + aes(x=x, y=y), data=d, cols=c("A", "B", "C") + + ) + + + coord_fixed() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.layer_scatterpie -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘scatterpie.Rmd’ + ... + 5 12.928774 -11.288549 4 0.34754260 3.144288 3.789556 2.295894 + 8 -126.506123 29.230687 5 0.95161857 3.029335 1.048951 2.471943 + 9 -68.685285 6.192712 6 0.04502772 3.203072 2.596539 4.439393 + + > ggplot() + geom_scatterpie(aes(x = long, y = lat, + + group = region), data = d, cols = LETTERS[1:4]) + coord_equal() + + When sourcing ‘scatterpie.R’: + Error: argument is of length zero + Execution halted + + ‘scatterpie.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘scatterpie.Rmd’ using rmarkdown + + Quitting from lines 52-54 [unnamed-chunk-3] (scatterpie.Rmd) + Error: processing vignette 'scatterpie.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘scatterpie.Rmd’ + + SUMMARY: processing the following file failed: + ‘scatterpie.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# scdtb + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mightymetrika/scdtb +* Source code: https://github.com/cran/scdtb +* Date/Publication: 2024-04-30 08:50:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "scdtb")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + ── Failure ('test-mixed_model_analysis.R:119:3'): mixed_model_analysis uses the .participant variable to label data points + when .participant is not NULL ── + res$plot$labels$shape (`actual`) not equal to "factor(part)" (`expected`). + + `actual` is NULL + `expected` is a character vector ('factor(part)') + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ] + Error: Test failures + Execution halted + ``` + +# scoringutils + +
+ +* Version: 1.2.2 +* GitHub: https://github.com/epiforecasts/scoringutils +* Source code: https://github.com/cran/scoringutils +* Date/Publication: 2023-11-29 15:50:10 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "scoringutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘scoringutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_predictions + > ### Title: Plot Predictions vs True Values + > ### Aliases: plot_predictions + > + > ### ** Examples + > + > library(ggplot2) + ... + + by = c("target_type", "location"), + + range = c(0, 50, 90, 95) + + ) + + + facet_wrap(~ location + target_type, scales = "free_y") + + + aes(fill = model, color = model) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘metric-details.Rmd’ using rmarkdown + --- finished re-building ‘metric-details.Rmd’ + + --- re-building ‘scoring-forecasts-directly.Rmd’ using rmarkdown + --- finished re-building ‘scoring-forecasts-directly.Rmd’ + + --- re-building ‘scoringutils.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘scoringutils.Rmd’ + ... + The following messages were produced when checking inputs: + 1. 144 values for `prediction` are NA in the data provided and the corresponding rows were removed. This may indicate a problem if unexpected. + + > example_quantile %>% make_NA(what = "truth", target_end_date >= + + "2021-07-15", target_end_date < "2021-05-22") %>% make_NA(what = "forecast", .... [TRUNCATED] + + When sourcing ‘scoringutils.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL + Execution halted + + ‘metric-details.Rmd’ using ‘UTF-8’... OK + ‘scoring-forecasts-directly.Rmd’ using ‘UTF-8’... OK + ‘scoringutils.Rmd’ using ‘UTF-8’... failed + ``` + +# scUtils + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/scUtils +* Date/Publication: 2020-06-25 16:20:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "scUtils")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(scUtils) + > + > test_check("scUtils") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-plots.R:59:3'): all kinds of colnames are allowed ──────────── + p$labels not equal to list(y = "Dim2", x = "Dim1", colour = "expression"). + Length mismatch: comparison on first 2 components + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# SCVA + +
+ +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/SCVA +* Date/Publication: 2020-01-09 22:50:10 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "SCVA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SCVA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphly + > ### Title: Interactive plot of single-case data + > ### Aliases: graphly + > ### Keywords: Single-case design Graph + > + > ### ** Examples + > + > data(AB) + > graphly(design = "AB", data = AB) + Error in pm[[2]] : subscript out of bounds + Calls: graphly -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# sdmTMB + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/pbs-assess/sdmTMB +* Source code: https://github.com/cran/sdmTMB +* Date/Publication: 2024-05-30 00:00:02 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "sdmTMB")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sdmTMB-Ex.R’ failed + The error most likely occurred in: + + > ### Name: emmeans.sdmTMB + > ### Title: Estimated marginal means with the 'emmeans' package with + > ### 'sdmTMB' + > ### Aliases: emmeans.sdmTMB + > + > ### ** Examples + > + ... + year2013 - year2017 -0.15358 0.259 959 -0.593 0.9342 + year2015 - year2017 0.03703 0.263 959 0.141 0.9990 + + P value adjustment: tukey method for comparing a family of 4 estimates + + > emmeans::emmip(fit2, year ~ depth_scaled, at = list(depth_scaled = seq(-2.5, + + 2.5, length.out = 50)), CIs = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 88.5Mb + sub-directories of 1Mb or more: + libs 86.4Mb + ``` + +# SDMtune + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/ConsBiol-unibern/SDMtune +* Source code: https://github.com/cran/SDMtune +* Date/Publication: 2023-07-03 12:20:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "SDMtune")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(SDMtune) + + _____ ____ __ ___ __ + / ___/ / __ \ / |/ // /_ __ __ ____ ___ + \__ \ / / / // /|_/ // __// / / // __ \ / _ \ + ___/ // /_/ // / / // /_ / /_/ // / / // __/ + ... + `expected` is a character vector ('Var2') + ── Failure ('test-plotCor.R:6:3'): The plot has the correct labels and text size ── + p$labels$y (`actual`) not equal to "Var1" (`expected`). + + `actual` is NULL + `expected` is a character vector ('Var1') + + [ FAIL 2 | WARN 0 | SKIP 55 | PASS 315 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic-use.Rmd’ + ... + [1] 0.8336850 0.8672387 + + > folds <- randomFolds(data, k = 4, only_presence = TRUE, + + seed = 25) + + > auc(cv_model) + + When sourcing ‘basic-use.R’: + Error: object 'cv_model' not found + Execution halted + + ‘basic-use.Rmd’ using ‘UTF-8’... failed + ‘hyper-tuning.Rmd’ using ‘UTF-8’... OK + ‘presence-absence.Rmd’ using ‘UTF-8’... OK + ‘var-selection.Rmd’ using ‘UTF-8’... OK + ``` + +# sedproxy + +
+ +* Version: 0.7.5 +* GitHub: https://github.com/EarthSystemDiagnostics/sedproxy +* Source code: https://github.com/cran/sedproxy +* Date/Publication: 2023-02-26 10:50:02 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "sedproxy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sedproxy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ClimToProxyClim + > ### Title: Simulate sediment archived proxy records from an input climate + > ### signal. + > ### Aliases: ClimToProxyClim + > + > ### ** Examples + > + ... + > + > PlotPFMs(PFM$everything, max.replicates = 1, stage.order = "seq") + + + facet_wrap(~stage) + Joining with `by = join_by(stage, scale)` + Scale for alpha is already present. + Adding another scale for alpha, which will replace the existing scale. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction-to-sedproxy.Rmd’ + ... + Timepoint(s) 1, 101 are in the mixed layer + + > PlotPFMs(PFM) + Joining with `by = join_by(stage, scale)` + Scale for alpha is already present. + Adding another scale for alpha, which will replace the existing scale. + + When sourcing ‘introduction-to-sedproxy.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘effect-of-climate-dependent-flux.Rmd’ using ‘UTF-8’... OK + ‘introduction-to-sedproxy.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘effect-of-climate-dependent-flux.Rmd’ using rmarkdown + ``` + +# see + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/easystats/see +* Source code: https://github.com/cran/see +* Date/Publication: 2024-09-06 04:30:02 UTC +* Number of recursive dependencies: 243 + +Run `revdepcheck::cloud_details(, "see")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘see-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_binomdensity + > ### Title: Add dot-densities for binary 'y' variables + > ### Aliases: geom_binomdensity + > + > ### ** Examples + > + > ## Don't show: + ... + 14. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 15. │ └─l$compute_geom_2(d, theme = plot$theme) + 16. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 17. │ └─self$geom$use_defaults(...) + 18. └─base::.handleSimpleError(...) + 19. └─rlang (local) h(simpleError(msg, call)) + 20. └─handlers[[1L]](cnd) + 21. └─cli::cli_abort(...) + 22. └─rlang::abort(...) + Execution halted + ``` + +# seedreg + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/seedreg +* Date/Publication: 2022-07-07 21:20:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "seedreg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘seedreg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lineplot + > ### Title: Graph: line chart + > ### Aliases: lineplot + > + > ### ** Examples + > + > data("substrate") + ... + 16. │ └─ggplot2 (local) setup_params(...) + 17. │ └─ggplot2:::make_summary_fun(...) + 18. │ └─rlang::as_function(fun.data) + 19. │ └─base::get(x, envir = env, mode = "function") + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +# semfindr + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/sfcheung/semfindr +* Source code: https://github.com/cran/semfindr +* Date/Publication: 2024-04-08 13:30:03 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "semfindr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘semfindr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cfa_dat2 + > ### Title: Sample Data: A CFA Model with an Influential Case + > ### Aliases: cfa_dat2 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + .x5 0.227 0.136 1.675 0.094 + .x6 0.472 0.108 4.378 0.000 + f1 0.073 0.063 1.161 0.245 + f2 0.149 0.078 1.926 0.054 + + > inf_out <- influence_stat(fit) + > gcd_plot(inf_out) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gcd_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(semfindr) + > + > test_check("semfindr") + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 13 | PASS 387 ] + + ... + 1. └─semfindr::index_plot(fit_est_change, "gcd") at test-index_plot.R:22:1 + 2. └─ggplot2:::`+.gg`(p, do.call(ggplot2::geom_point, point_aes)) + 3. └─ggplot2:::add_ggplot(e1, e2, e2name) + 4. ├─ggplot2::ggplot_add(object, p, objectname) + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 13 | PASS 387 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘semfindr.Rmd’ + ... + + Note: + - Only the first 10 case(s) is/are displayed. Set ‘first’ to NULL to display all cases. + - Cases sorted by Mahalanobis distance in decreasing order. + + > gcd_plot(fit_influence, largest_gcd = 3) + + ... + > gcd_plot(fit_influence, largest_gcd = 3) + + When sourcing ‘user_id.R’: + Error: argument is of length zero + Execution halted + + ‘casewise_scores.Rmd’ using ‘UTF-8’... OK + ‘selecting_cases.Rmd’ using ‘UTF-8’... OK + ‘semfindr.Rmd’ using ‘UTF-8’... failed + ‘user_id.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘casewise_scores.Rmd’ using rmarkdown + ``` + +# sensiPhy + +
+ +* Version: 0.8.5 +* GitHub: https://github.com/paternogbc/sensiPhy +* Source code: https://github.com/cran/sensiPhy +* Date/Publication: 2020-04-02 14:50:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "sensiPhy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sensiPhy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clade_physig + > ### Title: Influential clade detection - Phylogenetic signal + > ### Aliases: clade_physig + > + > ### ** Examples + > + > data(alien) + ... + 4 0.8975481 0.25 + 5 0.8827772 0.40 + + > sensi_plot(clade, "Bovidae") + Warning: Use of `nd$estimate` is discouraged. + ℹ Use `estimate` instead. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: sensi_plot ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘sensiPhy_vignette.Rmd’ + ... + + When sourcing ‘sensiPhy_vignette.R’: + Error: attempt to use zero-length variable name + Execution halted + + ‘sensiPhy_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# sglg + +
+ +* Version: 0.2.2 +* GitHub: NA +* Source code: https://github.com/cran/sglg +* Date/Publication: 2022-09-04 03:50:01 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "sglg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sglg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: deviance_residuals + > ### Title: Deviance Residuals for a Generalized Log-gamma Regression Model + > ### Aliases: deviance_residuals + > + > ### ** Examples + > + > # Example 1 + > n <- 300 + > error <- rglg(n,0,1,1) + > y <- 0.5 + error + > fit <- glg(y~1,data=as.data.frame(y)) + > deviance_residuals(fit) + Error in pm[[2]] : subscript out of bounds + Calls: deviance_residuals ... dots2plots -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# sgsR + +
+ +* Version: 1.4.5 +* GitHub: https://github.com/tgoodbody/sgsR +* Source code: https://github.com/cran/sgsR +* Date/Publication: 2024-03-03 15:10:02 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "sgsR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + ... + `expected` is a character vector ('zq90') + ── Failure ('test-utils-plot.R:19:3'): scatter messages ──────────────────────── + o1$labels$x (`actual`) not equal to "pzabove2" (`expected`). + + `actual` is NULL + `expected` is a character vector ('pzabove2') + + [ FAIL 2 | WARN 115 | SKIP 19 | PASS 508 ] + Error: Test failures + Execution halted + ``` + +# SHAPforxgboost + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/liuyanguu/SHAPforxgboost +* Source code: https://github.com/cran/SHAPforxgboost +* Date/Publication: 2023-05-29 17:20:07 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "SHAPforxgboost")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SHAPforxgboost-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatter.plot.diagonal + > ### Title: Make customized scatter plot with diagonal line and R2 printed. + > ### Aliases: scatter.plot.diagonal + > + > ### ** Examples + > + > scatter.plot.diagonal(data = iris, x = "Sepal.Length", y = "Petal.Length") + [1] "R2 is 0.76 ." + `geom_smooth()` using formula = 'y ~ x' + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatter.plot.diagonal ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ShapleyOutlier + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/ShapleyOutlier +* Date/Publication: 2023-02-20 10:30:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "ShapleyOutlier")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ShapleyOutlier-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MOE + > ### Title: Detecting cellwise outliers using Shapley values based on local + > ### outlyingness. + > ### Aliases: MOE + > + > ### ** Examples + > + ... + > mu <- rep(0,p) + > Sigma <- matrix(0.9, p, p); diag(Sigma) = 1 + > Sigma_inv <- solve(Sigma) + > x <- c(0,1,2,2.3,2.5) + > MOE_x <- MOE(x = x, mu = mu, Sigma = Sigma) + > plot(MOE_x) + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plot ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ShapleyOutlier_examples.Rmd’ + ... + + > rownames(phi_SCD) <- paste("Step", 0:(nrow(phi_SCD) - + + 1)) + + > plot(new_shapley(phi = phi_SCD), abbrev.var = FALSE, + + abbrev.obs = FALSE, sort.obs = FALSE, sort.var = FALSE) + + When sourcing ‘ShapleyOutlier_examples.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘ShapleyOutlier_examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ShapleyOutlier_examples.Rmd’ using rmarkdown + ``` + +# shinipsum + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Thinkr-open/shinipsum +* Source code: https://github.com/cran/shinipsum +* Date/Publication: 2024-02-09 15:50:05 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "shinipsum")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(shinipsum) + > + > test_check("shinipsum") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 3150 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + `a` has length 11, not length 10. + Backtrace: + ▆ + 1. └─base::lapply(...) at test-ggplot.R:3:3 + 2. └─shinipsum (local) FUN(X[[i]], ...) + 3. └─testthat::expect_length(a, expected_length) at test-ggplot.R:8:7 + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 3150 ] + Error: Test failures + Execution halted + ``` + +# signatureSurvival + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/signatureSurvival +* Date/Publication: 2023-07-19 11:10:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "signatureSurvival")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘signatureSurvival-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MKMplot + > ### Title: Multivariate Kaplan-Meier survival curve plot + > ### Aliases: MKMplot + > ### Keywords: multivariate survival analysis + > + > ### ** Examples + > + ... + Loading required package: survival + > require(ggplot2) + Loading required package: ggplot2 + > data(GSE50081) + > MKMplot(data=GSE50081,mol=56,X=c("t.stage","n.stage", "m.stage"),time="month", + + status="status1",sml="none",quant=c("No",-0.2,0.2),plotmethod="ggsurvplot", + + adjx = 5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: MKMplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.2Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +# SimCorrMix + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/AFialkowski/SimCorrMix +* Source code: https://github.com/cran/SimCorrMix +* Date/Publication: 2018-07-01 13:31:03 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "SimCorrMix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SimCorrMix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_simpdf_theory + > ### Title: Plot Simulated Probability Density Function and Target PDF by + > ### Distribution Name or Function for Continuous or Count Variables + > ### Aliases: plot_simpdf_theory + > ### Keywords: plot + > + > ### ** Examples + ... + + mix_sixths = c(0, 0)) + Total Simulation time: 0 minutes + > plot_simpdf_theory(Nmix$Y_mix[, 1], + + title = "Mixture of Normal Distributions", + + fx = function(x) 0.4 * dnorm(x, -2, 1) + 0.6 * dnorm(x, 2, 1), + + lower = -5, upper = 5) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cont_mixture.Rmd’ + ... + > sim_cdf_prob(sim_y = Nmix2$Y_mix[, 1], delta = y_star)$cumulative_prob + [1] 0.9504 + + > plot_simpdf_theory(sim_y = Nmix2$Y_mix[, 1], ylower = -10, + + yupper = 10, title = "PDF of Mixture of Normal Distributions", + + fx = fx, low .... [TRUNCATED] + + ... + + When sourcing ‘workflow.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cont_mixture.Rmd’ using ‘UTF-8’... failed + ‘corr_mixture.Rmd’ using ‘UTF-8’... OK + ‘method_comp.Rmd’ using ‘UTF-8’... OK + ‘variable_types.Rmd’ using ‘UTF-8’... OK + ‘workflow.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cont_mixture.Rmd’ using rmarkdown + + Quitting from lines 129-132 [unnamed-chunk-8] (cont_mixture.Rmd) + Error: processing vignette 'cont_mixture.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘cont_mixture.Rmd’ + + --- re-building ‘corr_mixture.Rmd’ using rmarkdown + --- finished re-building ‘corr_mixture.Rmd’ + ... + Quitting from lines 294-308 [unnamed-chunk-17] (workflow.Rmd) + Error: processing vignette 'workflow.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘workflow.Rmd’ + + SUMMARY: processing the following files failed: + ‘cont_mixture.Rmd’ ‘workflow.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘grid’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘PoisNor’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# SimMultiCorrData + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/AFialkowski/SimMultiCorrData +* Source code: https://github.com/cran/SimMultiCorrData +* Date/Publication: 2018-06-28 17:37:55 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "SimMultiCorrData")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dist_comp.Rmd’ + ... + + > 1 - pnorm(z_prime) + [1] 0.04999249 + + > plot_sim_pdf_theory(sim_y = H_exp$continuous_variable[, + + 1], Dist = "Exponential", params = 0.5) + + ... + Execution halted + + ‘benefits.Rmd’ using ‘UTF-8’... OK + ‘dist_comp.Rmd’ using ‘UTF-8’... failed + ‘errorloop.Rmd’ using ‘UTF-8’... OK + ‘functions.Rmd’ using ‘UTF-8’... OK + ‘method_comp.Rmd’ using ‘UTF-8’... OK + ‘sixth_validpdf.Rmd’ using ‘UTF-8’... failed + ‘variable_types.Rmd’ using ‘UTF-8’... OK + ‘workflow.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘benefits.Rmd’ using rmarkdown + --- finished re-building ‘benefits.Rmd’ + + --- re-building ‘dist_comp.Rmd’ using rmarkdown + + Quitting from lines 107-109 [unnamed-chunk-11] (dist_comp.Rmd) + Error: processing vignette 'dist_comp.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘dist_comp.Rmd’ + ... + + Quitting from lines 208-214 [unnamed-chunk-15] (sixth_validpdf.Rmd) + Error: processing vignette 'sixth_validpdf.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘sixth_validpdf.Rmd’ + + --- re-building ‘variable_types.Rmd’ using rmarkdown + --- finished re-building ‘variable_types.Rmd’ + + --- re-building ‘workflow.Rmd’ using rmarkdown + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ + ``` + +# SimNPH + +
+ +* Version: 0.5.5 +* GitHub: https://github.com/SimNPH/SimNPH +* Source code: https://github.com/cran/SimNPH +* Date/Publication: 2024-03-04 10:10:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "SimNPH")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(SimNPH) + Loading required package: SimDesign + Loading required package: survival + > + > test_check("SimNPH") + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 343 ] + ... + + `names(actual)`: "x" + `names(expected)`: "x" "y" + + `actual$y` is absent + `expected$y` is a character vector ('mpg') + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 343 ] + Error: Test failures + Execution halted + ``` + +# slendr + +
+ +* Version: 0.9.1 +* GitHub: https://github.com/bodkan/slendr +* Source code: https://github.com/cran/slendr +* Date/Publication: 2024-02-21 23:20:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "slendr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘slendr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: area + > ### Title: Calculate the area covered by the given slendr object + > ### Aliases: area + > + > ### ** Examples + > + > region_a <- region("A", center = c(20, 50), radius = 20) + ... + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggproto_parent(Coord, self)$setup_params(data) + 10. └─ggplot2 (local) setup_params(..., self = self) + 11. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 12. └─ggplot2:::check_logical(expand) + 13. └─ggplot2:::stop_input_type(...) + 14. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette-01-tutorial.Rmd’ + ... + dependencies automatically by running the function `setup_env()`. + + > init_env() + + When sourcing ‘vignette-01-tutorial.R’: + Error: Could not activate slendr's Python environment because it is not + present on your system ('Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2'). + ... + ‘vignette-01-tutorial.Rmd’ using ‘UTF-8’... failed + ‘vignette-02-grid-model.Rmd’ using ‘UTF-8’... failed + ‘vignette-03-interactions.Rmd’ using ‘UTF-8’... failed + ‘vignette-04-nonspatial-models.Rmd’ using ‘UTF-8’... failed + ‘vignette-05-tree-sequences.Rmd’ using ‘UTF-8’... failed + ‘vignette-06-locations.Rmd’ using ‘UTF-8’... failed + ‘vignette-07-backends.Rmd’ using ‘UTF-8’... failed + ‘vignette-08-nonslendr-tskit.Rmd’ using ‘UTF-8’... failed + ‘vignette-09-paper.Rmd’ using ‘UTF-8’... failed + ‘vignette-10-tracts.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.0Mb + sub-directories of 1Mb or more: + doc 3.7Mb + ``` + +# smallsets + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/lydialucchesi/smallsets +* Source code: https://github.com/cran/smallsets +* Date/Publication: 2023-12-05 00:00:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "smallsets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘smallsets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Smallset_Timeline + > ### Title: Smallset Timeline + > ### Aliases: Smallset_Timeline + > + > ### ** Examples + > + > set.seed(145) + > + > Smallset_Timeline( + + data = s_data, + + code = system.file("s_data_preprocess.R", package = "smallsets") + + ) + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘smallsets.Rmd’ + ... + > library(smallsets) + + > set.seed(145) + + > Smallset_Timeline(data = s_data, code = system.file("s_data_preprocess.R", + + package = "smallsets")) + + When sourcing ‘smallsets.R’: + Error: object is not coercible to a unit + Execution halted + + ‘smallsets.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘smallsets.Rmd’ using rmarkdown + + Quitting from lines 36-42 [timeline1] (smallsets.Rmd) + Error: processing vignette 'smallsets.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘smallsets.Rmd’ + + SUMMARY: processing the following file failed: + ‘smallsets.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘gurobi’ + ``` + +# spinifex + +
+ +* Version: 0.3.7.0 +* GitHub: https://github.com/nspyrison/spinifex +* Source code: https://github.com/cran/spinifex +* Date/Publication: 2024-01-29 14:40:02 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "spinifex")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(spinifex) + Loading required package: tourr + -------------------------------------------------------- + spinifex --- version 0.3.7.0 + Please share bugs, suggestions, and feature requests at: + ... + 2. │ └─base::withCallingHandlers(...) + 3. └─spinifex::play_tour_path(tour_path = tpath, data = dat_std, angle = 1) + 4. └─spinifex (local) render_type(frames = tour_df, ...) + 5. ├─plotly::ggplotly(p = gg, tooltip = "tooltip") + 6. └─plotly:::ggplotly.ggplot(p = gg, tooltip = "tooltip") + 7. └─plotly::gg2list(...) + + [ FAIL 3 | WARN 4 | SKIP 0 | PASS 80 ] + Error: Test failures + Execution halted + ``` + +# sport + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/gogonzo/sport +* Source code: https://github.com/cran/sport +* Date/Publication: 2024-01-08 23:50:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "sport")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > test_check("sport") + Loading required package: sport + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_output.R:30:3'): Scale is labelled 'r' ─────────────────────── + p$labels$y not identical to "r". + target is NULL, current is character + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7504 marked UTF-8 strings + ``` + +# spotoroo + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/TengMCing/spotoroo +* Source code: https://github.com/cran/spotoroo +* Date/Publication: 2023-08-21 05:50:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "spotoroo")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(spotoroo) + > + > test_check("spotoroo") + + -------------------------------- SPOTOROO 0.1.4 -------------------------------- + + ... + i Actually got a with text: + argument is of length zero + ── Failure ('test-plot_spotoroo.R:64:3'): plot_spotoroo() works ──────────────── + Expected `plot_spotoroo(result, type = "timeline")` to run without any errors. + i Actually got a with text: + argument is of length zero + + [ FAIL 2 | WARN 5 | SKIP 0 | PASS 65 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Clustering-hot-spots.Rmd’ + ... + + ──────────────────────────────────────────────────────────────────────────────── + + > plot_spotoroo(result, type = "def") + + > plot_spotoroo(result, type = "timeline") + + When sourcing ‘Clustering-hot-spots.R’: + Error: argument is of length zero + Execution halted + + ‘Clustering-hot-spots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Clustering-hot-spots.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘utils’ + All declared Imports should be used. + ``` + +# SqueakR + +
+ +* Version: 1.3.0 +* GitHub: https://github.com/osimon81/SqueakR +* Source code: https://github.com/cran/SqueakR +* Date/Publication: 2022-06-28 09:20:04 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "SqueakR")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘SqueakR.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘SqueakR.Rmd’ + ... + $ experimenters : NULL + $ experimental_data: list() + + > my_new_data <- add_timepoint_data(data_path = "../inst/extdata/Example_Mouse_Data.xlsx", + + t1 = 5, t2 = 25) + Adding call features Excel file to workspace... + + When sourcing ‘SqueakR.R’: + Error: `path` does not exist: ‘../inst/extdata/Example_Mouse_Data.xlsx’ + Execution halted + + ‘SqueakR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + doc 8.2Mb + ``` + +# stability + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/myaseen208/stability +* Source code: https://github.com/cran/stability +* Date/Publication: 2018-10-02 17:50:03 UTC +* Number of recursive dependencies: 47 + +Run `revdepcheck::cloud_details(, "stability")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘stability-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ammi_biplot + > ### Title: Additive Main Effects and Multiplicative Interaction (AMMI) + > ### Biplot + > ### Aliases: ammi_biplot ammi_biplot.default + > + > ### ** Examples + > + ... + > ammi_biplot( + + .data = ge_data + + , .y = Yield + + , .rep = Rep + + , .gen = Gen + + , .env = Env + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ammi_biplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# statgenGWAS + +
+ +* Version: 1.0.9 +* GitHub: https://github.com/Biometris/statgenGWAS +* Source code: https://github.com/cran/statgenGWAS +* Date/Publication: 2022-10-13 15:30:43 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "statgenGWAS")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("statgenGWAS") + + } + + test_GWAS.R................... 0 tests + test_GWAS.R................... 0 tests + ... + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86> + 3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90> + 4: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for + 5: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86> + 6: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90> + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.2Mb + sub-directories of 1Mb or more: + data 7.0Mb + libs 7.2Mb + ``` + +# statgenHTP + +
+ +* Version: 1.0.6.1 +* GitHub: https://github.com/Biometris/statgenHTP +* Source code: https://github.com/cran/statgenHTP +* Date/Publication: 2023-04-14 08:20:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "statgenHTP")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘statgenHTP-Ex.R’ failed + The error most likely occurred in: + + > ### Name: removeSerieOut + > ### Title: Replace outliers for series of observations by NA + > ### Aliases: removeSerieOut + > + > ### ** Examples + > + > ## Run the function to fit P-splines on a subset of genotypes. + ... + 18. │ └─ggplot2:::`+.gg`(...) + 19. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 20. │ ├─ggplot2::ggplot_add(object, p, objectname) + 21. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 22. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 23. └─base::.handleSimpleError(...) + 24. └─purrr (local) h(simpleError(msg, call)) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("statgenHTP") + + } + + test_TP.R..................... 0 tests + test_TP.R..................... 0 tests + ... + test_detectSerieOut.R......... 16 tests 1 fails Error in eval(expr, envir = e) : object 'serieOut1' not found + Calls: ... lapply -> FUN -> eval -> eval -> expect_inherits -> fun + In addition: Warning messages: + 1: 125 failed to parse. + 2: Ignoring unknown labels: + • `colour = ""` + 3: The following genotypes have less than 3 plotIds and are skipped in the outlier detection: + G12 + + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Overview_HTP.Rmd’ + ... + > outVator <- detectSerieOut(corrDat = spatCorrectedVator, + + predDat = predDat, coefDat = coefDat, trait = "EffpsII_corr", + + genotypes = sub .... [TRUNCATED] + + When sourcing ‘Overview_HTP.R’: + Error: ℹ In index: 1. + ℹ With name: y. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Overview_HTP.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Overview_HTP.Rmd’ using rmarkdown + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘asreml’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 9.0Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +# sugrrants + +
+ +* Version: 0.2.9 +* GitHub: https://github.com/earowang/sugrrants +* Source code: https://github.com/cran/sugrrants +* Date/Publication: 2024-03-12 05:20:03 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "sugrrants")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sugrrants-Ex.R’ failed + The error most likely occurred in: + + > ### Name: frame_calendar + > ### Title: Rearrange a temporal data frame to a calendar-based data format + > ### using linear algebra + > ### Aliases: frame_calendar prettify + > + > ### ** Examples + > + ... + + frame_calendar(x = Time, y = Hourly_Counts, date = Date, nrow = 4) + > + > # ggplot + > p1 <- calendar_df %>% + + ggplot(aes(x = .Time, y = .Hourly_Counts, group = Date)) + + + geom_line() + > prettify(p1, size = 3, label.padding = unit(0.15, "lines")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: prettify ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘frame-calendar.Rmd’ + ... + > p1 <- centre_calendar %>% ggplot(aes(x = .Time, y = .Hourly_Counts, + + group = Date)) + geom_line() + + > p1 + + > prettify(p1) + + When sourcing ‘frame-calendar.R’: + Error: argument is of length zero + Execution halted + + ‘frame-calendar.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘frame-calendar.Rmd’ using rmarkdown + ``` + +# superb + +
+ +* Version: 0.95.15 +* GitHub: https://github.com/dcousin3/superb +* Source code: https://github.com/cran/superb +* Date/Publication: 2024-08-17 19:00:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "superb")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘superb-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GRD + > ### Title: Generate random data + > ### Aliases: GRD + > + > ### ** Examples + > + > # Simplest example using all the default arguments: + ... + Difficulty; levels: 1, 2, 3, 4, 5 + 2.Within-Subject Factors ( 1 repeated measures ): + 3.Subjects per group ( 500 total subjects ): + 100 + ------------------------------------------------------------ + > # show the mean performance as a function of difficulty: + > superbPlot(dta, BSFactors = "Difficulty", variables="DV") + Error in superbPlot(dta, BSFactors = "Difficulty", variables = "DV") : + superb::ERROR: The function superbPlot.bar is not a known function for making plots with superbPlot. Exiting... + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("superb") + Loading required package: superb + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 93 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_compatibility.R:36:2'): TESTS (1/1) ──────────────────────────── + ... + 1. ├─testthat::expect_message(...) at test_superbPlot.R:810:5 + 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─superb::superbPlot(...) + + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 93 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CustomizingSuperbPlots.Rmd’ + ... + > mylabels <- c("Verbal", "Numerical", "Spatial", "Creativity", + + "Intrapersonal", "Interpersonal") + + > pltA <- superbPlot(dtaA, WSFactors = "Domain(6)", + + variables = mylabels, adjustments = list(purpose = "difference", + + decorrelation = .... [TRUNCATED] + + ... + ‘Vignette7.Rmd’ using ‘UTF-8’... failed + ‘Vignette8.Rmd’ using ‘UTF-8’... failed + ‘Vignette9.Rmd’ using ‘UTF-8’... failed + ‘VignetteA.Rmd’ using ‘UTF-8’... failed + ‘VignetteB.Rmd’ using ‘UTF-8’... failed + ‘VignetteC.Rmd’ using ‘UTF-8’... failed + ‘VignetteD.Rmd’ using ‘UTF-8’... OK + ‘VignetteE.Rmd’ using ‘UTF-8’... failed + ‘VignetteF.Rmd’ using ‘UTF-8’... failed + ‘VignetteG.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘CustomizingSuperbPlots.Rmd’ using rmarkdown + + Quitting from lines 91-107 [unnamed-chunk-4] (CustomizingSuperbPlots.Rmd) + Error: processing vignette 'CustomizingSuperbPlots.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.raincloud is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘CustomizingSuperbPlots.Rmd’ + + --- re-building ‘TheMakingOf.Rmd’ using rmarkdown + + ... + --- failed re-building ‘Vignette1.Rmd’ + + --- re-building ‘Vignette2.Rmd’ using rmarkdown + + Quitting from lines 39-48 [unnamed-chunk-2] (Vignette2.Rmd) + Error: processing vignette 'Vignette2.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘Vignette2.Rmd’ + + --- re-building ‘Vignette3.Rmd’ using rmarkdown + ``` + +# surveyexplorer + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/surveyexplorer +* Date/Publication: 2024-06-07 09:50:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "surveyexplorer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘surveyexplorer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: multi_freq + > ### Title: Generate an UpSet plot for multiple-choice questions + > ### Aliases: multi_freq + > + > ### ** Examples + > + > + ... + + > + > #Basic Upset plot + > + > #Use `group_by` to partition the question into several groups + > multi_freq(berlinbears, question = dplyr::starts_with('will_eat'), group_by + + = gender) + Error in as.unit(e2) : object is not coercible to a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit + Execution halted + ``` + +# survivalAnalysis + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/survivalAnalysis +* Date/Publication: 2022-02-11 14:00:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "survivalAnalysis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘survivalAnalysis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kaplan_meier_plot + > ### Title: Kaplan Meier plots from survival results. + > ### Aliases: kaplan_meier_plot + > + > ### ** Examples + > + > library(magrittr) + ... + + > survival::aml %>% + + analyse_survival(vars(time, status), x) %>% + + kaplan_meier_plot(break.time.by="breakByMonth", + + xlab=".OS.months", + + risk.table=TRUE, + + ggtheme=ggplot2::theme_bw(10)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘multivariate.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘univariate.Rmd’ + ... + ECOG 2-3 vs. ECOG 1-2 1.41 2.0 2.82 <0.001 + ECOG 1-2 vs. ECOG 2-3 0.35 0.5 0.71 <0.001 + + + + > kaplan_meier_plot(result) + + When sourcing ‘univariate.R’: + Error: argument is of length zero + Execution halted + + ‘multivariate.Rmd’ using ‘UTF-8’... OK + ‘univariate.Rmd’ using ‘UTF-8’... failed + ``` + +# survminer + +
+ +* Version: 0.4.9 +* GitHub: https://github.com/kassambara/survminer +* Source code: https://github.com/cran/survminer +* Date/Publication: 2021-03-09 09:50:03 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "survminer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘survminer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BRCAOV.survInfo + > ### Title: Breast and Ovarian Cancers Survival Information + > ### Aliases: BRCAOV.survInfo + > + > ### ** Examples + > + > data(BRCAOV.survInfo) + ... + The following object is masked from ‘package:survminer’: + + myeloma + + > fit <- survfit(Surv(times, patient.vital_status) ~ admin.disease_code, + + data = BRCAOV.survInfo) + > ggsurvplot(fit, data = BRCAOV.survInfo, risk.table = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggsurvplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(survminer) + Loading required package: ggplot2 + Loading required package: ggpubr + > + > test_check("survminer") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] + ... + 4. └─survminer (local) ``(...) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Informative_Survival_Plots.Rmd’ + ... + + + > fit <- survfit(Surv(times, patient.vital_status) ~ + + admin.disease_code, data = BRCAOV.survInfo) + + > ggsurvplot(fit, data = BRCAOV.survInfo, risk.table = TRUE) + + ... + > ggsurvplot(fit, data = lung, pval = TRUE, pval.method = TRUE) + + When sourcing ‘Specifiying_weights_in_log-rank_comparisons.R’: + Error: argument is of length zero + Execution halted + + ‘Informative_Survival_Plots.Rmd’ using ‘UTF-8’... failed + ‘Playing_with_fonts_and_texts.Rmd’ using ‘UTF-8’... failed + ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ using ‘UTF-8’... failed + ‘ggforest-show-interactions-hazard-ratio.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Informative_Survival_Plots.Rmd’ using rmarkdown + + Quitting from lines 66-72 [unnamed-chunk-4] (Informative_Survival_Plots.Rmd) + Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Informative_Survival_Plots.Rmd’ + + --- re-building ‘Playing_with_fonts_and_texts.Rmd’ using rmarkdown + + ... + --- failed re-building ‘Playing_with_fonts_and_texts.Rmd’ + + --- re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ using rmarkdown + + Quitting from lines 98-99 [unnamed-chunk-4] (Specifiying_weights_in_log-rank_comparisons.Rmd) + Error: processing vignette 'Specifiying_weights_in_log-rank_comparisons.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ + + --- re-building ‘ggforest-show-interactions-hazard-ratio.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 5.6Mb + ``` + +# survParamSim + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/yoshidk6/survParamSim +* Source code: https://github.com/cran/survParamSim +* Date/Publication: 2022-06-03 08:10:02 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "survParamSim")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘survParamSim.Rmd’ + ... + + "Lev+5FU")), depth = as.nu .... [TRUNCATED] + + > survfit.colon <- survfit(Surv(time, status) ~ rx, + + data = colon2) + + > survminer::ggsurvplot(survfit.colon) + + When sourcing ‘survParamSim.R’: + Error: argument is of length zero + Execution halted + + ‘survParamSim.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘survParamSim.Rmd’ using rmarkdown + + Quitting from lines 53-58 [plot_raw_data] (survParamSim.Rmd) + Error: processing vignette 'survParamSim.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘survParamSim.Rmd’ + + SUMMARY: processing the following file failed: + ‘survParamSim.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# survstan + +
+ +* Version: 0.0.7.1 +* GitHub: https://github.com/fndemarqui/survstan +* Source code: https://github.com/cran/survstan +* Date/Publication: 2024-04-12 16:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "survstan")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LRT.Rmd’ + ... + > ipass <- ipass %>% mutate(arm = as.factor(ipass$arm), + + arm = ifelse(arm == 1, "gefitinib", "carboplatin/paclitaxel")) + + > km <- survfit(Surv(time, status) ~ arm, data = ipass) + + > ggsurv(km) + + When sourcing ‘LRT.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LRT.Rmd’ using ‘UTF-8’... failed + ‘survstan.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘LRT.Rmd’ using rmarkdown + + Quitting from lines 31-42 [unnamed-chunk-2] (LRT.Rmd) + Error: processing vignette 'LRT.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘LRT.Rmd’ + + --- re-building ‘survstan.Rmd’ using rmarkdown + --- finished re-building ‘survstan.Rmd’ + + SUMMARY: processing the following file failed: + ‘LRT.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 80.3Mb + sub-directories of 1Mb or more: + libs 79.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# SVMMaj + +
+ +* Version: 0.2.9.2 +* GitHub: NA +* Source code: https://github.com/cran/SVMMaj +* Date/Publication: 2024-08-19 08:20:13 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "SVMMaj")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SVMMaj-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.q.svmmaj + > ### Title: SVM-Maj Algorithm + > ### Aliases: print.q.svmmaj svmmaj svmmaj.default + > + > ### ** Examples + > + > + ... + + > model3 <- svmmaj( + + diabetes$X, diabetes$y, weight.obs = weight.obs, + + spline.knots = 3, spline.degree = 2 + + ) + > plotWeights(model3, plotdim = c(2, 4)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotWeights ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘paper.Rnw’ + ... + + TP FP Precision + negative 0.741 0.259 0.879 + positive 0.817 0.183 0.636 + + > plotWeights(model.spline) + + When sourcing ‘paper.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘paper.Rnw’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘paper.Rnw’ using Sweave + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + + Error: processing vignette 'paper.Rnw' failed with diagnostics: + chunk 20 (label = splineweightsplot) + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building ‘paper.Rnw’ + + SUMMARY: processing the following file failed: + ‘paper.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Sysrecon + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/Sysrecon +* Date/Publication: 2023-02-20 08:50:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "Sysrecon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Sysrecon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Sysrecon + > ### Title: Sysrecon + > ### Aliases: Sysrecon + > + > ### ** Examples + > + > + ... + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic arguments: + • as.Date = as.Date + • yscale_mapping = yscale_mapping + • hang = hang + ℹ Did you misspell an argument name? + Error in as.unit(value) : object is not coercible to a unit + Calls: Sysrecon ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 38 marked UTF-8 strings + ``` + +# tabledown + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/masiraji/tabledown +* Source code: https://github.com/cran/tabledown +* Date/Publication: 2024-05-02 13:40:03 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "tabledown")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tabledown-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggreliability_plotly + > ### Title: A Function for Creating Item Response Theory based reliability + > ### plot based on plotly. + > ### Aliases: ggreliability_plotly + > + > ### ** Examples + > + ... + Iteration: 17, Log-Lik: -5351.363, Max-Change: 0.00011 + Iteration: 18, Log-Lik: -5351.363, Max-Change: 0.00054 + Iteration: 19, Log-Lik: -5351.363, Max-Change: 0.00012 + Iteration: 20, Log-Lik: -5351.363, Max-Change: 0.00035 + Iteration: 21, Log-Lik: -5351.363, Max-Change: 0.00010 + > + > plot <- ggreliability_plotly(data, model) + Error in pm[[2]] : subscript out of bounds + Calls: ggreliability_plotly -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 551 marked UTF-8 strings + ``` + +# tcgaViz + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/tcgaViz +* Date/Publication: 2023-04-04 15:40:02 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "tcgaViz")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + # `P-value adjusted` , Significance + + > plot(df, stats = stats) + + When sourcing ‘Tutorial.R’: + Error: ℹ In index: 1. + ℹ With name: value. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 35-43 [plot] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: value. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# TCIU + +
+ +* Version: 1.2.6 +* GitHub: https://github.com/SOCR/TCIU +* Source code: https://github.com/cran/TCIU +* Date/Publication: 2024-05-17 23:40:21 UTC +* Number of recursive dependencies: 163 + +Run `revdepcheck::cloud_details(, "TCIU")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TCIU-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fmri_image + > ### Title: interactive graph object of the fMRI image + > ### Aliases: fmri_image + > + > ### ** Examples + > + > fmri_generate = fmri_simulate_func(dim_data = c(64, 64, 40), mask = mask) + > fmri_image(fmri_generate$fmri_data, option='manually', voxel_location = c(40,22,33), time = 4) + Error in pm[[2]] : subscript out of bounds + Calls: fmri_image ... add_trace -> add_data -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tciu-LT-kimesurface.Rmd’ + ... + > require(ggplot2) + + > sample_save[[1]] + + > sample_save[[2]] + + When sourcing ‘tciu-LT-kimesurface.R’: + ... + + > fmri_image(fmri_generate$fmri_data, option = "manually", + + voxel_location = c(40, 22, 33), time = 4) + + When sourcing ‘tciu-fMRI-analytics.R’: + Error: subscript out of bounds + Execution halted + + ‘tciu-LT-kimesurface.Rmd’ using ‘UTF-8’... failed + ‘tciu-fMRI-analytics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tciu-LT-kimesurface.Rmd’ using rmarkdown + + Quitting from lines 159-160 [unnamed-chunk-5] (tciu-LT-kimesurface.Rmd) + Error: processing vignette 'tciu-LT-kimesurface.Rmd' failed with diagnostics: + unused arguments (list(1, 2), list(list("black", 0.727272727272727, 1, "butt", FALSE, TRUE), list("white", "black", 0.727272727272727, 1, TRUE), list("", "plain", "black", 16, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 4, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 4, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, + NULL, 1, -90, NULL, c(0, 0, 0, 4), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(3.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 3.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 3.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, + NULL, NULL, c(0, 3.2, 0, 3.2), NULL, TRUE), list("grey20", NULL, NULL, NULL, FALSE, TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 4, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), c(8, 8, 8, 8), 16, NULL, NULL, NULL, 1.2, NULL, NULL, 8, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, + NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, "bold", "black", 14, 0, NULL, NULL, NULL, NULL, NULL, FALSE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 16, list("grey92", NA, NULL, NULL, TRUE), list(), 8, NULL, NULL, list("white", NULL, NULL, NULL, FALSE, TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, TRUE), NULL, list(), NULL, list(), FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0.5, 1, NULL, + ... + Quitting from lines 184-185 [unnamed-chunk-5] (tciu-fMRI-analytics.Rmd) + Error: processing vignette 'tciu-fMRI-analytics.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘tciu-fMRI-analytics.Rmd’ + + SUMMARY: processing the following files failed: + ‘tciu-LT-kimesurface.Rmd’ ‘tciu-fMRI-analytics.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 14.1Mb + sub-directories of 1Mb or more: + data 1.5Mb + doc 12.0Mb + ``` + +# tcpl + +
+ +* Version: 3.1.0 +* GitHub: https://github.com/USEPA/CompTox-ToxCast-tcpl +* Source code: https://github.com/cran/tcpl +* Date/Publication: 2023-10-06 19:50:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "tcpl")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 2 | WARN 4 | SKIP 3 | PASS 55 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Data_processing-Archive_tcpl_v2.Rmd’ + ... + Loaded L4 AEID2 (7 rows; 0.03 secs) + Processed L5 AEID2 (7 rows; 0.08 secs) + Writing level 5 data for 2 ids... + Completed delete cascade for 2 ids (0.03 secs) + Writing level 5 complete. (0.03 secs) + Loaded L5 AEID1 (6 rows; 0.11 secs) + + When sourcing ‘Data_processing-Archive_tcpl_v2.R’: + Error: attempt to apply non-function + Execution halted + + ‘Assay_Registration.Rmd’ using ‘UTF-8’... OK + ‘Data_processing-Archive_tcpl_v2.Rmd’ using ‘UTF-8’... failed + ‘Data_processing.Rmd’ using ‘UTF-8’... OK + ‘Data_retrieval.Rmd’ using ‘UTF-8’... OK + ‘Introduction_Appendices.Rmd’ using ‘UTF-8’... OK + ``` + +# tern + +
+ +* Version: 0.9.5 +* GitHub: https://github.com/insightsengineering/tern +* Source code: https://github.com/cran/tern +* Date/Publication: 2024-06-21 04:40:06 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "tern")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tern-Ex.R’ failed + The error most likely occurred in: + + > ### Name: g_km + > ### Title: Kaplan-Meier plot + > ### Aliases: g_km kaplan_meier + > + > ### ** Examples + > + > library(dplyr) + ... + + control_surv = control_surv_timepoint(conf_level = 0.9), + + col = c("grey25", "grey50", "grey75"), + + annot_at_risk_title = FALSE, + + lty = 1:3, + + font_size = 8 + + ) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 4.5Mb + help 3.3Mb + ``` + +# thematic + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/rstudio/thematic +* Source code: https://github.com/cran/thematic +* Date/Publication: 2024-07-29 15:50:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "thematic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘thematic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sequential_gradient + > ### Title: Control parameters of the sequential colorscale + > ### Aliases: sequential_gradient + > + > ### ** Examples + > + > + > # Gradient from fg to accent + > fg <- sequential_gradient(1, 0) + > thematic_on("black", "white", "salmon", sequential = fg) + > ggplot2::qplot(1:10, 1:10, color = 1:10) + Warning: `qplot()` was deprecated in ggplot2 3.4.0. + Error in adjust_color(user_default$colour, bg, fg, accent) : + Internal error: adjust_color() expects an input of length 1 + Calls: ... -> -> update_defaults -> adjust_color + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(thematic) + > + > test_check("thematic") + [ FAIL 9 | WARN 1 | SKIP 7 | PASS 27 ] + + ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ + ... + 10. └─base::Map(...) + 11. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 12. └─thematic (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 13. ├─ggplot2::update_geom_defaults(...) + 14. │ └─ggplot2:::update_defaults(geom, "Geom", new, env = parent.frame()) + 15. └─thematic:::adjust_color(user_default$colour, bg, fg, accent) + + [ FAIL 9 | WARN 1 | SKIP 7 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +# Thermistor + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/Thermistor +* Date/Publication: 2024-04-05 15:43:02 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "Thermistor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Thermistor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_voltageCurve + > ### Title: Plot the V-DeltaT Curve + > ### Aliases: plot_voltageCurve + > + > ### ** Examples + > + > ### only target curve + ... + > ThVal <- CompValues$ThVal + > ThBeta <- CompValues$ThBeta + > Vnew <- voltageCurve(Tdata, R_id, Res, ThVal, ThBeta) + > plot_voltageCurve(Tdata, OnlyTarget = FALSE, Pdata = Vnew) + Warning in ggplot2::geom_line(ggplot2::aes(x = xid, y = Vdata, colour = "target", : + Ignoring unknown aesthetics: shape + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# tidybayes + +
+ +* Version: 3.0.6 +* GitHub: https://github.com/mjskay/tidybayes +* Source code: https://github.com/cran/tidybayes +* Date/Publication: 2023-08-12 23:30:02 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "tidybayes")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidybayes-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compare_levels + > ### Title: Compare the value of draws of some variable from a Bayesian + > ### model for different levels of a factor + > ### Aliases: compare_levels + > ### Keywords: manip + > + > ### ** Examples + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This is necessary because some tests fail otherwise; see https://github.com/hadley/testthat/issues/144 + > Sys.setenv("R_TESTS" = "") + > + > library(testthat) + > library(tidybayes) + > + > test_check("tidybayes") + ... + • test.geom_interval/grouped-intervals-h-stat.svg + • test.geom_pointinterval/grouped-pointintervals-h-stat.svg + • test.stat_dist_slabinterval/ccdfintervalh-using-args.svg + • test.stat_eye/one-parameter-horizontal-eye-mode-hdi.svg + • test.stat_eye/one-parameter-horizontal-half-eye.svg + • test.stat_eye/one-parameter-vertical-eye.svg + • test.stat_eye/one-parameter-vertical-halfeye.svg + • test.stat_eye/two-parameter-factor-horizontal-eye-fill.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tidy-brms.Rmd’ + ... + + ]) %>% median_qi(condition_mean = b_Intercept + r_condition, + + .width = c(0.95, 0 .... [TRUNCATED] + + When sourcing ‘tidy-brms.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + + When sourcing ‘tidybayes.R’: + Error: error in evaluating the argument 'object' in selecting a method for function 'sampling': object 'ABC_stan' not found + Execution halted + + ‘tidy-brms.Rmd’ using ‘UTF-8’... failed + ‘tidy-posterior.Rmd’ using ‘UTF-8’... failed + ‘tidy-rstanarm.Rmd’ using ‘UTF-8’... failed + ‘tidybayes-residuals.Rmd’ using ‘UTF-8’... failed + ‘tidybayes.Rmd’ using ‘UTF-8’... failed + ``` + +# tidycat + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/guyabel/tidycat +* Source code: https://github.com/cran/tidycat +* Date/Publication: 2021-08-02 04:20:01 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "tidycat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidycat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tidy_categorical + > ### Title: Expand broom::tidy() Outputs for Categorical Parameter Estimates + > ### Aliases: tidy_categorical + > + > ### ** Examples + > + > # strip ordering in factors (currently ordered factor not supported) + ... + > ggplot(data = d0, + + mapping = aes(x = level, colour = reference, + + y = estimate, ymin = conf.low, ymax = conf.high)) + + + facet_row(facets = vars(variable), scales = "free_x", space = "free") + + + geom_hline(yintercept = 0, linetype = "dashed") + + + geom_pointrange() + + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + Error in space$x : $ operator is invalid for atomic vectors + Calls: ... -> draw_panels -> -> init_gtable + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘intro.Rmd’ + ... + + > library(ggforce) + + > ggplot(data = d0, mapping = aes(x = level, y = estimate, + + colour = reference, ymin = conf.low, ymax = conf.high)) + + + facet_col(facets = .... [TRUNCATED] + + When sourcing ‘intro.R’: + Error: $ operator is invalid for atomic vectors + Execution halted + + ‘intro.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tidyr’ + All declared Imports should be used. + ``` + +# tidyCDISC + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/Biogen-Inc/tidyCDISC +* Source code: https://github.com/cran/tidyCDISC +* Date/Publication: 2023-03-16 14:20:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "tidyCDISC")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(tidyCDISC) + > library(shinyjs) + + Attaching package: 'shinyjs' + + ... + 6. ├─plotly::config(...) + 7. │ └─plotly:::modify_list(p$x$config, args) + 8. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) + 9. │ │ └─base::stopifnot(is.list(x), is.list(val)) + 10. │ └─x %||% list() + 11. └─plotly::layout(...) + + [ FAIL 1 | WARN 1 | SKIP 15 | PASS 91 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.0Mb + doc 1.8Mb + ``` + +# tidydr + +
+ +* Version: 0.0.5 +* GitHub: https://github.com/YuLab-SMU/tidydr +* Source code: https://github.com/cran/tidydr +* Date/Publication: 2023-03-08 09:20:02 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "tidydr")` for more info + +
+ +## Newly broken + +* checking whether package ‘tidydr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel -# inTextSummaryTable (default access) - -# inventorize (unknown) - -``` -#
-# -# * Version: 1.1.1 -# * GitHub: NA -# * Source code: https://github.com/cran/inventorize -# * Date/Publication: 2022-05-31 22:20:09 UTC -# * Number of recursive dependencies: 71 -# -# Run `revdepcheck::cloud_details(, "inventorize")` for more info -# -#
-# -# ## Newly broken -# -# * checking whether package ‘inventorize’ can be installed ... ERROR -# ``` -# Installation failed. -# See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. -# ``` -# -# ## Installation -# -# ### Devel -# -# ``` -# * installing *source* package ‘inventorize’ ... -# ** package ‘inventorize’ successfully unpacked and MD5 sums checked -# ** using staged installation -# ** R -# ** byte-compile and prepare package for lazy loading -# Error in pm[[2]] : subscript out of bounds -# Error: unable to load R code in package ‘inventorize’ -# Execution halted -# ERROR: lazy loading failed for package ‘inventorize’ -# * removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ -# -# -# ``` -# ### CRAN -# -# ``` -# * installing *source* package ‘inventorize’ ... -# ** package ‘inventorize’ successfully unpacked and MD5 sums checked -# ** using staged installation -# ** R -# ** byte-compile and prepare package for lazy loading -# Warning in qgamma(service_level, alpha, beta) : NaNs produced -# Warning in qgamma(service_level, alpha, beta) : NaNs produced -# ** help -# *** installing help indices -# ** building package indices -# ** testing if installed package can be loaded from temporary location -# ** testing if installed package can be loaded from final location -# ** testing if installed package keeps a record of temporary installation path -# * DONE (inventorize) -# -# -# ``` ``` -# karel (gganimate) - -# kDGLM (plotly) - -# latentcor (plotly) - -# lcars (device issue) - -# lemon (resolve theme) - -# lfproQC (plotly) - -# LMoFit (saved to disk) - -# manydata (plot slots) - -# MARVEL (ggnewscale) - -# MBNMAdose (cannot reproduce) - -# MBNMAtime (ggdist) - -# MetaNet (ggnewscale) - -# metR (fixed in dev) - -# migraph (missing labels) - -# MiMIR (plotly) +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'len0_null' not found +Error: unable to load R code in package ‘tidydr’ +Execution halted +ERROR: lazy loading failed for package ‘tidydr’ +* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ -# miRetrieve (plotly) - -# misspi (plotly) - -# mizer (cannot reproduce) - -# mlr3spatiotempcv (patchwork) - -# mlr3viz (patchwork) - -# modeltime.resample (plotly) - -# move (false positive) - -# mtb (missing labels) - -# neatmaps (plotly) - -# NetFACS (false positive) - -# NeuralSens (ggnewscale) - -# NHSRplotthedots (missing labels) - -# NIMAA (plotly) - -# OBIC (patchwork) - -# OmicNavigator (plotly) - -# oncomsm (patchwork) - -# pafr (missing labels) - -# patchwork (patchwork) - -# pathviewr (missing labels) - -# pcutils (patchwork) - -# pdxTrees (gganimate) - -# personalized (plotly) - -# phylepic (ggnewscale) - -# Plasmidprofiler (plotly) - -# platetools (faulty tests) - -# plotDK (missing labels) - -# plotly (plotly) - -# pmartR (unknown) ``` -#
-# -# * Version: 2.4.5 -# * GitHub: https://github.com/pmartR/pmartR -# * Source code: https://github.com/cran/pmartR -# * Date/Publication: 2024-05-21 15:50:02 UTC -# * Number of recursive dependencies: 149 -# -# Run `revdepcheck::cloud_details(, "pmartR")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(pmartR) -# > -# > test_check("pmartR") -# [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] -# -# ══ Skipped tests (11) ══════════════════════════════════════════════════════════ -# ... -# • plots/plot-spansres-color-high-color-low.svg -# • plots/plot-spansres.svg -# • plots/plot-statres-anova-volcano.svg -# • plots/plot-statres-anova.svg -# • plots/plot-statres-combined-volcano.svg -# • plots/plot-statres-combined.svg -# • plots/plot-statres-gtest.svg -# • plots/plot-totalcountfilt.svg -# Error: Test failures -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 10.4Mb -# sub-directories of 1Mb or more: -# R 1.5Mb -# help 1.5Mb -# libs 6.3Mb -# ``` -``` - -# pmxTools (ggdist) - -# posterior (ggdist) - -# PPQplan (plotly) - -# ppseq (plotly) - -# precrec (patchwork) - -# priorsense (ggdist) - -# ProAE (ggnewscale) - -# probably (missing labels) - -# processmapR (plotly) - -# psborrow (missing labels) - -# r2dii.plot (missing labels) - -# Radviz (accessing defaults) - -# rassta (plotly) - -# REddyProc (false positive) - -# redist (patchwork) - -# reReg (length 0 width) - -# reservr (patchwork) - -# rKOMICS (unknown) +### CRAN ``` -#
-# -# * Version: 1.3 -# * GitHub: NA -# * Source code: https://github.com/cran/rKOMICS -# * Date/Publication: 2023-06-29 22:40:03 UTC -# * Number of recursive dependencies: 128 -# -# Run `revdepcheck::cloud_details(, "rKOMICS")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘rKOMICS-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: msc.pca -# > ### Title: Prinicple Component Analysis based on MSC -# > ### Aliases: msc.pca -# > -# > ### ** Examples -# > -# > data(matrices) -# ... -# 11. │ └─base::withCallingHandlers(...) -# 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) -# 13. └─l$compute_geom_2(d, theme = plot$theme) -# 14. └─ggplot2 (local) compute_geom_2(..., self = self) -# 15. └─self$geom$use_defaults(...) -# 16. └─ggplot2 (local) use_defaults(..., self = self) -# 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) -# 18. └─cli::cli_abort(...) -# 19. └─rlang::abort(...) -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 24.8Mb -# sub-directories of 1Mb or more: -# extdata 24.0Mb -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘example.Rnw’ using Sweave -# Loading required package: viridisLite -# Warning: Removed 95 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 89 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 149 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 286 rows containing non-finite outside the scale range -# ... -# l.5 \usepackage -# {xcolor}^^M -# ! ==> Fatal error occurred, no output PDF file produced! -# --- failed re-building ‘example.Rnw’ -# -# SUMMARY: processing the following file failed: -# ‘example.Rnw’ -# -# Error: Vignette re-building failed. -# Execution halted -# ``` -``` - -# RKorAPClient (missing labels) - -# RNAseqQC (patchwork) - -# roahd (plotly) +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (tidydr) -# romic (plotly) -# roptions (plotly) - -# santaR (plot slots) - -# scdtb (missing labels) - -# scoringutils (ggdist) - -# scUtils (missing labels) - -# SCVA (plotly) - -# SDMtune (missing labels) - -# SeaVal (plotly) - -# sgsR (missing labels) - -# SHAPforxgboost (ggforce) - -# SHELF (unknown) - -``` -#
-# -# * Version: 1.10.0 -# * GitHub: https://github.com/OakleyJ/SHELF -# * Source code: https://github.com/cran/SHELF -# * Date/Publication: 2024-05-07 14:20:03 UTC -# * Number of recursive dependencies: 126 -# -# Run `revdepcheck::cloud_details(, "SHELF")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown -# ``` ``` - -# shinipsum (plot slots) - -# SimNPH (missing labels) - -# smallsets (patchwork) - -# spbal (empty sf) - -# spinifex (plotly) - -# sport (missing labels) - -# SqueakR (false positive) - -# statgenGWAS (device issue) - -# surveyexplorer (ggupset) - -# Sysrecon (patchwork) - -# tabledown (plotly) - -# TCIU (plotly) - -# tensorEVD (ggnewscale) - -# thematic (thematic) - -# tidybayes (ggdist) - -# tidycat (ggforce) - -# tidyCDISC (plotly) - -# tidydr (uses internals) - -# tidysdm (patchwork) - -# tidytreatment (ggdist) - -# timetk (plotly) - -# tinyarray (patchwork) - -# tornado (length 0 width) - -# TOSTER (ggdist) - -# TreatmentPatterns (plotly) - -# trelliscopejs (plotly) - -# tricolore (ggtern) - -# triptych (patchwork) - -# tsnet (ggdist) - -# umiAnalyzer (plotly) - -# valr (missing labels) - -# vivaldi (plotly) - -# vivid (ggnewscale) - -# vvshiny (plotly) - -# wilson (plotly) - -# xaringanthemer (default access) - -# yamlet (missing labels) +# tidysdm + +
+ +* Version: 0.9.5 +* GitHub: https://github.com/EvolEcolGroup/tidysdm +* Source code: https://github.com/cran/tidysdm +* Date/Publication: 2024-06-23 19:40:02 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "tidysdm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘a0_tidysdm_overview.Rmd’ + ... + > climate_vars <- names(climate_present) + + > lacerta_thin <- lacerta_thin %>% bind_cols(terra::extract(climate_present, + + lacerta_thin, ID = FALSE)) + + > lacerta_thin %>% plot_pres_vs_bg(class) + + When sourcing ‘a0_tidysdm_overview.R’: + Error: object is not a unit + Execution halted + + ‘a0_tidysdm_overview.Rmd’ using ‘UTF-8’... failed + ‘a1_palaeodata_application.Rmd’ using ‘UTF-8’... OK + ‘a2_tidymodels_additions.Rmd’ using ‘UTF-8’... OK + ‘a3_troubleshooting.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘a0_tidysdm_overview.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 2.0Mb + ``` + +# tidySEM + +
+ +* Version: 0.2.7 +* GitHub: https://github.com/cjvanlissa/tidySEM +* Source code: https://github.com/cran/tidySEM +* Date/Publication: 2024-06-04 09:46:01 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "tidySEM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidySEM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: edit_graph + > ### Title: Edit graph elements + > ### Aliases: edit_graph edit_nodes edit_edges + > + > ### ** Examples + > + > p <- prepare_graph(layout = get_layout("x", rows = 1)) + > p <- edit_graph(p, {colour = "blue"}, element = "nodes") + > plot(p) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(tidySEM) + Loading required package: OpenMx + To take full advantage of multiple cores, use: + mxOption(key='Number of Threads', value=parallel::detectCores()) #now + Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx) + Registered S3 method overwritten by 'tidySEM': + ... + 4. └─tidySEM:::.plot_edges_internal(p, df_edges) + 5. └─ggplot2:::`+.gg`(p, do.call(geom_path, argslist)) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 17 | WARN 1 | SKIP 6 | PASS 65 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Plotting_graphs.Rmd’ + ... + + > suppressWarnings({ + + HS.model <- " visual =~ x1 + x2 + x3\n textual =~ x4 + x5 + x6\n speed =~ x7 + x8 + x9 " + + .... [TRUNCATED] + + > p <- graph_sem(model = fit, text_size = 2, fix_coord = TRUE) + + ... + + ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK + ‘Plotting_graphs.Rmd’ using ‘UTF-8’... failed + ‘SMART_LCA_checklist.Rmd’ using ‘UTF-8’... OK + ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK + ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK + ‘lca_lcga.Rmd’ using ‘UTF-8’... OK + ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK + ‘sem_graph.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Generating_syntax.Rmd’ using rmarkdown + --- finished re-building ‘Generating_syntax.Rmd’ + + --- re-building ‘Plotting_graphs.Rmd’ using rmarkdown + + Quitting from lines 77-80 [unnamed-chunk-5] (Plotting_graphs.Rmd) + Error: processing vignette 'Plotting_graphs.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Plotting_graphs.Rmd’ + ... + Quitting from lines 48-51 [unnamed-chunk-3] (sem_graph.Rmd) + Error: processing vignette 'sem_graph.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘sem_graph.Rmd’ + + SUMMARY: processing the following files failed: + ‘Plotting_graphs.Rmd’ ‘sem_graph.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# tidytreatment + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/bonStats/tidytreatment +* Source code: https://github.com/cran/tidytreatment +* Date/Publication: 2022-02-21 09:00:07 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "tidytreatment")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘use-tidytreatment-BART.Rmd’ + ... + + by = ".row") %>% ggplot() + stat_halfeye(aes(x = z, y = fit)) + + + facet_wrap(~c1, l .... [TRUNCATED] + + When sourcing ‘use-tidytreatment-BART.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘use-tidytreatment-BART.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘use-tidytreatment-BART.Rmd’ using rmarkdown + + Quitting from lines 163-177 [plot-tidy-bart] (use-tidytreatment-BART.Rmd) + Error: processing vignette 'use-tidytreatment-BART.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + ... + NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("white", NA, NULL, NULL, TRUE), list(NULL, "grey20", NULL, NULL, TRUE), NULL, NULL, NULL, list("grey92", + NULL, NULL, NULL, FALSE, "grey92", TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", + NULL, NULL, list("grey85", "grey20", NULL, NULL, TRUE), NULL, NULL, "on", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘use-tidytreatment-BART.Rmd’ + + SUMMARY: processing the following file failed: + ‘use-tidytreatment-BART.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘bartMachine’ + ``` + +# timeplyr + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/NicChr/timeplyr +* Source code: https://github.com/cran/timeplyr +* Date/Publication: 2024-08-17 13:40:02 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "timeplyr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘timeplyr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: time_ggplot + > ### Title: Quick time-series ggplot + > ### Aliases: time_ggplot + > + > ### ** Examples + > + > library(dplyr) + ... + > data.table::setDTthreads(threads = 2L) + > collapse::set_collapse(nthreads = 1L) + > ## End(Don't show) + > # It's as easy as this + > AirPassengers %>% + + ts_as_tibble() %>% + + time_ggplot(time, value) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# timetk + +
+ +* Version: 2.9.0 +* GitHub: https://github.com/business-science/timetk +* Source code: https://github.com/cran/timetk +* Date/Publication: 2023-10-31 22:30:02 UTC +* Number of recursive dependencies: 205 + +Run `revdepcheck::cloud_details(, "timetk")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 7. └─timetk:::plot_time_series.grouped_df(...) + 8. ├─timetk::plot_time_series(...) + 9. └─timetk:::plot_time_series.data.frame(...) + 10. ├─plotly::ggplotly(g, dynamicTicks = TRUE) + 11. └─plotly:::ggplotly.ggplot(g, dynamicTicks = TRUE) + 12. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 406 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2750 marked UTF-8 strings + ``` + +# tinyarray + +
+ +* Version: 2.4.2 +* GitHub: https://github.com/xjsun1221/tinyarray +* Source code: https://github.com/cran/tinyarray +* Date/Publication: 2024-06-13 14:20:02 UTC +* Number of recursive dependencies: 243 + +Run `revdepcheck::cloud_details(, "tinyarray")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tinyarray-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box_surv + > ### Title: box_surv + > ### Aliases: box_surv + > + > ### ** Examples + > + > if(requireNamespace("ggpubr",quietly = TRUE)) { + + k = box_surv(log2(exp_hub1+1),exprSet_hub1,meta1);k[[1]] + + }else{ + + warning("Package 'ggpubr' needed for this function to work. + + Please install it by install.packages('ggpubr')") + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: box_surv ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ComplexHeatmap’ + ``` + +# tipmap + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/Boehringer-Ingelheim/tipmap +* Source code: https://github.com/cran/tipmap +* Date/Publication: 2023-08-14 10:30:03 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "tipmap")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + + MAP Prior MCMC sample: + mean sd 2.5% 50% 97.5% + theta_resp_pred 1.43 0.356 0.661 1.44 2.1 + + > plot(map_mcmc)$forest_model + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘expert_elicitation.Rmd’ using ‘UTF-8’... OK + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘expert_elicitation.Rmd’ using rmarkdown + ``` + +# tornado + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/bertcarnell/tornado +* Source code: https://github.com/cran/tornado +* Date/Publication: 2024-01-21 17:30:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "tornado")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tornado-Ex.R’ failed + The error most likely occurred in: + + > ### Name: importance.cv.glmnet + > ### Title: Plot Variable Importance for a GLMNET model + > ### Aliases: importance.cv.glmnet + > + > ### ** Examples + > + > if (requireNamespace("glmnet", quietly = TRUE)) + ... + + form <- formula(mpg ~ cyl*wt*hp) + + mf <- model.frame(form, data = mtcars) + + mm <- model.matrix(mf, mf) + + gtest <- glmnet::cv.glmnet(x = mm, y = mtcars$mpg, family = "gaussian") + + imp <- importance(gtest, mtcars, form, nperm = 50) + + plot(imp) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (require(testthat)) + + { + + library(tornado) + + + + test_check("tornado") + + } + Loading required package: testthat + ... + 2. └─tornado:::plot.tornado_plot(torn, plot = FALSE, xlabel = "Probability of Class 1") + 3. └─ggplot2:::`+.gg`(...) + 4. └─ggplot2:::add_ggplot(e1, e2, e2name) + 5. ├─ggplot2::ggplot_add(object, p, objectname) + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 28 | WARN 14 | SKIP 0 | PASS 86 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tornadoVignette.Rmd’ + ... + > lm1 <- lm(mpg ~ cyl * wt * hp, data = mtcars) + + > torn1 <- tornado::tornado(lm1, type = "PercentChange", + + alpha = 0.1) + + > plot(torn1, xlabel = "MPG", geom_bar_control = list(width = 0.4)) + + When sourcing ‘tornadoVignette.R’: + Error: argument is of length zero + Execution halted + + ‘tornadoVignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tornadoVignette.Rmd’ using rmarkdown + + Quitting from lines 106-109 [lm1] (tornadoVignette.Rmd) + Error: processing vignette 'tornadoVignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘tornadoVignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘tornadoVignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# TOSTER + +
+ +* Version: 0.8.3 +* GitHub: NA +* Source code: https://github.com/cran/TOSTER +* Date/Publication: 2024-05-08 16:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "TOSTER")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TOSTER-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dataTOSTone + > ### Title: TOST One Sample T-Test + > ### Aliases: dataTOSTone + > + > ### ** Examples + > + > library("TOSTER") + ... + N Mean Median SD SE + ───────────────────────────────────────────────────────────────────────── + Sepal.Width 150 3.057333 3.000000 0.4358663 0.03558833 + ───────────────────────────────────────────────────────────────────────── + + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.727272727272727, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.727272727272727, 1, TRUE), list("", "plain", "black", 16, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.727272727272727, 0.727272727272727, 1, 1, "", 5.62335685623357, 2.18181818181818, 19, TRUE), 8, c(8, 8, 8, 8), NULL, NULL, list(NULL, NULL, "#333333", NULL, NULL, NULL, NULL, + NULL, c(10, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 4, 0), NULL, TRUE), NULL, list(NULL, NULL, "#333333", NULL, NULL, NULL, 90, NULL, c(0, 10, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 4), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, "#333333", NULL, NULL, NULL, NULL, NULL, c(5, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NU + Calls: ... -> -> -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(TOSTER) + + Attaching package: 'TOSTER' + + The following object is masked from 'package:testthat': + ... + 26. └─base::Map(...) + 27. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 28. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 29. └─layer$compute_geom_2(key, single_params, theme) + 30. └─ggplot2 (local) compute_geom_2(..., self = self) + 31. └─self$geom$use_defaults(...) + + [ FAIL 8 | WARN 0 | SKIP 0 | PASS 1034 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘IntroTOSTt.Rmd’ + ... + mean of x mean of y + 0.75 2.33 + + + > plot(res1, type = "cd") + + When sourcing ‘IntroTOSTt.R’: + ... + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, "bold", NULL, 11, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, list + Execution halted + + ‘IntroTOSTt.Rmd’ using ‘UTF-8’... failed + ‘IntroductionToTOSTER.Rmd’ using ‘UTF-8’... OK + ‘SMD_calcs.Rmd’ using ‘UTF-8’... OK + ‘correlations.Rmd’ using ‘UTF-8’... OK + ‘robustTOST.Rmd’ using ‘UTF-8’... failed + ‘the_ftestTOSTER.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘IntroTOSTt.Rmd’ using rmarkdown + ``` + +# TreatmentPatterns + +
+ +* Version: 2.6.9 +* GitHub: https://github.com/darwin-eu/TreatmentPatterns +* Source code: https://github.com/cran/TreatmentPatterns +* Date/Publication: 2024-09-02 12:40:06 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "TreatmentPatterns")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 22. ├─testthat::expect_s3_class(output$charAgePlot$html, "html") at test-CharacterizationPlots.R:50:9 + 23. │ └─testthat::quasi_label(enquo(object), arg = "object") + 24. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 25. ├─output$charAgePlot + 26. └─shiny:::`$.shinyoutput`(output, charAgePlot) + 27. └─.subset2(x, "impl")$getOutput(name) + + [ FAIL 1 | WARN 39 | SKIP 21 | PASS 138 ] + Error: Test failures + Execution halted + ``` + +# TreatmentSelection + +
+ +* Version: 2.1.1 +* GitHub: NA +* Source code: https://github.com/cran/TreatmentSelection +* Date/Publication: 2017-08-11 18:55:47 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "TreatmentSelection")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TreatmentSelection-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compare.trtsel + > ### Title: compare the performance of two treatment selection markers + > ### Aliases: compare.trtsel + > + > ### ** Examples + > + > + ... + > # Plot treatment effect curves with pointwise confidence intervals + > ## use more bootstraps in practice + > compare(x = trtsel.Y1, x2 = trtsel.Y2, + + bootstraps = 10, plot = TRUE, + + ci = "horizontal", conf.bands = TRUE) + Bootstrap bias-correction will be implemented to correct for over-optimism bias in estimation. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: compare ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# TreeDep + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/TreeDep +* Date/Publication: 2018-12-02 17:50:03 UTC +* Number of recursive dependencies: 32 + +Run `revdepcheck::cloud_details(, "TreeDep")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TreeDep-Ex.R’ failed + The error most likely occurred in: + + > ### Name: TreeDep_plot + > ### Title: TreeDep_plot - Generates a plot for selected variables and + > ### dates. + > ### Aliases: TreeDep_plot + > + > ### ** Examples + > + ... + + start_day = 25, + + stop_day = 3) + Warning: Removed 12 rows containing missing values or values outside the scale range + (`geom_line()`). + Warning: Removed 12 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# TreeDist + +
+ +* Version: 2.9.1 +* GitHub: https://github.com/ms609/TreeDist +* Source code: https://github.com/cran/TreeDist +* Date/Publication: 2024-09-07 09:20:02 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "TreeDist")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘treespace.Rmd’ + ... + [1] "Epoch: 3 finished. 212 datapoints changed bestmatch" + [1] "Epoch: 4 started" + [1] "Epoch: 4 finished. 203 datapoints changed bestmatch" + [1] "Epoch: 5 started" + [1] "Epoch: 5 finished. 165 datapoints changed bestmatch" + [1] "---- Esom Training Finished ----" + + ... + + ‘Generalized-RF.Rmd’ using ‘UTF-8’... OK + ‘Robinson-Foulds.Rmd’ using ‘UTF-8’... OK + ‘Using-TreeDist.Rmd’ using ‘UTF-8’... OK + ‘compare-treesets.Rmd’ using ‘UTF-8’... OK + ‘different-leaves.Rmd’ using ‘UTF-8’... OK + ‘information.Rmd’ using ‘UTF-8’... OK + ‘landscapes.Rmd’ using ‘UTF-8’... OK + ‘treespace.Rmd’ using ‘UTF-8’... failed + ‘using-distances.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Generalized-RF.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.7Mb + sub-directories of 1Mb or more: + doc 1.2Mb + libs 5.9Mb + ``` + +# treeheatr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/trang1618/treeheatr +* Source code: https://github.com/cran/treeheatr +* Date/Publication: 2020-11-19 21:00:03 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "treeheatr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘treeheatr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw_tree + > ### Title: Draws the conditional decision tree. + > ### Aliases: draw_tree + > + > ### ** Examples + > + > x <- compute_tree(penguins, target_lab = 'species') + > draw_tree(x$dat, x$fit, x$term_dat, x$layout) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: draw_tree ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘explore.Rmd’ + ... + + > library(treeheatr) + + > penguins <- na.omit(penguins) + + > heat_tree(penguins, target_lab = "species") + + When sourcing ‘explore.R’: + Error: argument is of length zero + Execution halted + + ‘explore.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘explore.Rmd’ using rmarkdown + + Quitting from lines 33-36 [unnamed-chunk-2] (explore.Rmd) + Error: processing vignette 'explore.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘explore.Rmd’ + + SUMMARY: processing the following file failed: + ‘explore.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# trelliscopejs + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/hafen/trelliscopejs +* Source code: https://github.com/cran/trelliscopejs +* Date/Publication: 2021-02-01 08:00:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "trelliscopejs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(trelliscopejs) + > + > test_check("trelliscopejs") + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 4. └─base::lapply(...) + 5. └─trelliscopejs (local) FUN(X[[i]], ...) + 6. ├─base::do.call(plotly::ggplotly, c(list(p = q), plotly_args)) + 7. ├─plotly (local) ``(p = ``) + 8. └─plotly:::ggplotly.ggplot(p = ``) + 9. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# tricolore + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/jschoeley/tricolore +* Source code: https://github.com/cran/tricolore +* Date/Publication: 2024-05-15 15:00:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "tricolore")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tricolore-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ColorKeySextant + > ### Title: Sextant Scheme Legend + > ### Aliases: ColorKeySextant + > ### Keywords: internal + > + > ### ** Examples + > + ... + 3. ├─ggtern::ggplot_build(x) + 4. └─ggtern:::ggplot_build.ggplot(x) + 5. └─ggtern:::layers_add_or_remove_mask(plot) + 6. └─ggint$plot_theme(plot) + 7. └─ggplot2:::validate_theme(theme) + 8. └─base::mapply(...) + 9. └─ggplot2 (local) ``(...) + 10. └─cli::cli_abort(...) + 11. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘choropleth_maps_with_tricolore.Rmd’ + ... + + > plot_educ <- ggplot(euro_example) + geom_sf(aes(fill = rgb, + + geometry = geometry), size = 0.1) + scale_fill_identity() + + > plot_educ + + When sourcing ‘choropleth_maps_with_tricolore.R’: + Error: The `tern.axis.ticks.length.major` theme element must be a + object. + Execution halted + + ‘choropleth_maps_with_tricolore.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown + + Quitting from lines 61-72 [unnamed-chunk-4] (choropleth_maps_with_tricolore.Rmd) + Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics: + The `tern.axis.ticks.length.major` theme element must be a + object. + --- failed re-building ‘choropleth_maps_with_tricolore.Rmd’ + + SUMMARY: processing the following file failed: + ‘choropleth_maps_with_tricolore.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# triptych + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/aijordan/triptych +* Source code: https://github.com/cran/triptych +* Date/Publication: 2024-06-13 15:50:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "triptych")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘triptych-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.triptych + > ### Title: Plot methods for the triptych classes + > ### Aliases: plot.triptych autoplot.triptych plot.triptych_murphy + > ### autoplot.triptych_murphy plot.triptych_reliability + > ### autoplot.triptych_reliability plot.triptych_roc autoplot.triptych_roc + > ### plot.triptych_mcbdsc autoplot.triptych_mcbdsc + > + > ### ** Examples + > + > data(ex_binary, package = "triptych") + > tr <- triptych(ex_binary) + > + > dplyr::slice(tr, 1, 3, 6, 9) |> autoplot() + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# tsnet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/bsiepe/tsnet +* Source code: https://github.com/cran/tsnet +* Date/Publication: 2024-02-28 11:30:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "tsnet")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, + NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.2, 0, 2.2), NULL, TRUE), list("grey70", 0.5, NULL, NULL, FALSE, "grey70", TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), list("gray70", 0.5, NULL, NULL, + FALSE, "gray70", FALSE), NULL, NULL, list("gray70", 0.5, NULL, NULL, FALSE, "gray70", FALSE), NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("white", + NA, NULL, NULL, TRUE), list(), NULL, NULL, NULL, list("grey87", NULL, NULL, NULL, FALSE, "grey87", TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, + TRUE), "topleft", NULL, NULL, list("gray90", NA, NULL, NULL, FALSE), NULL, NULL, "on", "inside", list(NULL, NULL, "black", 0.8, NULL, NULL, NULL, NULL, c(6, 6, 6, 6), NULL, FALSE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + + [ FAIL 1 | WARN 14 | SKIP 0 | PASS 108 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 163.4Mb + sub-directories of 1Mb or more: + libs 162.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# UBayFS + +
+ +* Version: 1.0 +* GitHub: https://github.com/annajenul/UBayFS +* Source code: https://github.com/cran/UBayFS +* Date/Publication: 2023-03-07 10:50:02 UTC +* Number of recursive dependencies: 188 + +Run `revdepcheck::cloud_details(, "UBayFS")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘BFS_UBayFS.Rmd’ + ... + ( 21,23,28 ) + ( 21,27,28 ) + ( 21,23,24 ) + + > plot(model) + [1] "Warning: multiple optimal feature sets, plotting first feature set." + + ... + ( 2,3,7,8,14,22,23,26,27,28 ) + + > plot(model) + + When sourcing ‘UBayFS.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘BFS_UBayFS.Rmd’ using ‘UTF-8’... failed + ‘UBayFS.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘BFS_UBayFS.Rmd’ using rmarkdown + + Quitting from lines 147-150 [unnamed-chunk-8] (BFS_UBayFS.Rmd) + Error: processing vignette 'BFS_UBayFS.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘BFS_UBayFS.Rmd’ + + --- re-building ‘UBayFS.Rmd’ using rmarkdown + ... + Quitting from lines 306-309 [unnamed-chunk-12] (UBayFS.Rmd) + Error: processing vignette 'UBayFS.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘UBayFS.Rmd’ + + SUMMARY: processing the following files failed: + ‘BFS_UBayFS.Rmd’ ‘UBayFS.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Umatrix + +
+ +* Version: 4.0.1 +* GitHub: NA +* Source code: https://github.com/cran/Umatrix +* Date/Publication: 2024-08-17 06:30:17 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "Umatrix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Umatrix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotMatrix + > ### Title: plotMatrix + > ### Aliases: plotMatrix + > + > ### ** Examples + > + > data("Hepta") + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +# umiAnalyzer + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/sfilges/umiAnalyzer +* Source code: https://github.com/cran/umiAnalyzer +* Date/Publication: 2021-11-25 08:40:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "umiAnalyzer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘umiAnalyzer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AmpliconPlot + > ### Title: Generate Amplicon plots + > ### Aliases: AmpliconPlot + > + > ### ** Examples + > + > library(umiAnalyzer) + ... + > + > main = system.file('extdata', package = 'umiAnalyzer') + > samples <- list.dirs(path = main, full.names = FALSE, recursive = FALSE) + > simsen <- createUmiExperiment(experimentName = 'example',mainDir = main,sampleNames = samples) + > simsen <- filterUmiObject(simsen) + > + > amplicon_plot <- AmpliconPlot(simsen) + Error in pm[[2]] : subscript out of bounds + Calls: AmpliconPlot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# UnalR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/estadisticaun/UnalR +* Source code: https://github.com/cran/UnalR +* Date/Publication: 2024-05-25 17:20:05 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "UnalR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘UnalR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Plot.Apiladas + > ### Title: Cree un gráfico de barras apiladas dinámico/estático y flexible + > ### Aliases: Plot.Apiladas + > + > ### ** Examples + > + > ## Don't show: + ... + + legend.direction = "vertical"), gg.Bar = list(width = 0.6, color = "#000000"), + + gg.Texto = list(subtitle = "»»»", tag = "®", caption = "Información Disponible desde 2009-1"))) + Warning: + ¡Ha ingresado un dataframe que no está de forma condensada, es decir, + para cada categoría existe más de un valor para un mismo punto del eje X! + Se sumará los valores por defectos para dichos puntos que gocen de +1 valor + + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(UnalR) + > + > test_check("UnalR") + Starting 2 test processes + [ FAIL 2 | WARN 4 | SKIP 1 | PASS 50 ] + + ... + 7. └─UnalR::Plot.Series(...) + 8. └─ggplot2:::`+.gg`(...) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 4 | SKIP 1 | PASS 50 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + R 2.3Mb + data 2.0Mb + help 2.6Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 312859 marked UTF-8 strings + ``` + +# unmconf + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/unmconf +* Date/Publication: 2024-09-09 22:00:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "unmconf")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘unmconf.Rmd’ + ... + 9 -1.05 1 5.63 -0.447 1 1 1.55 TRUE TRUE + 10 0.620 0 1.66 -1.71 1 1 1.37 TRUE TRUE + + > bayesplot::mcmc_intervals(unm_mod, prob_outer = 0.95, + + regex_pars = "(beta|lambda|gamma|delta|zeta).+") + geom_point(aes(value, + + name), .... [TRUNCATED] + + When sourcing ‘unmconf.R’: + Error: argument is of length zero + Execution halted + + ‘unmconf.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘unmconf.Rmd’ using rmarkdown + ``` + +# usmap + +
+ +* Version: 0.7.1 +* GitHub: https://github.com/pdil/usmap +* Source code: https://github.com/cran/usmap +* Date/Publication: 2024-03-21 04:20:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "usmap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘usmap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: .east_north_central + > ### Title: East North Central census division + > ### Aliases: .east_north_central + > ### Keywords: datasets + > + > ### ** Examples + > + > plot_usmap(include = .east_north_central, labels = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_usmap ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + ... + • data/statepov.svg + • plot/arizona-county-map-with-labels-and-fill.svg + • plot/example-data-state-map-with-custom-linewidth.svg + • plot/new-england-state-map-with-labels-excluding-maine.svg + • plot/southeastern-states-map-with-labels.svg + • plot/state-map-with-labels.svg + • plot/state-map-with-major-rivers.svg + • plot/state-population-map-with-blue-outlines.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘usmap1.Rmd’ + ... + + > knitr::opts_chunk$set(collapse = TRUE, comment = "#>") + + > usmap::plot_usmap() + + When sourcing ‘usmap1.R’: + Error: argument is of length zero + ... + + > usmap::plot_usmap("states", labels = TRUE) + + When sourcing ‘usmap3.R’: + Error: argument is of length zero + Execution halted + + ‘usmap1.Rmd’ using ‘UTF-8’... failed + ‘usmap2.Rmd’ using ‘UTF-8’... failed + ‘usmap3.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘usmap1.Rmd’ using rmarkdown + + Quitting from lines 26-27 [unnamed-chunk-1] (usmap1.Rmd) + Error: processing vignette 'usmap1.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘usmap1.Rmd’ + + --- re-building ‘usmap2.Rmd’ using rmarkdown + + ... + Quitting from lines 26-27 [unnamed-chunk-1] (usmap3.Rmd) + Error: processing vignette 'usmap3.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘usmap3.Rmd’ + + SUMMARY: processing the following files failed: + ‘usmap1.Rmd’ ‘usmap2.Rmd’ ‘usmap3.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 17 marked UTF-8 strings + ``` + +# vannstats + +
+ +* Version: 1.3.4.14 +* GitHub: NA +* Source code: https://github.com/cran/vannstats +* Date/Publication: 2023-04-15 04:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "vannstats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vannstats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qq + > ### Title: Simplified Normal (Q-Q) Plot + > ### Aliases: qq + > + > ### ** Examples + > + > data <- mtcars + > + > qq(data,mpg,cyl) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: qq ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vDiveR + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/vDiveR +* Date/Publication: 2024-01-09 20:20:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "vDiveR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vDiveR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_entropy + > ### Title: Entropy plot + > ### Aliases: plot_entropy + > + > ### ** Examples + > + > plot_entropy(proteins_1host) + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + Scale for linetype is already present. + Adding another scale for linetype, which will replace the existing scale. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘DT’ ‘maps’ ‘readr’ + All declared Imports should be used. + ``` + +# venn + +
+ +* Version: 1.12 +* GitHub: https://github.com/dusadrian/venn +* Source code: https://github.com/cran/venn +* Date/Publication: 2024-01-08 11:40:05 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "venn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘venn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: venn + > ### Title: Draw and display a Venn diagram + > ### Aliases: venn + > ### Keywords: functions + > + > ### ** Examples + > + ... + > + > + > # producing a ggplot2 graphics + > venn(x, ilabels = "counts", ggplot = TRUE) + > + > # increasing the border size + > venn(x, ilabels = "counts", ggplot = TRUE, size = 1.5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: venn ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vimpclust + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/vimpclust +* Date/Publication: 2021-01-08 09:30:03 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "vimpclust")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘sparsewkm.Rmd’ + ... + restecg 3.1e-02 0.000 0.000 0.000 0.000 + exang 2.3e-01 0.182 0.138 0.106 0.046 + slope 3.2e-01 0.231 0.188 0.151 0.077 + thal 1.2e-01 0.058 0.023 0.000 0.000 + + > plot(res, what = "weights.features") + + When sourcing ‘sparsewkm.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘groupsparsewkm.Rmd’ using ‘UTF-8’... OK + ‘sparsewkm.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘groupsparsewkm.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘mclust’ ‘rlang’ + All declared Imports should be used. + ``` + +# vip + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/koalaverse/vip +* Source code: https://github.com/cran/vip +* Date/Publication: 2023-08-21 09:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "vip")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vip-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vi + > ### Title: Variable importance + > ### Aliases: vi vi.default + > + > ### ** Examples + > + > # + ... + 8 drat 0.0265 0.0564 + 9 carb 0.00898 0.00885 + 10 disp -0.000824 0.00744 + > + > # Plot variable importance scores + > vip(vis, include_type = TRUE, all_permutations = TRUE, + + geom = "point", aesthetics = list(color = "forestgreen", size = 3)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: vip ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > if (requireNamespace("tinytest", quietly = TRUE)) { + + home <- length(unclass(packageVersion("vip"))[[1L]]) == 4 + + tinytest::test_package("vip", at_home = home) + + } + + Attaching package: 'vip' + + ... + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 1 tests OK + test_pkg_nnet.R............... 2 tests OK + test_pkg_nnet.R............... 3 tests OK Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'C50', 'caret', 'Cubist', 'earth', 'gbm', 'glmnet', 'h2o', + 'lightgbm', 'mixOmics', 'mlr', 'mlr3', 'neuralnet', 'parsnip', + 'partykit', 'pls', 'randomForest', 'ranger', 'RSNNS', 'sparklyr', + 'tidymodels', 'workflows', 'xgboost' + ``` + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘randomForest’, ‘glmnet’, ‘C50’, ‘Cubist’, ‘caret’, ‘partykit’, ‘earth’, ‘gbm’, ‘h2o’, ‘sparklyr’, ‘ranger’, ‘xgboost’, ‘lightgbm’ + ``` + +# VirtualPop + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/willekens/VirtualPop +* Source code: https://github.com/cran/VirtualPop +* Date/Publication: 2024-03-18 10:30:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "VirtualPop")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Piecewise_exponential.Rmd’ + ... + > H <- VirtualPop::H_pw(x, breakpoints, rates) + + > dd <- data.frame(x = x, y = exp(-H)) + + > p <- survminer::ggsurvplot(KM, data = data.frame(pw_sample), + + conf.int = TRUE, ggtheme = theme_bw()) + + When sourcing ‘Piecewise_exponential.R’: + Error: argument is of length zero + Execution halted + + ‘MultistateLH.Rmd’ using ‘UTF-8’... OK + ‘Piecewise_exponential.Rmd’ using ‘UTF-8’... failed + ‘Tutorial.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MultistateLH.Rmd’ using knitr + --- finished re-building ‘MultistateLH.Rmd’ + + --- re-building ‘Piecewise_exponential.Rmd’ using knitr + ``` + +# viscomp + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/georgiosseitidis/viscomp +* Source code: https://github.com/cran/viscomp +* Date/Publication: 2023-01-16 09:50:02 UTC +* Number of recursive dependencies: 137 + +Run `revdepcheck::cloud_details(, "viscomp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘viscomp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: loccos + > ### Title: Leaving One Component Combination Out Scatter plot + > ### Aliases: loccos + > + > ### ** Examples + > + > data(nmaMACE) + > loccos(model = nmaMACE, combination = c("B")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: loccos ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vivaldi + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/GreshamLab/vivaldi +* Source code: https://github.com/cran/vivaldi +* Date/Publication: 2023-03-21 20:10:02 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "vivaldi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vivaldi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: snv_location + > ### Title: snv_location + > ### Aliases: snv_location + > + > ### ** Examples + > + > # Example 1: + ... + 6 m2 PB1 234 G A minor 0.010 0.990 + 7 m2 PB1 266 G A minor 0.022 0.978 + 8 m2 PB2 199 A G minor 0.043 0.957 + 9 m2 PB2 88 G A major 0.055 0.945 + 10 m2 PB2 180 C T minor 0.011 0.989 + > + > snv_location(df) + Error in pm[[2]] : subscript out of bounds + Calls: snv_location -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-snv_location.R:13:3'): expect output ───────────────────────── + Expected `snv_location(df)` to run without any errors. + i Actually got a with text: + subscript out of bounds + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette.Rmd’ + ... + |a_3_fb | 96| + |a_3_iv | 94| + |b_1_fb | 82| + |b_1_iv | 91| + + > snv_location(DF_filt_SNVs) + + When sourcing ‘vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + doc 5.4Mb + extdata 1.1Mb + ``` + +# voiceR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/voiceR +* Date/Publication: 2023-09-12 20:30:02 UTC +* Number of recursive dependencies: 179 + +Run `revdepcheck::cloud_details(, "voiceR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘voiceR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: comparisonPlots + > ### Title: Create boxplots for extracted audio features + > ### Aliases: comparisonPlots + > + > ### ** Examples + > + > comparisonPlots(testAudioData, by = "Condition") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: comparisonPlots ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 4. └─(function() {... + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 30 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + Audios 1.1Mb + data 6.5Mb + ``` + +# volcano3D + +
+ +* Version: 2.0.9 +* GitHub: https://github.com/KatrionaGoldmann/volcano3D +* Source code: https://github.com/cran/volcano3D +* Date/Publication: 2023-05-17 11:00:02 UTC +* Number of recursive dependencies: 166 + +Run `revdepcheck::cloud_details(, "volcano3D")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘volcano3D-Ex.R’ failed + The error most likely occurred in: + + > ### Name: boxplot_trio + > ### Title: Boxplot to compare groups + > ### Aliases: boxplot_trio + > ### Keywords: hplot + > + > ### ** Examples + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Vignette.rmd’ + ... + > plot1 <- boxplot_trio(syn_polar, value = "COBL", text_size = 7, + + test = "polar_padj", my_comparisons = list(c("Lymphoid", + + "Myeloid" .... [TRUNCATED] + + When sourcing ‘Vignette.R’: + Error: ℹ In index: 1. + ℹ With name: row. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Vignette.rmd’ using ‘UTF-8’... failed + ‘Vignette_2x3.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Vignette.rmd’ using rmarkdown + ``` + +# voluModel + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/hannahlowens/voluModel +* Source code: https://github.com/cran/voluModel +* Date/Publication: 2024-08-20 22:50:01 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "voluModel")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘voluModel-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pointCompMap + > ### Title: Comparative point mapping + > ### Aliases: pointCompMap + > ### Keywords: plotting + > + > ### ** Examples + > + ... + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggproto_parent(Coord, self)$setup_params(data) + 10. └─ggplot2 (local) setup_params(..., self = self) + 11. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 12. └─ggplot2:::check_logical(expand) + 13. └─ggplot2:::stop_input_type(...) + 14. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘a_Introduction.Rmd’ using rmarkdown + + Quitting from lines 44-58 [show points] (a_Introduction.Rmd) + Error: processing vignette 'a_Introduction.Rmd' failed with diagnostics: + `expand` must be a logical vector, not the number 0.05. + --- failed re-building ‘a_Introduction.Rmd’ + + --- re-building ‘b_RasterProcessing.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘a_Introduction.Rmd’ + ... + + returnclass = "sf")[1] + + > pointMap(occs = occurrences, ptCol = "orange", landCol = "black", + + spName = "Steindachneria argentea", ptSize = 3, land = land) + Using decimalLongitude and decimalLatitude + as x and y coordinates, respectively. + + ... + + When sourcing ‘e_GLMWorkflow.R’: + Error: invalid font type + Execution halted + + ‘a_Introduction.Rmd’ using ‘UTF-8’... failed + ‘b_RasterProcessing.Rmd’ using ‘UTF-8’... OK + ‘c_DataSampling.Rmd’ using ‘UTF-8’... failed + ‘d_Visualization.Rmd’ using ‘UTF-8’... failed + ‘e_GLMWorkflow.Rmd’ using ‘UTF-8’... failed + ``` + +# vsd + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/vsd +* Date/Publication: 2021-05-11 09:40:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "vsd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vsd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vsd + > ### Title: Visualizing Survival Data + > ### Aliases: vsd vsd.formula vsd.Surv vsd.coxph vsd.survfit vsd.survfitcox + > ### vsd.flexsurvreg + > + > ### ** Examples + > + ... + • `linetype = "Strata"` + • `shape = "Strata"` + + > + > # parametric models are also supported with flexsurv + > vsd(flexsurv::flexsurvreg(Surv(rectime, censrec) ~ group, data = flexsurv::bc, dist = 'gengamma'), + + .include = c("par")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: vsd ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘flexsurv’ + All declared Imports should be used. + ``` + +# vvshiny + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/vvshiny +* Date/Publication: 2023-07-19 15:30:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "vvshiny")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 1. ├─vvshiny::ggplotly_with_legend(p, color = "grp", mapping_table = list(grp = "Group")) at test-ggplotly_with_legend.R:15:3 + 2. │ ├─plotly::ggplotly(plot) %>% ... + 3. │ ├─plotly::ggplotly(plot) + 4. │ └─plotly:::ggplotly.ggplot(plot) + 5. │ └─plotly::gg2list(...) + 6. └─plotly::layout(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 60 ] + Error: Test failures + Execution halted + ``` + +# walker + +
+ +* Version: 1.0.10 +* GitHub: https://github.com/helske/walker +* Source code: https://github.com/cran/walker +* Date/Publication: 2024-08-30 06:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "walker")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘walker.Rmd’ + ... + For each parameter, n_eff is a crude measure of effective sample size, + and Rhat is the potential scale reduction factor on split chains (at + convergence, Rhat=1). + + > mcmc_areas(as.matrix(fit$stanfit), regex_pars = c("sigma_y", + + "sigma_rw1")) + + When sourcing ‘walker.R’: + Error: argument is of length zero + Execution halted + + ‘walker.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘walker.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 161.5Mb + sub-directories of 1Mb or more: + libs 160.1Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# WVPlots + +
+ +* Version: 1.3.8 +* GitHub: https://github.com/WinVector/WVPlots +* Source code: https://github.com/cran/WVPlots +* Date/Publication: 2024-04-22 20:40:07 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "WVPlots")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘WVPlots-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ScatterHist + > ### Title: Plot a scatter plot with marginals. + > ### Aliases: ScatterHist + > + > ### ** Examples + > + > + ... + 10. └─ggplot2:::ggplot_build.ggplot(x) + 11. └─layout$setup(data, plot$data, plot$plot_env) + 12. └─ggplot2 (local) setup(..., self = self) + 13. └─self$coord$setup_params(data) + 14. └─ggplot2 (local) setup_params(..., self = self) + 15. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 16. └─ggplot2:::check_logical(expand) + 17. └─ggplot2:::stop_input_type(...) + 18. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if (requireNamespace("tinytest", quietly=TRUE) ) { + + if (requireNamespace('data.table', quietly = TRUE)) { + + # don't multi-thread during CRAN checks + + data.table::setDTthreads(1) + + } + + tinytest::test_package("WVPlots") + ... + 18. └─ggplot2:::ggplot_build.ggplot(x) + 19. └─layout$setup(data, plot$data, plot$plot_env) + 20. └─ggplot2 (local) setup(..., self = self) + 21. └─self$coord$setup_params(data) + 22. └─ggplot2 (local) setup_params(..., self = self) + 23. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 24. └─ggplot2:::check_logical(expand) + 25. └─ggplot2:::stop_input_type(...) + 26. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘WVPlots_concept.Rmd’ + ... + > frm$absY <- abs(frm$y) + + > frm$posY = frm$y > 0 + + > WVPlots::ScatterHist(frm, "x", "y", smoothmethod = "lm", + + title = "Example Linear Fit") + + ... + > frm$posY = frm$y > 0 + + > WVPlots::ScatterHist(frm, "x", "y", title = "Example Fit") + + When sourcing ‘WVPlots_examples.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘WVPlots_concept.Rmd’ using ‘UTF-8’... failed + ‘WVPlots_examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘WVPlots_concept.Rmd’ using rmarkdown + ``` + +# xaringanthemer + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/gadenbuie/xaringanthemer +* Source code: https://github.com/cran/xaringanthemer +* Date/Publication: 2022-08-20 18:40:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "xaringanthemer")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(xaringanthemer) + > + > test_check("xaringanthemer") + [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-ggplot2.R:267:3'): theme_xaringan_restore_defaults() restores defaults ── + res$after_restore$line_colour (`actual`) not equal to res$original$colour (`expected`). + + `actual` is a character vector ('#0088ff') + `expected` is an S3 object of class , a call + + [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘xaringanthemer.Rmd’ + ... + Warning in file(con, "r") : + cannot open file './../man/fragments/_quick-intro.Rmd': No such file or directory + + Quitting from lines 43-43 [unnamed-chunk-2] (xaringanthemer.Rmd) + + When tangling ‘xaringanthemer.Rmd’: + Error: cannot open the connection + Execution halted + + ‘ggplot2-themes.Rmd’ using ‘UTF-8’... OK + ‘template-variables.Rmd’ using ‘UTF-8’... OK + ‘xaringanthemer.Rmd’ using ‘UTF-8’... failed + ``` + +# yamlet + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/bergsmat/yamlet +* Source code: https://github.com/cran/yamlet +* Date/Publication: 2024-03-29 13:30:02 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "yamlet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘yamlet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplot_add.ggplot_isometric + > ### Title: Add Isometry to Plot Object + > ### Aliases: ggplot_add.ggplot_isometric + > ### Keywords: internal + > + > ### ** Examples + > + ... + ismtrc> library(magrittr) + + ismtrc> library(ggplot2) + + ismtrc> data.frame(x = 1:5, y = 3:7) %>% + ismtrc+ ggplot(aes(x, y)) + geom_point() + isometric() + Error in ggplot_add.ggplot_isometric(object, p, objectname) : + "x" %in% names(plot$labels) is not TRUE + Calls: example ... ggplot_add -> ggplot_add.ggplot_isometric -> stopifnot + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(yamlet) + + Attaching package: 'yamlet' + + The following object is masked from 'package:stats': + + ... + ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ + • empty test (2): 'test-yamlet.R:1346:1', 'test-yamlet.R:1351:1' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-yamlet.R:843:1'): ggplot.resolved is stable ────────────────── + `print(x %>% ggplot(map) + geom_point())` did not produce any warnings. + + [ FAIL 1 | WARN 0 | SKIP 2 | PASS 516 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘scripted-html.Rmd’ using rmarkdown + ``` From 6d48584c6c3396bc108218487f60fa577da5a767 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 13 Sep 2024 11:12:23 +0200 Subject: [PATCH 126/264] Ink and paper settings for built-in themes (re: #6059) (#6063) * abstract away theme colours * add snapshot test * add news bullet --- NEWS.md | 2 + R/theme-defaults.R | 142 ++++---- man/ggtheme.Rd | 42 ++- .../theme/theme-with-inverted-colours.svg | 332 ++++++++++++++++++ tests/testthat/test-theme.R | 18 + 5 files changed, 466 insertions(+), 70 deletions(-) create mode 100644 tests/testthat/_snaps/theme/theme-with-inverted-colours.svg diff --git a/NEWS.md b/NEWS.md index a4bce3f6be..5df6059f0f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Built-in `theme_*()` functions now have `ink` and `paper` arguments to control + foreground and background colours respectively (@teunbrand) * The `summary()` method for ggplots is now more terse about facets (@teunbrand, #5989). * `guide_bins()`, `guide_colourbar()` and `guide_coloursteps()` gain an `angle` diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 77b36e243e..8be7999d4d 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -11,6 +11,7 @@ #' legend titles, the plot title and tag text. #' @param base_line_size base size for line elements #' @param base_rect_size base size for rect elements +#' @param ink,paper colour for foreground and background elements respectively. #' #' @details #' \describe{ @@ -106,7 +107,8 @@ NULL theme_grey <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { # The half-line (base-fontsize / 2) sets up the basic vertical # rhythm of the theme. Most margins will be set to this value. @@ -124,16 +126,16 @@ theme_grey <- function(base_size = 11, base_family = "", # Elements in this first block aren't used directly, but are inherited # by others line = element_line( - colour = "black", linewidth = base_line_size, + colour = ink, linewidth = base_line_size, linetype = 1, lineend = "butt" ), rect = element_rect( - fill = "white", colour = "black", + fill = paper, colour = ink, linewidth = base_rect_size, linetype = 1 ), text = element_text( family = base_family, face = "plain", - colour = "black", size = base_size, + colour = ink, size = base_size, lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), @@ -144,7 +146,7 @@ theme_grey <- function(base_size = 11, base_family = "", margins = margin(half_line, half_line, half_line, half_line), geom = element_geom( - ink = "black", paper = "white", accent = "#3366FF", + ink = ink, paper = paper, accent = "#3366FF", linewidth = base_line_size, borderwidth = base_line_size, linetype = 1L, bordertype = 1L, family = base_family, fontsize = base_size, @@ -154,14 +156,14 @@ theme_grey <- function(base_size = 11, base_family = "", axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, - axis.text = element_text(size = rel(0.8), colour = "grey30"), + axis.text = element_text(size = rel(0.8), colour = col_mix(ink, paper, 0.305)), axis.text.x = element_text(margin = margin(t = 0.8 * half_line / 2), vjust = 1), axis.text.x.top = element_text(margin = margin(b = 0.8 * half_line / 2), vjust = 0), axis.text.y = element_text(margin = margin(r = 0.8 * half_line / 2), hjust = 1), axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line / 2), hjust = 0), axis.text.r = element_text(margin = margin(l = 0.8 * half_line / 2, r = 0.8 * half_line / 2), hjust = 0.5), - axis.ticks = element_line(colour = "grey20"), + axis.ticks = element_line(colour = col_mix(ink, paper, 0.2)), axis.ticks.length = rel(0.5), axis.ticks.length.x = NULL, axis.ticks.length.x.top = NULL, @@ -210,19 +212,19 @@ theme_grey <- function(base_size = 11, base_family = "", legend.box.background = element_blank(), legend.box.spacing = rel(2), - panel.background = element_rect(fill = "grey92", colour = NA), + panel.background = element_rect(fill = col_mix(ink, paper, 0.925), colour = NA), panel.border = element_blank(), - panel.grid = element_line(colour = "white"), + panel.grid = element_line(colour = paper), panel.grid.minor = element_line(linewidth = rel(0.5)), panel.spacing = NULL, panel.spacing.x = NULL, panel.spacing.y = NULL, panel.ontop = FALSE, - strip.background = element_rect(fill = "grey85", colour = NA), + strip.background = element_rect(fill = col_mix(ink, paper, 0.854), colour = NA), strip.clip = "on", strip.text = element_text( - colour = "grey10", + colour = col_mix(ink, paper, 0.105), size = rel(0.8), margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) ), @@ -235,7 +237,7 @@ theme_grey <- function(base_size = 11, base_family = "", strip.switch.pad.grid = unit(half_line / 2, "pt"), strip.switch.pad.wrap = unit(half_line / 2, "pt"), - plot.background = element_rect(colour = "white"), + plot.background = element_rect(colour = paper), plot.title = element_text( # font size "large" size = rel(1.2), hjust = 0, vjust = 1, @@ -274,24 +276,29 @@ theme_gray <- theme_grey theme_bw <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { # Starts with theme_grey and then modify some parts theme_grey( base_size = base_size, base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( # white background and dark border - panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(colour = "grey20"), + panel.background = element_rect(fill = paper, colour = NA), + panel.border = element_rect(colour = col_mix(ink, paper, 0.2)), # make gridlines dark, same contrast with white as in theme_grey - panel.grid = element_line(colour = "grey92"), + panel.grid = element_line(colour = col_mix(ink, paper, 0.925)), panel.grid.minor = element_line(linewidth = rel(0.5)), # contour strips to match panel contour - strip.background = element_rect(fill = "grey85", colour = "grey20"), + strip.background = element_rect( + fill = col_mix(ink, paper, 0.851), + colour = col_mix(ink, paper, 0.2) + ), complete = TRUE ) @@ -302,7 +309,8 @@ theme_bw <- function(base_size = 11, base_family = "", theme_linedraw <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { half_line <- base_size / 2 # Starts with theme_bw and then modify some parts @@ -312,25 +320,26 @@ theme_linedraw <- function(base_size = 11, base_family = "", base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( # black text and ticks on the axes - axis.text = element_text(colour = "black", size = rel(0.8)), - axis.ticks = element_line(colour = "black", linewidth = rel(0.5)), + axis.text = element_text(colour = ink, size = rel(0.8)), + axis.ticks = element_line(colour = ink, linewidth = rel(0.5)), # NB: match the *visual* thickness of axis ticks to the panel border # 0.5 clipped looks like 0.25 # pure black panel border and grid lines, but thinner - panel.border = element_rect(colour = "black", linewidth = rel(1)), - panel.grid = element_line(colour = "black"), + panel.border = element_rect(colour = ink, linewidth = rel(1)), + panel.grid = element_line(colour = ink), panel.grid.major = element_line(linewidth = rel(0.1)), panel.grid.minor = element_line(linewidth = rel(0.05)), # strips with black background and white text - strip.background = element_rect(fill = "black"), + strip.background = element_rect(fill = ink), strip.text = element_text( - colour = "white", + colour = paper, size = rel(0.8), margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) ), @@ -344,7 +353,8 @@ theme_linedraw <- function(base_size = 11, base_family = "", theme_light <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { half_line <- base_size / 2 # Starts with theme_grey and then modify some parts @@ -353,25 +363,26 @@ theme_light <- function(base_size = 11, base_family = "", base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( # white panel with light grey border - panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(colour = "grey70", linewidth = rel(1)), + panel.background = element_rect(fill = paper, colour = NA), + panel.border = element_rect(colour = col_mix(ink, paper, 0.705), linewidth = rel(1)), # light grey, thinner gridlines # => make them slightly darker to keep acceptable contrast - panel.grid = element_line(colour = "grey87"), + panel.grid = element_line(colour = col_mix(ink, paper, 0.871)), panel.grid.major = element_line(linewidth = rel(0.5)), panel.grid.minor = element_line(linewidth = rel(0.25)), # match axes ticks thickness to gridlines and colour to panel border - axis.ticks = element_line(colour = "grey70", linewidth = rel(0.5)), + axis.ticks = element_line(colour = col_mix(ink, paper, 0.705), linewidth = rel(0.5)), # dark strips with light text (inverse contrast compared to theme_grey) - strip.background = element_rect(fill = "grey70", colour = NA), + strip.background = element_rect(fill = col_mix(ink, paper, 0.705), colour = NA), strip.text = element_text( - colour = "white", + colour = paper, size = rel(0.8), margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) ), @@ -386,7 +397,8 @@ theme_light <- function(base_size = 11, base_family = "", theme_dark <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { half_line <- base_size / 2 # Starts with theme_grey and then modify some parts @@ -395,24 +407,25 @@ theme_dark <- function(base_size = 11, base_family = "", base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( # dark panel - panel.background = element_rect(fill = "grey50", colour = NA), + panel.background = element_rect(fill = col_mix(ink, paper, 0.5), colour = NA), # inverse grid lines contrast compared to theme_grey # make them thinner and try to keep the same visual contrast as in theme_light - panel.grid = element_line(colour = "grey42"), + panel.grid = element_line(colour = col_mix(ink, paper, 0.42)), panel.grid.major = element_line(linewidth = rel(0.5)), panel.grid.minor = element_line(linewidth = rel(0.25)), # match axes ticks thickness to gridlines - axis.ticks = element_line(colour = "grey20", linewidth = rel(0.5)), + axis.ticks = element_line(colour = col_mix(ink, paper, 0.2), linewidth = rel(0.5)), # dark strips with light text (inverse contrast compared to theme_grey) - strip.background = element_rect(fill = "grey15", colour = NA), + strip.background = element_rect(fill = col_mix(ink, paper, 0.15), colour = NA), strip.text = element_text( - colour = "grey90", + colour = col_mix(ink, paper, 0.9), size = rel(0.8), margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) ), @@ -426,17 +439,19 @@ theme_dark <- function(base_size = 11, base_family = "", theme_minimal <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { # Starts with theme_bw and remove most parts theme_bw( base_size = base_size, base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( - axis.ticks = element_blank(), + axis.ticks = element_blank(), legend.background = element_blank(), legend.key = element_blank(), panel.background = element_blank(), @@ -453,13 +468,15 @@ theme_minimal <- function(base_size = 11, base_family = "", theme_classic <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { theme_bw( base_size = base_size, base_family = base_family, header_family = header_family, base_line_size = base_line_size, - base_rect_size = base_rect_size + base_rect_size = base_rect_size, + ink = ink, paper = paper ) %+replace% theme( # no background and no grid @@ -485,7 +502,8 @@ theme_classic <- function(base_size = 11, base_family = "", theme_void <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { half_line <- base_size / 2 # Only keep indispensable text: legend and plot titles @@ -494,7 +512,7 @@ theme_void <- function(base_size = 11, base_family = "", rect = element_blank(), text = element_text( family = base_family, face = "plain", - colour = "black", size = base_size, + colour = ink, size = base_size, lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), @@ -563,21 +581,22 @@ theme_void <- function(base_size = 11, base_family = "", theme_test <- function(base_size = 11, base_family = "", header_family = NULL, base_line_size = base_size / 22, - base_rect_size = base_size / 22) { + base_rect_size = base_size / 22, + ink = "black", paper = "white") { half_line <- base_size / 2 t <- theme( line = element_line( - colour = "black", linewidth = base_line_size, + colour = ink, linewidth = base_line_size, linetype = 1, lineend = "butt" ), rect = element_rect( - fill = "white", colour = "black", + fill = paper, colour = ink, linewidth = base_rect_size, linetype = 1 ), text = element_text( family = base_family, face = "plain", - colour = "black", size = base_size, + colour = ink, size = base_size, lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), @@ -585,7 +604,7 @@ theme_test <- function(base_size = 11, base_family = "", spacing = unit(half_line, "pt"), margins = margin(half_line, half_line, half_line, half_line), geom = element_geom( - ink = "black", paper = "white", accent = "#3366FF", + ink = ink, paper = paper, accent = "#3366FF", linewidth = base_line_size, borderwidth = base_line_size, family = base_family, fontsize = base_size, linetype = 1L, @@ -595,12 +614,12 @@ theme_test <- function(base_size = 11, base_family = "", axis.line = element_blank(), axis.line.x = NULL, axis.line.y = NULL, - axis.text = element_text(size = rel(0.8), colour = "grey30"), + axis.text = element_text(size = rel(0.8), colour = col_mix(ink, paper, 0.305)), axis.text.x = element_text(margin = margin(t = 0.8 * half_line / 2), vjust = 1), axis.text.x.top = element_text(margin = margin(b = 0.8 * half_line / 2), vjust = 0), axis.text.y = element_text(margin = margin(r = 0.8 * half_line / 2), hjust = 1), axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line / 2), hjust = 0), - axis.ticks = element_line(colour = "grey20"), + axis.ticks = element_line(colour = col_mix(ink, paper, 0.2)), axis.ticks.length = rel(0.5), axis.ticks.length.x = NULL, axis.ticks.length.x.top = NULL, @@ -651,8 +670,8 @@ theme_test <- function(base_size = 11, base_family = "", legend.box.background = element_blank(), legend.box.spacing = rel(2), - panel.background = element_rect(fill = "white", colour = NA), - panel.border = element_rect(colour = "grey20"), + panel.background = element_rect(fill = paper, colour = NA), + panel.border = element_rect(colour = col_mix(ink, paper, 0.2)), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.spacing = NULL, @@ -660,10 +679,13 @@ theme_test <- function(base_size = 11, base_family = "", panel.spacing.y = NULL, panel.ontop = FALSE, - strip.background = element_rect(fill = "grey85", colour = "grey20"), + strip.background = element_rect( + fill = col_mix(ink, paper, 0.851), + colour = col_mix(ink, paper, 0.2) + ), strip.clip = "on", strip.text = element_text( - colour = "grey10", + colour = col_mix(ink, paper, 0.105), size = rel(0.8), margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) ), @@ -676,7 +698,7 @@ theme_test <- function(base_size = 11, base_family = "", strip.switch.pad.grid = rel(0.5), strip.switch.pad.wrap = rel(0.5), - plot.background = element_rect(colour = "white"), + plot.background = element_rect(colour = paper), plot.title = element_text( size = rel(1.2), hjust = 0, vjust = 1, diff --git a/man/ggtheme.Rd b/man/ggtheme.Rd index 642319bcc9..e86accb182 100644 --- a/man/ggtheme.Rd +++ b/man/ggtheme.Rd @@ -18,7 +18,9 @@ theme_grey( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_gray( @@ -26,7 +28,9 @@ theme_gray( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_bw( @@ -34,7 +38,9 @@ theme_bw( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_linedraw( @@ -42,7 +48,9 @@ theme_linedraw( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_light( @@ -50,7 +58,9 @@ theme_light( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_dark( @@ -58,7 +68,9 @@ theme_dark( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_minimal( @@ -66,7 +78,9 @@ theme_minimal( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_classic( @@ -74,7 +88,9 @@ theme_classic( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_void( @@ -82,7 +98,9 @@ theme_void( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) theme_test( @@ -90,7 +108,9 @@ theme_test( base_family = "", header_family = NULL, base_line_size = base_size/22, - base_rect_size = base_size/22 + base_rect_size = base_size/22, + ink = "black", + paper = "white" ) } \arguments{ @@ -105,6 +125,8 @@ legend titles, the plot title and tag text.} \item{base_line_size}{base size for line elements} \item{base_rect_size}{base size for rect elements} + +\item{ink, paper}{colour for foreground and background elements respectively.} } \description{ These are complete themes which control all non-data display. Use diff --git a/tests/testthat/_snaps/theme/theme-with-inverted-colours.svg b/tests/testthat/_snaps/theme/theme-with-inverted-colours.svg new file mode 100644 index 0000000000..812529cf9f --- /dev/null +++ b/tests/testthat/_snaps/theme/theme-with-inverted-colours.svg @@ -0,0 +1,332 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Strip title + + + + + + + + +2 +3 +4 +5 +6 +7 +20 +30 +40 + + + +displ +hwy + +drv + + + + + + +4 +f +r +Subtitle +Main title +Caption +A + + diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 9c10202504..36ad577c65 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -840,6 +840,24 @@ test_that("Strips can render custom elements", { expect_doppelganger("custom strip elements can render", plot) }) +test_that("theme ink and paper settings work", { + + p <- ggplot(mpg, aes(displ, hwy, colour = drv)) + + geom_point() + + facet_wrap(~"Strip title") + + labs( + title = "Main title", + subtitle = "Subtitle", + tag = "A", + caption = "Caption" + ) + + expect_doppelganger( + "Theme with inverted colours", + p + theme_gray(ink = "white", paper = "black") + ) +}) + test_that("legend margins are correct when using relative key sizes", { df <- data_frame(x = 1:3, y = 1:3, a = letters[1:3]) From c3dd767f28aed273197ec3f674b5dc51092cff7f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Fri, 13 Sep 2024 14:01:52 +0200 Subject: [PATCH 127/264] Fix for `position_dodge(preserve = "single")` with location based data (#6000) * fallback for location based data * Warn when x/xmin are absent --- R/position-dodge.R | 11 +++++++++-- tests/testthat/test-position_dodge.R | 16 ++++++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) diff --git a/R/position-dodge.R b/R/position-dodge.R index ec4b64cdad..78d4a9a45f 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -106,6 +106,11 @@ PositionDodge <- ggproto("PositionDodge", Position, reverse = NULL, setup_params = function(self, data) { flipped_aes <- has_flipped_aes(data, default = self$orientation == "y") + check_required_aesthetics( + if (flipped_aes) "y|ymin" else "x|xmin", + names(data), snake_class(self) + ) + data <- flip_data(data, flipped_aes) if (is.null(data$xmin) && is.null(data$xmax) && is.null(self$width)) { cli::cli_warn(c( @@ -117,8 +122,10 @@ PositionDodge <- ggproto("PositionDodge", Position, if (identical(self$preserve, "total")) { n <- NULL } else { - n <- vec_unique(data[c("group", "PANEL", "xmin")]) - n <- vec_group_id(n[c("PANEL", "xmin")]) + data$xmin <- data$xmin %||% data$x + cols <- intersect(colnames(data), c("group", "PANEL", "xmin")) + n <- vec_unique(data[cols]) + n <- vec_group_id(n[setdiff(cols, "group")]) n <- max(tabulate(n, attr(n, "n"))) } diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index 1d7127a239..9107de1d92 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -37,3 +37,19 @@ test_that("position_dodge() can reverse the dodge order", { ld <- get_layer_data(p + geom_col(position = position_dodge(reverse = FALSE))) expect_equal(ld$label[order(ld$x)], c("A", "A", "B", "B", "C")) }) + +test_that("position_dodge warns about missing required aesthetics", { + + # Bit of a contrived geom to not have a required 'x' aesthetic + GeomDummy <- ggproto(NULL, GeomPoint, required_aes = NULL, optional_aes = "x") + + p <- ggplot(mtcars, aes(cyl, disp, colour = factor(vs))) + + layer( + geom = GeomDummy, + stat = "identity", + position = position_dodge(width = 0.5), + mapping = aes(x = NULL) + ) + + expect_error(ggplot_build(p), "requires the following missing aesthetics") +}) From d7428813349253c4e6ffbfd9744be6e33e6c2c13 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:34:33 +0200 Subject: [PATCH 128/264] fallback when constructor call is missing (#6095) --- R/plot-construction.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/plot-construction.R b/R/plot-construction.R index 14f2badaed..e6a86139eb 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -196,7 +196,7 @@ new_layer_names <- function(layer, existing) { new_name <- layer$name if (is.null(new_name)) { # Construct a name from the layer's call - new_name <- call_name(layer$constructor) + new_name <- call_name(layer$constructor) %||% snake_class(layer$geom) if (new_name %in% existing) { names <- c(existing, new_name) From 842e6becbddb9e2b02bc45ffebe5c1adf806f4a1 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 16 Sep 2024 11:13:52 +0200 Subject: [PATCH 129/264] Fix linetype regression (#6097) * don't set `na.value = "blank"` * add test --- R/scale-linetype.R | 4 ++-- R/scale-manual.R | 2 +- man/scale_linetype.Rd | 6 +++--- man/scale_manual.Rd | 2 +- tests/testthat/test-scale-manual.R | 7 +++++++ 5 files changed, 14 insertions(+), 7 deletions(-) diff --git a/R/scale-linetype.R b/R/scale-linetype.R index bc4fa0ce71..d4ea6df26d 100644 --- a/R/scale-linetype.R +++ b/R/scale-linetype.R @@ -35,7 +35,7 @@ #' scale_linetype_identity() + #' facet_grid(linetype ~ .) + #' theme_void(20) -scale_linetype <- function(name = waiver(), ..., na.value = "blank") { +scale_linetype <- function(name = waiver(), ..., na.value = NA) { discrete_scale( "linetype", name = name, palette = pal_linetype(), @@ -46,7 +46,7 @@ scale_linetype <- function(name = waiver(), ..., na.value = "blank") { #' @rdname scale_linetype #' @export -scale_linetype_binned <- function(name = waiver(), ..., na.value = "blank") { +scale_linetype_binned <- function(name = waiver(), ..., na.value = NA) { binned_scale( "linetype", name = name, palette = pal_binned(pal_linetype()), diff --git a/R/scale-manual.R b/R/scale-manual.R index bcd0624094..7fc9094070 100644 --- a/R/scale-manual.R +++ b/R/scale-manual.R @@ -119,7 +119,7 @@ scale_shape_manual <- function(..., values, breaks = waiver(), na.value = NA) { #' @seealso #' Other linetype scales: [scale_linetype()], [scale_linetype_identity()]. #' @export -scale_linetype_manual <- function(..., values, breaks = waiver(), na.value = "blank") { +scale_linetype_manual <- function(..., values, breaks = waiver(), na.value = NA) { manual_scale("linetype", values, breaks, ..., na.value = na.value) } diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index 9b57b40978..cc5fa67cb4 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -7,13 +7,13 @@ \alias{scale_linetype_discrete} \title{Scale for line patterns} \usage{ -scale_linetype(name = waiver(), ..., na.value = "blank") +scale_linetype(name = waiver(), ..., na.value = NA) -scale_linetype_binned(name = waiver(), ..., na.value = "blank") +scale_linetype_binned(name = waiver(), ..., na.value = NA) scale_linetype_continuous(...) -scale_linetype_discrete(name = waiver(), ..., na.value = "blank") +scale_linetype_discrete(name = waiver(), ..., na.value = NA) } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If diff --git a/man/scale_manual.Rd b/man/scale_manual.Rd index 92205f3013..d49cd0f526 100644 --- a/man/scale_manual.Rd +++ b/man/scale_manual.Rd @@ -32,7 +32,7 @@ scale_size_manual(..., values, breaks = waiver(), na.value = NA) scale_shape_manual(..., values, breaks = waiver(), na.value = NA) -scale_linetype_manual(..., values, breaks = waiver(), na.value = "blank") +scale_linetype_manual(..., values, breaks = waiver(), na.value = NA) scale_linewidth_manual(..., values, breaks = waiver(), na.value = NA) diff --git a/tests/testthat/test-scale-manual.R b/tests/testthat/test-scale-manual.R index 3d87268c41..2ad47425f7 100644 --- a/tests/testthat/test-scale-manual.R +++ b/tests/testthat/test-scale-manual.R @@ -176,3 +176,10 @@ test_that("NAs from palette are not translated (#5929)", { s3$train(c("8", "6", "4")) expect_equal(s3$map(c("4", "6", "8", "10")), c("a", NA, "c", NA)) }) + +test_that("numeric linetype palettes are mapped correctly (#6096)", { + x <- c(LETTERS[1:3], NA) + sc <- scale_linetype_manual(values = 1:5) + sc$train(x) + expect_equal(sc$map(x), c(1L, 2L, 3L, NA)) +}) From a33953f93108a78953cd2f48115f95c6c8a7d611 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 09:32:16 +0200 Subject: [PATCH 130/264] Fix 6088 (#6106) * when there is nothing to stack, exit via `var = NULL` * add test --- R/position-stack.R | 12 +++++++----- tests/testthat/test-position-stack.R | 6 ++++++ 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/R/position-stack.R b/R/position-stack.R index 6d77269a1f..de23456625 100644 --- a/R/position-stack.R +++ b/R/position-stack.R @@ -153,8 +153,14 @@ PositionStack <- ggproto("PositionStack", Position, setup_params = function(self, data) { flipped_aes <- has_flipped_aes(data) data <- flip_data(data, flipped_aes) + var <- self$var %||% stack_var(data) + if (!vec_duplicate_any(data$x)) { + # We skip stacking when all data have different x positions so that + # there is nothing to stack + var <- NULL + } list( - var = self$var %||% stack_var(data), + var = var, fill = self$fill, vjust = self$vjust, reverse = self$reverse, @@ -185,10 +191,6 @@ PositionStack <- ggproto("PositionStack", Position, if (is.null(params$var)) { return(data) } - if (!vec_duplicate_any(data$x)) { - # Every x is unique, nothing to stack here - return(flip_data(data, params$flipped_aes)) - } negative <- data$ymax < 0 negative[is.na(negative)] <- FALSE diff --git a/tests/testthat/test-position-stack.R b/tests/testthat/test-position-stack.R index 6a9353a300..54c6b858e8 100644 --- a/tests/testthat/test-position-stack.R +++ b/tests/testthat/test-position-stack.R @@ -25,6 +25,12 @@ test_that("negative and positive values are handled separately", { expect_equal(dat$ymin[dat$x == 2], c(0, -3)) expect_equal(dat$ymax[dat$x == 2], c(2, 0)) + + # Test only negatives #6088 + df <- data_frame0(x = c(1, 1, 2, 2), y = c(-1, -1, -1, -1), g = LETTERS[1:4]) + dat <- get_layer_data(ggplot(df, aes(x, y, fill = factor(g))) + geom_col()) + expect_equal(dat$ymax, dat$ymin + 1) + expect_equal(dat$ymin, c(-2, -1, -2, -1)) }) test_that("can request reverse stacking", { From f87ea347bfb7666f3b13e53dc60e96b16ad48b5e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 09:38:57 +0200 Subject: [PATCH 131/264] fix missing `labels` slot (#6010) --- R/plot.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/plot.R b/R/plot.R index 6bdcabc23f..97a1e96102 100644 --- a/R/plot.R +++ b/R/plot.R @@ -130,7 +130,8 @@ ggplot.default <- function(data = NULL, mapping = aes(), ..., coordinates = coord_cartesian(default = TRUE), facet = facet_null(), plot_env = environment, - layout = ggproto(NULL, Layout) + layout = ggproto(NULL, Layout), + labels = list() ), class = c("gg", "ggplot")) set_last_plot(p) From 7f6d5bf91ac1d50bbdd74ed554bf8524badd2448 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 10:04:11 +0200 Subject: [PATCH 132/264] Fix regression from #6027 (#6098) * fallback for numeric expand * add test --- R/coord-.R | 3 +++ tests/testthat/test-coord-.R | 17 +++++++++++++++++ 2 files changed, 20 insertions(+) diff --git a/R/coord-.R b/R/coord-.R index 0d0bb5ecb9..11f498c9b8 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -246,6 +246,9 @@ render_axis <- function(panel_params, axis, scale, position, theme) { # Elaborates an 'expand' argument for every side (top, right, bottom or left) parse_coord_expand <- function(expand) { + if (is.numeric(expand) && all(expand %in% c(0, 1))) { + expand <- as.logical(expand) + } check_logical(expand) if (anyNA(expand)) { cli::cli_abort("{.arg expand} cannot contain missing values.") diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index 6a50369bbc..f1e910c807 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -75,6 +75,23 @@ test_that("coords append a column to the layout correctly", { expect_equal(test$COORD, c(1, 2, 1)) }) +test_that("parse_coord_expand parses correctly", { + + p <- parse_coord_expand(FALSE) + expect_equal(p, rep(FALSE, 4)) + + p <- parse_coord_expand(c(FALSE, TRUE)) + expect_equal(p, c(FALSE, TRUE, FALSE, TRUE)) + + p <- parse_coord_expand(c(top = FALSE, left = FALSE)) + expect_equal(p, c(FALSE, TRUE, TRUE, FALSE)) + + # Dependencies might use `expand = 1` + p <- parse_coord_expand(c(1, 0)) + expect_equal(p, c(TRUE, FALSE, TRUE, FALSE)) + +}) + test_that("coord expand takes a vector", { base <- ggplot() + lims(x = c(0, 10), y = c(0, 10)) From 171664bb1e04c41e4968e6c33050a7c58a520166 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 11:16:12 +0200 Subject: [PATCH 133/264] Label accessor (#6078) * guides merge aesthetics * add getter for completed plot labels * incorporate getter in tests * document --- NAMESPACE | 1 + NEWS.md | 2 + R/guide-colorbar.R | 1 + R/guide-legend.R | 1 + R/labels.R | 33 +++++++++++++++++ man/labs.Rd | 7 ++++ tests/testthat/test-labels.R | 71 +++++++++++++----------------------- 7 files changed, 70 insertions(+), 46 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index f0ccf3bec1..1220e7e6ef 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -426,6 +426,7 @@ export(get_alt_text) export(get_element_tree) export(get_geom_defaults) export(get_guide_data) +export(get_labs) export(get_last_plot) export(get_layer_data) export(get_layer_grob) diff --git a/NEWS.md b/NEWS.md index 5df6059f0f..8d7f8760d0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* New `get_labs()` function for retrieving completed plot labels + (@teunbrand, #6008). * Built-in `theme_*()` functions now have `ink` and `paper` arguments to control foreground and background colours respectively (@teunbrand) * The `summary()` method for ggplots is now more terse about facets diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index 586caee124..c7c424c2ac 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -273,6 +273,7 @@ GuideColourbar <- ggproto( merge = function(self, params, new_guide, new_params) { new_params$key$.label <- new_params$key$.value <- NULL params$key <- vec_cbind(params$key, new_params$key) + params$aesthetic <- union(params$aesthetic, new_params$aesthetic) return(list(guide = self, params = params)) }, diff --git a/R/guide-legend.R b/R/guide-legend.R index 671acf1a1c..37aad2e3f0 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -204,6 +204,7 @@ GuideLegend <- ggproto( cli::cli_warn("Duplicated {.arg override.aes} is ignored.") } params$override.aes <- params$override.aes[!duplicated(nms)] + params$aesthetic <- union(params$aesthetic, new_params$aesthetic) list(guide = self, params = params) }, diff --git a/R/labels.R b/R/labels.R index 20cc929d37..50e3776555 100644 --- a/R/labels.R +++ b/R/labels.R @@ -179,6 +179,39 @@ ggtitle <- function(label, subtitle = waiver()) { labs(title = label, subtitle = subtitle) } +#' @rdname labs +#' @export +#' @param plot A ggplot object +#' @description +#' `get_labs()` retrieves completed labels from a plot. +get_labs <- function(plot = get_last_plot()) { + plot <- ggplot_build(plot) + + labs <- plot$plot$labels + + xy_labs <- rename( + c(x = plot$layout$resolve_label(plot$layout$panel_scales_x[[1]], labs), + y = plot$layout$resolve_label(plot$layout$panel_scales_y[[1]], labs)), + c(x.primary = "x", x.secondary = "x.sec", + y.primary = "y", y.secondary = "y.sec") + ) + + labs <- defaults(xy_labs, labs) + + guides <- plot$plot$guides + if (length(guides$aesthetics) == 0) { + return(labs) + } + + for (aes in guides$aesthetics) { + param <- guides$get_params(aes) + aes <- param$aesthetic # Can have length > 1 when guide was merged + title <- vec_set_names(rep(list(param$title), length(aes)), aes) + labs <- defaults(title, labs) + } + labs +} + #' Extract alt text from a plot #' #' This function returns a text that can be used as alt-text in webpages etc. diff --git a/man/labs.Rd b/man/labs.Rd index 6fc7e9aa08..5d6fb93b52 100644 --- a/man/labs.Rd +++ b/man/labs.Rd @@ -5,6 +5,7 @@ \alias{xlab} \alias{ylab} \alias{ggtitle} +\alias{get_labs} \title{Modify axis, legend, and plot labels} \usage{ labs( @@ -22,6 +23,8 @@ xlab(label) ylab(label) ggtitle(label, subtitle = waiver()) + +get_labs(plot = get_last_plot()) } \arguments{ \item{...}{A list of new name-value pairs. The name should be an aesthetic.} @@ -44,6 +47,8 @@ rlang \link[rlang:as_function]{lambda} function notation.} \item{label}{The title of the respective axis (for \code{xlab()} or \code{ylab()}) or of the plot (for \code{ggtitle()}).} + +\item{plot}{A ggplot object} } \description{ Good labels are critical for making your plots accessible to a wider @@ -52,6 +57,8 @@ variable name. Use the plot \code{title} and \code{subtitle} to explain the main findings. It's common to use the \code{caption} to provide information about the data source. \code{tag} can be used for adding identification tags to differentiate between multiple plots. + +\code{get_labs()} retrieves completed labels from a plot. } \details{ You can also set axis and legend labels in the individual scales (using diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index 60f5165c1b..6a26578c0b 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -52,15 +52,13 @@ test_that("setting guide labels works", { test_that("Labels from default stat mapping are overwritten by default labels", { p <- ggplot(mpg, aes(displ, hwy)) + geom_density2d() - labels <- ggplot_build(p)$plot$labels + labels <- get_labs(p) expect_equal(labels$colour[1], "colour") expect_true(attr(labels$colour, "fallback")) p <- p + geom_smooth(aes(color = drv), method = "lm", formula = y ~ x) - labels <- ggplot_build(p)$plot$labels - - expect_equal(labels$colour, "drv") + expect_equal(get_labs(p)$colour, "drv") }) test_that("Labels can be extracted from attributes", { @@ -68,8 +66,8 @@ test_that("Labels can be extracted from attributes", { attr(df$mpg, "label") <- "Miles per gallon" p <- ggplot(df, aes(mpg, disp)) + geom_point() - labels <- ggplot_build(p)$plot$labels + labels <- get_labs(p) expect_equal(labels$x, "Miles per gallon") expect_equal(labels$y, "disp") }) @@ -79,14 +77,10 @@ test_that("Labels from static aesthetics are ignored (#6003)", { df <- data.frame(x = 1, y = 1, f = 1) p <- ggplot(df, aes(x, y, colour = f)) + geom_point() - labels <- ggplot_build(p)$plot$labels - - expect_equal(labels$colour, "f") + expect_equal(get_labs(p)$colour, "f") p <- ggplot(df, aes(x, y, colour = f)) + geom_point(colour = "blue") - labels <- ggplot_build(p)$plot$labels - - expect_null(labels$colour) + expect_null(get_labs(p)$colour) }) test_that("alt text is returned", { @@ -140,24 +134,25 @@ test_that("position axis label hierarchy works as intended", { geom_point(size = 5) p <- ggplot_build(p) + resolve_label <- function(x) p$layout$resolve_label(x, p$plot$labels) # In absence of explicit title, get title from mapping expect_identical( - p$layout$resolve_label(p$layout$panel_scales_x[[1]], p$plot$labels), + resolve_label(p$layout$panel_scales_x[[1]]), list(secondary = NULL, primary = "foo") ) expect_identical( - p$layout$resolve_label(p$layout$panel_scales_y[[1]], p$plot$labels), + resolve_label(p$layout$panel_scales_y[[1]]), list(primary = "bar", secondary = NULL) ) # Scale name overrules mapping label expect_identical( - p$layout$resolve_label(scale_x_continuous("Baz"), p$plot$labels), + resolve_label(scale_x_continuous("Baz")), list(secondary = NULL, primary = "Baz") ) expect_identical( - p$layout$resolve_label(scale_y_continuous("Qux"), p$plot$labels), + resolve_label(scale_y_continuous("Qux")), list(primary = "Qux", secondary = NULL) ) @@ -167,23 +162,23 @@ test_that("position axis label hierarchy works as intended", { p$plot$layers ) expect_identical( - p$layout$resolve_label(scale_x_continuous("Baz"), p$plot$labels), + resolve_label(scale_x_continuous("Baz")), list(secondary = NULL, primary = "quuX") ) expect_identical( - p$layout$resolve_label(scale_y_continuous("Qux"), p$plot$labels), + resolve_label(scale_y_continuous("Qux")), list(primary = "corgE", secondary = NULL) ) # Secondary axis names work xsec <- scale_x_continuous("Baz", sec.axis = dup_axis(name = "grault")) expect_identical( - p$layout$resolve_label(xsec, p$plot$labels), + resolve_label(xsec), list(secondary = "grault", primary = "quuX") ) ysec <- scale_y_continuous("Qux", sec.axis = dup_axis(name = "garply")) expect_identical( - p$layout$resolve_label(ysec, p$plot$labels), + resolve_label(ysec), list(primary = "corgE", secondary = "garply") ) @@ -194,12 +189,12 @@ test_that("position axis label hierarchy works as intended", { p$plot$layers ) expect_identical( - p$layout$resolve_label(xsec, p$plot$labels), + resolve_label(xsec), list(secondary = "waldo", primary = "quuX") ) ysec <- scale_y_continuous("Qux", sec.axis = dup_axis(name = "garply")) expect_identical( - p$layout$resolve_label(ysec, p$plot$labels), + resolve_label(ysec), list(primary = "corgE", secondary = "fred") ) }) @@ -220,16 +215,11 @@ test_that("moving guide positions lets titles follow", { ), p$plot$layers ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_x[[1]], p$plot$labels), - list(secondary = NULL, primary = "baz") - ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_y[[1]], p$plot$labels), - list(primary = "qux", secondary = NULL) - ) + labs <- get_labs(p) + expect <- list(x = "baz", x.sec = NULL, y = "qux", y.sec = NULL) + expect_identical(labs[names(expect)], expect) - # Guides at secondary positions (changes order of primary/secondary) + # Guides at secondary positions p$layout$setup_panel_guides( guides_list( list(x = guide_axis("baz", position = "top"), @@ -237,14 +227,8 @@ test_that("moving guide positions lets titles follow", { ), p$plot$layers ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_x[[1]], p$plot$labels), - list(primary = "baz", secondary = NULL) - ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_y[[1]], p$plot$labels), - list(secondary = NULL, primary = "qux") - ) + labs <- get_labs(p) + expect_identical(labs[names(expect)], expect) # Primary guides at secondary positions with # secondary guides at primary positions @@ -257,14 +241,9 @@ test_that("moving guide positions lets titles follow", { ), p$plot$layers ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_x[[1]], p$plot$labels), - list(primary = "baz", secondary = "quux") - ) - expect_identical( - p$layout$resolve_label(p$layout$panel_scales_y[[1]], p$plot$labels), - list(secondary = "corge", primary = "qux") - ) + labs <- get_labs(p) + expect[c("x.sec", "y.sec")] <- list("quux", "corge") + expect_identical(labs[names(expect)], expect) }) # Visual tests ------------------------------------------------------------ From 5184f5e39f862b8a14827b98ad883cc71b541f94 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 12:38:07 +0200 Subject: [PATCH 134/264] Clean up orphan functions and tiny one-off helpers (#6022) * replace single use internal functions * move helper to location where it is used * remove orphan functions * replace and remove redundant `adjust_breaks()` function * replace `df_rows()` with `vec_slice()` * inline `f_as_facets_list()` * inline `find_origin()` * inline `firstUpper()` * replace `has_name()` * replace `interleave()` with `vec_interleave()` * remove `cunion()` * inline `is_dotted_var()` * inline `is_facets()` * inline `is_labeller()` * inline `is_missing_arg()` * replace `is_npc()` (we partially backport `unitType()`) * inline `is_scalar_numeric()` * inline `is.margin()` * inline `is.sec_axis()` * inline `is.subclass()` * inline `is_triple_bang()` * remove `justify_grobs()` * inline `label_variable()` * more responsibility for `parse_axes_labeling()`, so that it is less distracting * remove `resolve_guide()` * inline revalue * simplify `scale_flip_position()` * remove `as.quoted()` (note there is still `as_quoted()`) * replace `simplify_formula()` with `simplify()` * inline `single_value()` * inline `update_guides()` * inline `is_column_vec()` and better name for `validate_column_vec()` * remove/replace `wrap_as_facets_list()` (by `compact_facets()` * finishing touches * `parse_axes_labeling` uses parent call * elaborate on regex pattern * Revert "inline `is_labeller()`" This reverts commit 9976913a361d4e3a040e5c09131d60e8973c2a93. * Revert "inline `is.sec_axis()`" This reverts commit 1bdc20d2dc48eec0fd6d1f45b7405856273689ac. * Revert "replace single use internal functions" This reverts commit 20fa50f80612fdd28dc71e28fdab281e68a83b1f. * Collection of test functions for user-facing components * apply tests when applicable * redocument * abolish `uniquecols()`'s rownames * move `is.*()` functions to class definitions --- DESCRIPTION | 1 - NAMESPACE | 15 ++-- R/aes-evaluation.R | 9 ++- R/aes.R | 15 +++- R/compat-plyr.R | 102 +++------------------------ R/coord-.R | 17 +++-- R/coord-cartesian-.R | 2 +- R/coord-map.R | 2 +- R/coord-sf.R | 17 ++--- R/facet-.R | 59 ++++++---------- R/facet-grid-.R | 4 +- R/facet-wrap.R | 8 +-- R/fortify.R | 2 +- R/geom-.R | 5 +- R/geom-defaults.R | 2 +- R/geom-hex.R | 31 -------- R/geom-label.R | 2 +- R/geom-violin.R | 2 +- R/ggproto.R | 8 +-- R/grob-dotstack.R | 4 +- R/guide-.R | 9 ++- R/guides-.R | 48 +++---------- R/labeller.R | 26 ++----- R/layer.R | 14 ++-- R/limits.R | 2 +- R/margins.R | 83 ++-------------------- R/performance.R | 7 -- R/plot-build.R | 11 ++- R/plot-construction.R | 11 ++- R/plot.R | 15 ++-- R/position-.R | 4 ++ R/quick-plot.R | 5 -- R/save.R | 2 +- R/scale-.R | 12 ++-- R/scale-colour.R | 2 +- R/scale-view.R | 17 ----- R/stat-.R | 4 ++ R/stat-bin2d.R | 15 +--- R/stat-summary-bin.R | 3 +- R/stat-summary.R | 10 +++ R/theme-elements.R | 4 ++ R/theme.R | 21 +++--- R/utilities-break.R | 10 +-- R/utilities-matrix.R | 25 ------- R/utilities.R | 86 +++------------------- man/ggproto.Rd | 5 -- man/is.Coord.Rd | 12 ---- man/is.facet.Rd | 15 ---- man/is.ggplot.Rd | 15 ---- man/is.theme.Rd | 15 ---- man/is_tests.Rd | 63 +++++++++++++++++ tests/testthat/_snaps/compat-plyr.md | 16 ----- tests/testthat/_snaps/margins.md | 4 -- tests/testthat/_snaps/utilities.md | 4 -- tests/testthat/test-compat-plyr.R | 6 -- tests/testthat/test-facet-.R | 22 +++--- tests/testthat/test-margins.R | 3 - tests/testthat/test-stat-bin2d.R | 4 +- tests/testthat/test-utilities.R | 4 -- 59 files changed, 281 insertions(+), 660 deletions(-) delete mode 100644 R/utilities-matrix.R delete mode 100644 man/is.Coord.Rd delete mode 100644 man/is.facet.Rd delete mode 100644 man/is.ggplot.Rd delete mode 100644 man/is.theme.Rd create mode 100644 man/is_tests.Rd delete mode 100644 tests/testthat/_snaps/compat-plyr.md delete mode 100644 tests/testthat/_snaps/margins.md delete mode 100644 tests/testthat/test-compat-plyr.R delete mode 100644 tests/testthat/test-margins.R diff --git a/DESCRIPTION b/DESCRIPTION index b4cd9ec950..ff587e4b88 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -276,7 +276,6 @@ Collate: 'utilities-break.R' 'utilities-grid.R' 'utilities-help.R' - 'utilities-matrix.R' 'utilities-patterns.R' 'utilities-resolution.R' 'utilities-tidy-eval.R' diff --git a/NAMESPACE b/NAMESPACE index 1220e7e6ef..5737492a00 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -84,8 +84,6 @@ S3method(guide_train,default) S3method(guide_transform,default) S3method(heightDetails,titleGrob) S3method(heightDetails,zeroGrob) -S3method(interleave,default) -S3method(interleave,unit) S3method(limits,Date) S3method(limits,POSIXct) S3method(limits,POSIXlt) @@ -126,8 +124,6 @@ S3method(scale_type,logical) S3method(scale_type,numeric) S3method(scale_type,ordered) S3method(scale_type,sfc) -S3method(single_value,default) -S3method(single_value,factor) S3method(summary,ggplot) S3method(vec_cast,character.mapped_discrete) S3method(vec_cast,double.mapped_discrete) @@ -464,9 +460,20 @@ export(guide_transform) export(guides) export(has_flipped_aes) export(is.Coord) +export(is.coord) +export(is.element) export(is.facet) +export(is.geom) export(is.ggplot) export(is.ggproto) +export(is.guide) +export(is.guides) +export(is.layer) +export(is.mapping) +export(is.margin) +export(is.position) +export(is.scale) +export(is.stat) export(is.theme) export(label_both) export(label_bquote) diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index 5554b54772..8e47ebcd1e 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -219,12 +219,10 @@ stage_scaled <- function(start = NULL, after_stat = NULL, after_scale = NULL) { } # Regex to determine if an identifier refers to a calculated aesthetic +# The pattern includes ye olde '...var...' syntax, which was +# deprecated in 3.4.0 in favour of `after_stat()` match_calculated_aes <- "^\\.\\.([a-zA-Z._]+)\\.\\.$" -is_dotted_var <- function(x) { - grepl(match_calculated_aes, x) -} - # Determine if aesthetic is calculated is_calculated_aes <- function(aesthetics, warn = FALSE) { vapply(aesthetics, is_calculated, warn = warn, logical(1), USE.NAMES = FALSE) @@ -246,7 +244,8 @@ is_calculated <- function(x, warn = FALSE) { if (is.null(x) || is.atomic(x)) { FALSE } else if (is.symbol(x)) { - res <- is_dotted_var(as.character(x)) + # Test if x is a dotted variable + res <- grepl(match_calculated_aes, as.character(x)) if (res && warn) { what <- I(paste0("The dot-dot notation (`", x, "`)")) var <- gsub(match_calculated_aes, "\\1", as.character(x)) diff --git a/R/aes.R b/R/aes.R index 4120657222..d739289b0e 100644 --- a/R/aes.R +++ b/R/aes.R @@ -102,6 +102,10 @@ aes <- function(x, y, ...) { rename_aes(aes) } +#' @export +#' @rdname is_tests +is.mapping <- function(x) inherits(x, "uneval") + # Wrap symbolic objects in quosures but pull out constants out of # quosures for backward-compatibility new_aesthetic <- function(x, env = globalenv()) { @@ -177,7 +181,12 @@ standardise_aes_names <- function(x) { x <- sub("color", "colour", x, fixed = TRUE) # convert old-style aesthetics names to ggplot version - revalue(x, ggplot_global$base_to_ggplot) + convert <- ggplot_global$base_to_ggplot + convert <- convert[names(convert) %in% x] + if (length(convert) > 0) { + x[match(names(convert), x)] <- convert + } + x } # x is a list of aesthetic mappings, as generated by aes() @@ -448,7 +457,9 @@ arg_enquos <- function(name, frame = caller_env()) { quo <- inject(enquo0(!!sym(name)), frame) expr <- quo_get_expr(quo) - if (!is_missing(expr) && is_triple_bang(expr)) { + is_triple_bang <- !is_missing(expr) && + is_bang(expr) && is_bang(expr[[2]]) && is_bang(expr[[c(2, 2)]]) + if (is_triple_bang) { # Evaluate `!!!` operand and create a list of quosures env <- quo_get_env(quo) xs <- eval_bare(expr[[2]][[2]][[2]], env) diff --git a/R/compat-plyr.R b/R/compat-plyr.R index efc2865a0c..bb3ea73cb9 100644 --- a/R/compat-plyr.R +++ b/R/compat-plyr.R @@ -166,84 +166,7 @@ join_keys <- function(x, y, by) { list(x = keys[seq_len(n_x)], y = keys[n_x + seq_len(n_y)], n = attr(keys, "n")) } -#' Replace specified values with new values, in a factor or character vector -#' -#' An easy to use substitution of elements in a string-like vector (character or -#' factor). If `x` is a character vector the matching elements will be replaced -#' directly and if `x` is a factor the matching levels will be replaced -#' -#' @param x A character or factor vector -#' @param replace A named character vector with the names corresponding to the -#' elements to replace and the values giving the replacement. -#' -#' @return A vector of the same class as `x` with the given values replaced -#' -#' @keywords internal -#' @noRd -#' -revalue <- function(x, replace) { - if (is.character(x)) { - replace <- replace[names(replace) %in% x] - if (length(replace) == 0) return(x) - x[match(names(replace), x)] <- replace - } else if (is.factor(x)) { - lev <- levels(x) - replace <- replace[names(replace) %in% lev] - if (length(replace) == 0) return(x) - lev[match(names(replace), lev)] <- replace - levels(x) <- lev - } else if (!is.null(x)) { - stop_input_type(x, "a factor or character vector") - } - x -} -# Iterate through a formula and return a quoted version -simplify_formula <- function(x) { - if (length(x) == 2 && x[[1]] == as.name("~")) { - return(simplify(x[[2]])) - } - if (length(x) < 3) - return(list(x)) - op <- x[[1]] - a <- x[[2]] - b <- x[[3]] - if (op == as.name("+") || op == as.name("*") || op == - as.name("~")) { - c(simplify(a), simplify(b)) - } - else if (op == as.name("-")) { - c(simplify(a), bquote(-.(x), list(x = simplify(b)))) - } - else { - list(x) - } -} -#' Create a quoted version of x -#' -#' This function captures the special meaning of formulas in the context of -#' facets in ggplot2, where `+` have special meaning. It works as -#' `plyr::as.quoted` but only for the special cases of `character`, `call`, and -#' `formula` input as these are the only situations relevant for ggplot2. -#' -#' @param x A formula, string, or call to be quoted -#' @param env The environment to a attach to the quoted expression. -#' -#' @keywords internal -#' @noRd -#' -as.quoted <- function(x, env = parent.frame()) { - x <- if (is.character(x)) { - lapply(x, function(x) parse(text = x)[[1]]) - } else if (is.formula(x)) { - simplify_formula(x) - } else if (is.call(x)) { - as.list(x)[-1] - } else { - cli::cli_abort("Must be a character vector, call, or formula.") - } - attributes(x) <- list(env = env, class = 'quoted') - x -} + # round a number to a given precision round_any <- function(x, accuracy, f = round) { check_numeric(x) @@ -286,29 +209,20 @@ dapply <- function(df, by, fun, ..., drop = TRUE) { } # Shortcut when only one group - if (all(vapply(grouping_cols, single_value, logical(1)))) { + has_single_group <- all(vapply( + grouping_cols, + function(x) identical(as.character(levels(x) %||% attr(x, "n")), "1"), + logical(1) + )) + if (has_single_group) { return(apply_fun(df)) } ids <- id(grouping_cols, drop = drop) group_rows <- split_with_index(seq_len(nrow(df)), ids) result <- lapply(seq_along(group_rows), function(i) { - cur_data <- df_rows(df, group_rows[[i]]) + cur_data <- vec_slice(df, group_rows[[i]]) apply_fun(cur_data) }) vec_rbind0(!!!result) } - -single_value <- function(x, ...) { - UseMethod("single_value") -} -#' @export -single_value.default <- function(x, ...) { - # This is set by id() used in creating the grouping var - identical(attr(x, "n"), 1L) -} -#' @export -single_value.factor <- function(x, ...) { - # Panels are encoded as factor numbers and can never be missing (NA) - identical(levels(x), "1") -} diff --git a/R/coord-.R b/R/coord-.R index 11f498c9b8..6764cf62a3 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -226,11 +226,18 @@ Coord <- ggproto("Coord", } ) -#' Is this object a coordinate system? -#' -#' @export is.Coord -#' @keywords internal -is.Coord <- function(x) inherits(x, "Coord") + +#' @export +#' @rdname is_tests +is.coord <- function(x) inherits(x, "Coord") + +#' @export +#' @rdname is_tests +#' @usage is.Coord(x) # Deprecated +is.Coord <- function(x) { + deprecate_soft0("3.5.2", "is.Coord()", "is.coord()") + is.coord(x) +} # Renders an axis with the correct orientation or zeroGrob if no axis should be # generated diff --git a/R/coord-cartesian-.R b/R/coord-cartesian-.R index 885918c3d1..1b13d9c6c0 100644 --- a/R/coord-cartesian-.R +++ b/R/coord-cartesian-.R @@ -163,7 +163,7 @@ view_scales_from_scale <- function(scale, coord_limits = NULL, expand = TRUE) { } panel_guides_grob <- function(guides, position, theme, labels = NULL) { - if (!inherits(guides, "Guides")) { + if (!is.guides(guides)) { return(zeroGrob()) } pair <- guides$get_position(position) diff --git a/R/coord-map.R b/R/coord-map.R index d300d33dce..3ba9260206 100644 --- a/R/coord-map.R +++ b/R/coord-map.R @@ -157,7 +157,7 @@ CoordMap <- ggproto("CoordMap", Coord, transform = function(self, data, panel_params) { trans <- mproject(self, data$x, data$y, panel_params$orientation) - out <- cunion(trans[c("x", "y")], data) + out <- data_frame0(!!!defaults(trans[c("x", "y")], data)) out$x <- rescale(out$x, 0:1, panel_params$x.proj) out$y <- rescale(out$y, 0:1, panel_params$y.proj) diff --git a/R/coord-sf.R b/R/coord-sf.R index f129947dc0..c31af6d393 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -545,11 +545,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, label_axes <- label_axes %|W|% "" } - if (is.character(label_axes)) { - label_axes <- parse_axes_labeling(label_axes) - } else if (!is.list(label_axes)) { - cli::cli_abort("Panel labeling format not recognized.") - } + label_axes <- parse_axes_labeling(label_axes) if (is.character(label_graticule)) { label_graticule <- unlist(strsplit(label_graticule, "")) @@ -582,9 +578,14 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, ) } -parse_axes_labeling <- function(x) { - labs <- unlist(strsplit(x, "")) - list(top = labs[1], right = labs[2], bottom = labs[3], left = labs[4]) +parse_axes_labeling <- function(x, call = caller_env()) { + if (is.character(x)) { + x <- unlist(strsplit(x, "")) + x <- list(top = x[1], right = x[2], bottom = x[3], left = x[4]) + } else if (!is.list(x)) { + cli::cli_abort("Panel labeling format not recognized.", call = call) + } + x } # This function does two things differently from standard breaks: diff --git a/R/facet-.R b/R/facet-.R index 2e349f6f97..8faafc1428 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -266,6 +266,10 @@ Facet <- ggproto("Facet", NULL, } ) +#' @export +#' @rdname is_tests +is.facet <- function(x) inherits(x, "Facet") + # Helpers ----------------------------------------------------------------- #' Quote faceting variables @@ -353,13 +357,6 @@ get_strip_labels <- function(plot = get_last_plot()) { plot$plot$facet$format_strip_labels(layout, params) } -#' Is this object a faceting specification? -#' -#' @param x object to test -#' @keywords internal -#' @export -is.facet <- function(x) inherits(x, "Facet") - # A "special" value, currently not used but could be used to determine # if faceting is active NO_PANEL <- -1L @@ -418,7 +415,14 @@ as_facets_list <- function(x) { # distinct facet dimensions and `+` defines multiple facet variables # inside each dimension. if (is_formula(x)) { - return(f_as_facets_list(x)) + if (length(x) == 2) { + rows <- f_as_facets(NULL) + cols <- f_as_facets(x) + } else { + rows <- f_as_facets(x[-3]) + cols <- f_as_facets(x[-2]) + } + return(list(rows, cols)) } # For backward-compatibility with facet_wrap() @@ -437,7 +441,7 @@ as_facets_list <- function(x) { } validate_facets <- function(x) { - if (inherits(x, "uneval")) { + if (is.mapping(x)) { cli::cli_abort("Please use {.fn vars} to supply facet variables.") } # Native pipe have higher precedence than + so any type of gg object can be @@ -451,10 +455,9 @@ validate_facets <- function(x) { x } - # Flatten a list of quosures objects to a quosures object, and compact it compact_facets <- function(x) { - + x <- as_facets_list(x) proxy <- vec_proxy(x) is_list <- vapply(proxy, vec_is_list, logical(1)) proxy[is_list] <- lapply(proxy[is_list], unclass) @@ -501,18 +504,10 @@ simplify <- function(x) { } } -f_as_facets_list <- function(f) { - lhs <- function(x) if (length(x) == 2) NULL else x[-3] - rhs <- function(x) if (length(x) == 2) x else x[-2] - - rows <- f_as_facets(lhs(f)) - cols <- f_as_facets(rhs(f)) - - list(rows, cols) -} - as_facets <- function(x) { - if (is_facets(x)) { + is_facets <- is.list(x) && length(x) > 0 && + all(vapply(x, is_quosure, logical(1))) + if (is_facets) { return(x) } @@ -533,27 +528,13 @@ f_as_facets <- function(f) { env <- f_env(f) %||% globalenv() # as.quoted() handles `+` specifications - vars <- as.quoted(f) + vars <- simplify(f) - # `.` in formulas is ignored - vars <- discard_dots(vars) + # `.` in formulas is discarded + vars <- vars[!vapply(vars, identical, logical(1), as.name("."))] as_quosures(vars, env, named = TRUE) } -discard_dots <- function(x) { - x[!vapply(x, identical, logical(1), as.name("."))] -} - -is_facets <- function(x) { - if (!is.list(x)) { - return(FALSE) - } - if (!length(x)) { - return(FALSE) - } - all(vapply(x, is_quosure, logical(1))) -} - # When evaluating variables in a facet specification, we evaluate bare # variables and expressions slightly differently. Bare variables should diff --git a/R/facet-grid-.R b/R/facet-grid-.R index a0b6e31931..784e394885 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -219,8 +219,8 @@ grid_as_facets_list <- function(rows, cols) { check_object(cols, is_quosures, "a {.fn vars} specification", allow_null = TRUE) list( - rows = compact_facets(as_facets_list(rows)), - cols = compact_facets(as_facets_list(cols)) + rows = compact_facets(rows), + cols = compact_facets(cols) ) } diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 8564f319b7..4650d12dd8 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -177,7 +177,7 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", labeller <- check_labeller(labeller) # Flatten all facets dimensions into a single one - facets <- wrap_as_facets_list(facets) + facets <- compact_facets(facets) if (lifecycle::is_present(switch) && !is.null(switch)) { deprecate_warn0("2.2.0", "facet_wrap(switch)", "facet_wrap(strip.position)") @@ -213,12 +213,6 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", ) } -# Returns a quosures object -wrap_as_facets_list <- function(x) { - facets_list <- as_facets_list(x) - compact_facets(facets_list) -} - #' @rdname ggplot2-ggproto #' @format NULL #' @usage NULL diff --git a/R/fortify.R b/R/fortify.R index 5b5b7c5171..da4bcf7892 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -82,7 +82,7 @@ fortify.default <- function(model, data, ...) { "or an object coercible by {.fn fortify}, or a valid ", "{.cls data.frame}-like object coercible by {.fn as.data.frame}" ) - if (inherits(model, "uneval")) { + if (is.mapping(model)) { msg <- c( paste0(msg, ", not ", obj_type_friendly(model), "."), "i" = "Did you accidentally pass {.fn aes} to the {.arg data} argument?" diff --git a/R/geom-.R b/R/geom-.R index 5b6a2af09d..c5a1ab275d 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -183,7 +183,7 @@ Geom <- ggproto("Geom", modified_aes <- data_frame0(!!!compact(modified_aes)) - data <- cunion(modified_aes, data) + data <- data_frame0(!!!defaults(modified_aes, data)) } # Override mappings with params @@ -236,6 +236,9 @@ Geom <- ggproto("Geom", ) +#' @export +#' @rdname is_tests +is.geom <- function(x) inherits(x, "Geom") eval_from_theme <- function(aesthetics, theme) { themed <- is_themed_aes(aesthetics) diff --git a/R/geom-defaults.R b/R/geom-defaults.R index 65974f841a..b185990fbb 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -98,7 +98,7 @@ get_geom_defaults <- function(geom, theme = theme_get()) { if (is.character(geom)) { geom <- check_subclass(geom, "Geom") } - if (inherits(geom, "Geom")) { + if (is.geom(geom)) { out <- geom$use_defaults(data = NULL, theme = theme) return(out) } diff --git a/R/geom-hex.R b/R/geom-hex.R index 6badb8f87a..152227a40b 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -118,34 +118,3 @@ GeomHex <- ggproto("GeomHex", Geom, rename_size = TRUE ) - - -# Draw hexagon grob -# Modified from code by Nicholas Lewin-Koh and Martin Maechler -# -# @param x positions of hex centres -# @param y positions -# @param size vector of hex sizes -# @param gp graphical parameters -# @keyword internal -# -# THIS IS NO LONGER USED BUT LEFT IF CODE SOMEWHERE ELSE RELIES ON IT -hexGrob <- function(x, y, size = rep(1, length(x)), gp = gpar()) { - if (length(y) != length(x)) { - cli::cli_abort("{.arg x} and {.arg y} must have the same length") - } - - dx <- resolution(x, FALSE) - dy <- resolution(y, FALSE) / sqrt(3) / 2 * 1.15 - - hexC <- hexbin::hexcoords(dx, dy, n = 1) - - n <- length(x) - - polygonGrob( - x = rep.int(hexC$x, n) * rep(size, each = 6) + rep(x, each = 6), - y = rep.int(hexC$y, n) * rep(size, each = 6) + rep(y, each = 6), - default.units = "native", - id.lengths = rep(6, n), gp = gp - ) -} diff --git a/R/geom-label.R b/R/geom-label.R index 4168c98d94..6f21478da0 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -78,7 +78,7 @@ GeomLabel <- ggproto("GeomLabel", Geom, data <- coord$transform(data, panel_params) data$vjust <- compute_just(data$vjust, data$y, data$x, data$angle) data$hjust <- compute_just(data$hjust, data$x, data$y, data$angle) - if (!inherits(label.padding, "margin")) { + if (!is.margin("margin")) { label.padding <- rep(label.padding, length.out = 4) } diff --git a/R/geom-violin.R b/R/geom-violin.R index 17a2d40e94..9976e5b8a4 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -223,7 +223,7 @@ create_quantile_segment_frame <- function(data, draw_quantiles) { # We have two rows per segment drawn. Each segment gets its own group. data_frame0( - x = interleave(violin.xminvs, violin.xmaxvs), + x = vec_interleave(violin.xminvs, violin.xmaxvs), y = rep(ys, each = 2), group = rep(ys, each = 2) ) diff --git a/R/ggproto.R b/R/ggproto.R index 0af8a5a5ab..6165a9707d 100644 --- a/R/ggproto.R +++ b/R/ggproto.R @@ -98,6 +98,9 @@ ggproto <- function(`_class` = NULL, `_inherit` = NULL, ...) { e } +#' @export +#' @rdname is_tests +is.ggproto <- function(x) inherits(x, "ggproto") #' @export #' @rdname ggproto @@ -106,11 +109,6 @@ ggproto_parent <- function(parent, self) { structure(list(parent = parent, self = self), class = "ggproto_parent") } -#' @param x An object to test. -#' @export -#' @rdname ggproto -is.ggproto <- function(x) inherits(x, "ggproto") - fetch_ggproto <- function(x, name) { res <- NULL diff --git a/R/grob-dotstack.R b/R/grob-dotstack.R index 75ca9e81ed..d3463c18bd 100644 --- a/R/grob-dotstack.R +++ b/R/grob-dotstack.R @@ -14,15 +14,13 @@ dotstackGrob <- function( y <- unit(y, default.units) if (!is.unit(dotdia)) dotdia <- unit(dotdia, default.units) - if (!is_npc(dotdia)) + if (!unitType(dotdia) == "npc") cli::cli_warn("Unit type of dotdia should be {.val npc}") grob(x = x, y = y, stackaxis = stackaxis, dotdia = dotdia, stackposition = stackposition, stackdir = stackdir, stackratio = stackratio, name = name, gp = gp, vp = vp, cl = "dotstackGrob") } -# Only cross-version reliable way to check the unit of a unit object -is_npc <- function(x) isTRUE(grepl('^[^+^-^\\*]*[^s]npc$', as.character(x))) #' @export makeContext.dotstackGrob <- function(x) { diff --git a/R/guide-.R b/R/guide-.R index 4cb77ee7bb..dd63949cd2 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -66,6 +66,10 @@ new_guide <- function(..., available_aes = "any", super) { ) } +#' @export +#' @rdname is_tests +is.guide <- function(x) inherits(x, "Guide") + #' @section Guides: #' #' The `guide_*()` functions, such as `guide_legend()` return an object that @@ -377,7 +381,7 @@ Guide <- ggproto( # Renders tickmarks build_ticks = function(key, elements, params, position = params$position, length = elements$ticks_length) { - if (!inherits(elements, "element")) { + if (!is.element(elements)) { elements <- elements$ticks } if (!inherits(elements, "element_line")) { @@ -519,7 +523,8 @@ opposite_position <- function(position) { top = "bottom", bottom = "top", left = "right", - right = "left" + right = "left", + position ) } diff --git a/R/guides-.R b/R/guides-.R index fcd65bb94a..d250c78025 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -69,7 +69,7 @@ NULL guides <- function(...) { args <- list2(...) if (length(args) > 0) { - if (is.list(args[[1]]) && !inherits(args[[1]], "guide")) args <- args[[1]] + if (is.list(args[[1]]) && !is.guide(args[[1]])) args <- args[[1]] args <- rename_aes(args) } @@ -109,18 +109,9 @@ guides <- function(...) { NULL } -update_guides <- function(p, guides) { - p <- plot_clone(p) - if (inherits(p$guides, "Guides")) { - old <- p$guides - new <- ggproto(NULL, old) - new$add(guides) - p$guides <- new - } else { - p$guides <- guides - } - p -} +#' @export +#' @rdname is_tests +is.guides <- function(x) inherits(x, "Guides") # Class ------------------------------------------------------------------- @@ -151,7 +142,7 @@ Guides <- ggproto( if (is.null(guides)) { return(invisible()) } - if (inherits(guides, "Guides")) { + if (is.guides(guides)) { guides <- guides$guides } self$guides <- defaults(guides, self$guides) @@ -350,13 +341,8 @@ Guides <- ggproto( # Find guide for aesthetic-scale combination # Hierarchy is in the order: # plot + guides(XXX) + scale_ZZZ(guide = XXX) > default(i.e., legend) - guide <- resolve_guide( - aesthetic = aesthetics[idx], - scale = scales[[idx]], - guides = guides, - default = default, - null = missing - ) + guide <- guides[[aesthetics[idx]]] %||% scales[[idx]]$guide %|W|% + default %||% missing if (isFALSE(guide)) { deprecate_warn0("3.3.4", I("The `guide` argument in `scale_*()` cannot be `FALSE`. This "), I('"none"')) @@ -870,24 +856,6 @@ include_layer_in_guide <- function(layer, matched) { isTRUE(layer$show.legend) } -# Simplify legend position to one of horizontal/vertical/inside -legend_position <- function(position) { - if (length(position) == 1) { - if (position %in% c("top", "bottom")) { - "horizontal" - } else { - "vertical" - } - } else { - "inside" - } -} - -# resolve the guide from the scale and guides -resolve_guide <- function(aesthetic, scale, guides, default = "none", null = "none") { - guides[[aesthetic]] %||% scale$guide %|W|% default %||% null -} - # validate guide object validate_guide <- function(guide) { # if guide is specified by character, then find the corresponding guide @@ -898,7 +866,7 @@ validate_guide <- function(guide) { guide <- fun() } } - if (inherits(guide, "Guide")) { + if (is.guide(guide)) { return(guide) } if (inherits(guide, "guide") && is.list(guide)) { diff --git a/R/labeller.R b/R/labeller.R index f23f22b459..4ca220c2b4 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -114,21 +114,17 @@ label_value <- function(labels, multi_line = TRUE) { # currently needed for Roxygen class(label_value) <- c("function", "labeller") -# Helper for label_both -label_variable <- function(labels, multi_line = TRUE) { - if (multi_line) { - row <- as.list(names(labels)) - } else { - row <- list(paste(names(labels), collapse = ", ")) - } - lapply(row, rep, nrow(labels) %||% length(labels[[1]])) -} - #' @rdname labellers #' @export label_both <- function(labels, multi_line = TRUE, sep = ": ") { value <- label_value(labels, multi_line = multi_line) - variable <- label_variable(labels, multi_line = multi_line) + + if (isTRUE(multi_line)) { + row <- as.list(names(labels)) + } else { + row <- list(paste(names(labels), collapse = ", ")) + } + variable <- lapply(row, rep, nrow(labels) %||% length(labels[[1]])) if (multi_line) { out <- vector("list", length(value)) @@ -176,14 +172,6 @@ label_parsed <- function(labels, multi_line = TRUE) { } class(label_parsed) <- c("function", "labeller") -find_names <- function(expr) { - if (is.call(expr)) { - unlist(lapply(expr[-1], find_names)) - } else if (is.name(expr)) { - as.character(expr) - } -} - #' Label with mathematical expressions #' #' `label_bquote()` offers a flexible way of labelling diff --git a/R/layer.R b/R/layer.R index 8acb438c9e..3fd89cf3f7 100644 --- a/R/layer.R +++ b/R/layer.R @@ -58,8 +58,8 @@ #' `NA`, the default, includes if any aesthetics are mapped. #' `FALSE` never includes, and `TRUE` always includes. #' It can also be a named logical vector to finely select the aesthetics to -#' display. To include legend keys for all levels, even -#' when no data exists, use `TRUE`. If `NA`, all levels are shown in legend, +#' display. To include legend keys for all levels, even +#' when no data exists, use `TRUE`. If `NA`, all levels are shown in legend, #' but unobserved levels are omitted. #' @param inherit.aes If `FALSE`, overrides the default aesthetics, #' rather than combining with them. This is most useful for helper functions @@ -202,8 +202,12 @@ layer <- function(geom = NULL, stat = NULL, ) } +#' @export +#' @rdname is_tests +is.layer <- function(x) inherits(x, "Layer") + validate_mapping <- function(mapping, call = caller_env()) { - if (!inherits(mapping, "uneval")) { + if (!is.mapping(mapping)) { msg <- "{.arg mapping} must be created by {.fn aes}." # Native pipe have higher precedence than + so any type of gg object can be # expected here, not just ggplot @@ -419,7 +423,7 @@ Layer <- ggproto("Layer", NULL, } stat_data <- cleanup_mismatched_data(stat_data, nrow(data), "after_stat") - cunion(stat_data, data) + data_frame0(!!!defaults(stat_data, data)) }, compute_geom_1 = function(self, data) { @@ -468,8 +472,6 @@ Layer <- ggproto("Layer", NULL, } ) -is.layer <- function(x) inherits(x, "Layer") - check_subclass <- function(x, subclass, argname = to_lower_ascii(subclass), env = parent.frame(), diff --git a/R/limits.R b/R/limits.R index 087c4c11d0..2e31220ec8 100644 --- a/R/limits.R +++ b/R/limits.R @@ -80,7 +80,7 @@ lims <- function(...) { args <- list2(...) - if (!all(has_name(args))) { + if (!is_named2(args)) { cli::cli_abort("All arguments must be named.") } env <- current_env() diff --git a/R/margins.R b/R/margins.R index 176072b4de..7104a7d330 100644 --- a/R/margins.R +++ b/R/margins.R @@ -8,9 +8,10 @@ margin <- function(t = 0, r = 0, b = 0, l = 0, unit = "pt") { class(u) <- c("margin", class(u)) u } -is.margin <- function(x) { - inherits(x, "margin") -} + +#' @export +#' @rdname is_tests +is.margin <- function(x) inherits(x, "margin") #' Create a text grob with the proper location and margins #' @@ -151,82 +152,6 @@ heightDetails.titleGrob <- function(x) { sum(x$heights) } -#' Justifies a grob within a larger drawing area -#' -#' `justify_grobs()` can be used to take one or more grobs and draw them justified inside a larger -#' drawing area, such as the cell in a gtable. It is needed to correctly place [`titleGrob`]s -#' with margins. -#' -#' @param grobs The single grob or list of grobs to justify. -#' @param x,y x and y location of the reference point relative to which justification -#' should be performed. If `NULL`, justification will be done relative to the -#' enclosing drawing area (i.e., `x = hjust` and `y = vjust`). -#' @param hjust,vjust Horizontal and vertical justification of the grob relative to `x` and `y`. -#' @param int_angle Internal angle of the grob to be justified. When justifying a text -#' grob with rotated text, this argument can be used to make `hjust` and `vjust` operate -#' relative to the direction of the text. -#' @param debug If `TRUE`, aids visual debugging by drawing a solid -#' rectangle behind the complete grob area. -#' -#' @noRd -justify_grobs <- function(grobs, x = NULL, y = NULL, hjust = 0.5, vjust = 0.5, - int_angle = 0, debug = FALSE) { - if (!inherits(grobs, "grob")) { - if (is.list(grobs)) { - return(lapply(grobs, justify_grobs, x, y, hjust, vjust, int_angle, debug)) - } - else { - stop_input_type(grobs, as_cli("an individual {.cls grob} or list of {.cls grob} objects")) - } - } - - if (inherits(grobs, "zeroGrob")) { - return(grobs) - } - - # adjust hjust and vjust according to internal angle - just <- rotate_just(int_angle, hjust, vjust) - - x <- x %||% unit(just$hjust, "npc") - y <- y %||% unit(just$vjust, "npc") - - - if (isTRUE(debug)) { - children <- gList( - rectGrob(gp = gg_par(fill = "lightcyan", col = NA)), - grobs - ) - } - else { - children <- gList(grobs) - } - - - result_grob <- gTree( - children = children, - vp = viewport( - x = x, - y = y, - width = grobWidth(grobs), - height = grobHeight(grobs), - just = unlist(just) - ) - ) - - - if (isTRUE(debug)) { - #cat("x, y:", c(x, y), "\n") - #cat("E - hjust, vjust:", c(hjust, vjust), "\n") - grobTree( - result_grob, - pointsGrob(x, y, pch = 20, gp = gg_par(col = "mediumturquoise")) - ) - } else { - result_grob - } -} - - #' Rotate justification parameters counter-clockwise #' #' @param angle angle of rotation, in degrees diff --git a/R/performance.R b/R/performance.R index b26b1a7072..7676ed31d6 100644 --- a/R/performance.R +++ b/R/performance.R @@ -10,13 +10,6 @@ mat_2_df <- function(x, col_names = colnames(x)) { data_frame0(!!!cols, .size = nrow(x)) } -df_col <- function(x, name) .subset2(x, name) - -df_rows <- function(x, i) { - cols <- lapply(x, `[`, i = i) - data_frame0(!!!cols, .size = length(i)) -} - # More performant modifyList without recursion modify_list <- function(old, new) { for (i in names(new)) old[[i]] <- new[[i]] diff --git a/R/plot-build.R b/R/plot-build.R index 36f33616fd..c7e641c8e6 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -288,7 +288,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot_margin <- calc_element("plot.margin", theme) plot_table <- gtable_add_padding(plot_table, plot_margin) - if (inherits(theme$plot.background, "element")) { + if (is.element(theme$plot.background)) { plot_table <- gtable_add_grob(plot_table, element_render(theme, "plot.background"), t = 1, l = 1, b = -1, r = -1, name = "background", z = -Inf) @@ -408,11 +408,10 @@ table_add_tag <- function(table, label, theme) { x <- unit(position[1], "npc") y <- unit(position[2], "npc") } - # Do manual placement of tag - tag <- justify_grobs( - tag, x = x, y = y, - hjust = element$hjust, vjust = element$vjust, - int_angle = element$angle, debug = element$debug + # Re-render with manual positions + tag <- element_grob( + element, x = x, y = y, label = label, + margin_y = TRUE, margin_x = TRUE ) if (location == "plot") { table <- gtable_add_grob( diff --git a/R/plot-construction.R b/R/plot-construction.R index e6a86139eb..b021b630e9 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -149,7 +149,16 @@ ggplot_add.labels <- function(object, plot, object_name) { } #' @export ggplot_add.Guides <- function(object, plot, object_name) { - update_guides(plot, object) + if (is.guides(plot$guides)) { + # We clone the guides object to prevent modify-in-place of guides + old <- plot$guides + new <- ggproto(NULL, old) + new$add(object) + plot$guides <- new + } else { + plot$guides <- object + } + plot } #' @export ggplot_add.uneval <- function(object, plot, object_name) { diff --git a/R/plot.R b/R/plot.R index 97a1e96102..f6a6aaeb49 100644 --- a/R/plot.R +++ b/R/plot.R @@ -111,7 +111,7 @@ ggplot <- function(data = NULL, mapping = aes(), ..., #' @export ggplot.default <- function(data = NULL, mapping = aes(), ..., environment = parent.frame()) { - if (!missing(mapping) && !inherits(mapping, "uneval")) { + if (!missing(mapping) && !is.mapping(mapping)) { cli::cli_abort(c( "{.arg mapping} must be created with {.fn aes}.", "x" = "You've supplied {.obj_type_friendly {mapping}}." @@ -148,6 +148,13 @@ ggplot.function <- function(data = NULL, mapping = aes(), ..., )) } +#' Reports whether x is a type of object +#' @param x An object to test +#' @keywords internal +#' @export +#' @name is_tests +is.ggplot <- function(x) inherits(x, "ggplot") + plot_clone <- function(plot) { p <- plot p$scales <- plot$scales$clone() @@ -155,12 +162,6 @@ plot_clone <- function(plot) { p } -#' Reports whether x is a ggplot object -#' @param x An object to test -#' @keywords internal -#' @export -is.ggplot <- function(x) inherits(x, "ggplot") - #' Explicitly draw plot #' #' Generally, you do not need to print or plot a ggplot2 plot explicitly: the diff --git a/R/position-.R b/R/position-.R index 559c6c68d0..88d6f914a9 100644 --- a/R/position-.R +++ b/R/position-.R @@ -69,6 +69,10 @@ Position <- ggproto("Position", } ) +#' @export +#' @rdname is_tests +is.position <- function(x) inherits(x, "Position") + #' Convenience function to transform all position variables. #' #' @param trans_x,trans_y Transformation functions for x and y aesthetics. diff --git a/R/quick-plot.R b/R/quick-plot.R index 0ef5852cfb..38cfd895fc 100644 --- a/R/quick-plot.R +++ b/R/quick-plot.R @@ -173,8 +173,3 @@ qplot <- function(x, y, ..., data, facets = NULL, margins = FALSE, #' @export #' @rdname qplot quickplot <- qplot - -is.constant <- function(x) { - is_I_call <- function(x) is.call(x) && identical(x[[1]], quote(I)) - vapply(x, is_I_call, logical(1)) -} diff --git a/R/save.R b/R/save.R index acc4176162..ffe6945410 100644 --- a/R/save.R +++ b/R/save.R @@ -182,7 +182,7 @@ parse_dpi <- function(dpi, call = caller_env()) { print = 300, retina = 320, ) - } else if (is_scalar_numeric(dpi)) { + } else if (is_bare_numeric(dpi, n = 1L)) { dpi } else { stop_input_type(dpi, "a single number or string", call = call) diff --git a/R/scale-.R b/R/scale-.R index fd0bbd444f..878cc602b9 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -357,6 +357,10 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name = ) } +#' @export +#' @rdname is_tests +is.scale <- function(x) inherits(x, "Scale") + #' @section Scales: #' #' All `scale_*` functions like [scale_x_continuous()] return a `Scale*` @@ -1379,13 +1383,7 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, # In place modification of a scale to change the primary axis scale_flip_position <- function(scale) { - scale$position <- switch(scale$position, - top = "bottom", - bottom = "top", - left = "right", - right = "left", - scale$position - ) + scale$position <- opposite_position(scale$position) invisible() } diff --git a/R/scale-colour.R b/R/scale-colour.R index 71255e2033..19cdda1396 100644 --- a/R/scale-colour.R +++ b/R/scale-colour.R @@ -197,7 +197,7 @@ scale_fill_binned <- function(..., # helper function to make sure that the provided scale is of the correct # type (i.e., is continuous and works with the provided aesthetic) check_scale_type <- function(scale, name, aesthetic, scale_is_discrete = FALSE, call = caller_env()) { - if (!is.ggproto(scale) || !inherits(scale, "Scale")) { + if (!is.ggproto(scale) || !is.scale(scale)) { cli::cli_abort(c( "The {.arg type} argument must return a continuous scale for the {.field {aesthetic}} aesthetic.", "x" = "The provided object is not a scale function." diff --git a/R/scale-view.R b/R/scale-view.R index de78ebffb6..3cf18147ec 100644 --- a/R/scale-view.R +++ b/R/scale-view.R @@ -90,23 +90,6 @@ view_scale_secondary <- function(scale, limits = scale$get_limits(), } } -view_scale_empty <- function() { - ggproto(NULL, ViewScale, - is_empty = function() TRUE, - is_discrete = function() NA, - dimension = function() c(0, 1), - get_limits = function() c(0, 1), - get_breaks = function() NULL, - get_breaks_minor = function() NULL, - get_labels = function(breaks = NULL) breaks, - rescale = function(x) cli::cli_abort("Not implemented."), - map = function(x) cli::cli_abort("Not implemented."), - make_title = function(title) title, - break_positions = function() NULL, - break_positions_minor = function() NULL - ) -} - ViewScale <- ggproto("ViewScale", NULL, # map, rescale, and make_title need a reference # to the original scale diff --git a/R/stat-.R b/R/stat-.R index 2d56937b06..11cdbc67d6 100644 --- a/R/stat-.R +++ b/R/stat-.R @@ -218,3 +218,7 @@ Stat <- ggproto("Stat", } ) + +#' @export +#' @rdname is_tests +is.stat <- function(x) inherits(x, "Stat") diff --git a/R/stat-bin2d.R b/R/stat-bin2d.R index 69f57ebee3..bdb69db23a 100644 --- a/R/stat-bin2d.R +++ b/R/stat-bin2d.R @@ -104,7 +104,7 @@ dual_param <- function(x, default = list(x = NULL, y = NULL)) { } bin2d_breaks <- function(scale, breaks = NULL, origin = NULL, binwidth = NULL, - bins = 30, right = TRUE) { + bins = 30, closed = "right") { # Bins for categorical data should take the width of one level, # and should show up centered over their tick marks. All other parameters # are ignored. @@ -138,18 +138,7 @@ bin2d_breaks <- function(scale, breaks = NULL, origin = NULL, binwidth = NULL, if (length(breaks) > 1 && breaks[length(breaks) - 1] >= range[2]) { breaks <- breaks[-length(breaks)] } - - adjust_breaks(breaks, right) -} - -adjust_breaks <- function(x, right = TRUE) { - diddle <- 1e-07 * stats::median(diff(x)) - if (right) { - fuzz <- c(-diddle, rep.int(diddle, length(x) - 1)) - } else { - fuzz <- c(rep.int(-diddle, length(x) - 1), diddle) - } - sort(x) + fuzz + bins(breaks, closed)$fuzzy } bin_loc <- function(x, id) { diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index d94b6ddab9..a56bea189e 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -82,7 +82,8 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, flipped_aes = FALSE, width = NULL) { data <- flip_data(data, flipped_aes) x <- flipped_names(flipped_aes)$x - breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, right = right) + breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, + closed = if (right) "right" else "left") data$bin <- cut(data$x, breaks, include.lowest = TRUE, labels = FALSE) out <- dapply(data, "bin", fun %||% function(df) mean_se(df$y)) diff --git a/R/stat-summary.R b/R/stat-summary.R index 6476021fc5..a32eda8ca0 100644 --- a/R/stat-summary.R +++ b/R/stat-summary.R @@ -222,6 +222,16 @@ summarise_by_x <- function(data, summary, ...) { merge(summary, unique, by = c("x", "group"), sort = FALSE) } +# Return unique columns +# This is used for figuring out which columns are constant within a group +# +# @keyword internal +uniquecols <- function(df) { + df <- df[1, sapply(df, is_unique), drop = FALSE] + attr(df, "row.names") <- .set_row_names(nrow(df)) + df +} + #' A selection of summary functions from Hmisc #' #' @description diff --git a/R/theme-elements.R b/R/theme-elements.R index 747bb0cf78..7e5de2f777 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -202,6 +202,10 @@ element_geom <- function( pointsize = 1.5, pointshape = 19 ) +#' @export +#' @rdname is_tests +is.element <- function(x) inherits(x, "element") + #' @export print.element <- function(x, ...) utils::str(x) diff --git a/R/theme.R b/R/theme.R index 43c379f9b6..2eedd300c5 100644 --- a/R/theme.R +++ b/R/theme.R @@ -529,7 +529,7 @@ theme <- function(..., # If complete theme set all non-blank elements to inherit from blanks if (complete) { elements <- lapply(elements, function(el) { - if (inherits(el, "element") && !inherits(el, "element_blank")) { + if (is.element(el) && !inherits(el, "element_blank")) { el$inherit.blank <- TRUE } el @@ -543,6 +543,10 @@ theme <- function(..., ) } +#' @export +#' @rdname is_tests +is.theme <- function(x) inherits(x, "theme") + # check whether theme is complete is_theme_complete <- function(x) isTRUE(attr(x, "complete", exact = TRUE)) @@ -894,7 +898,9 @@ combine_elements <- function(e1, e2) { } # If e2 is 'richer' than e1, fill e2 with e1 parameters - if (is.subclass(e2, e1)) { + is_subclass <- !any(inherits(e2, class(e1), which = TRUE) == 0) + is_subclass <- is_subclass && length(setdiff(class(e2), class(e1)) > 0) + if (is_subclass) { new <- defaults(e1, e2) e2[names(new)] <- new return(e2) @@ -903,17 +909,6 @@ combine_elements <- function(e1, e2) { e1 } -is.subclass <- function(x, y) { - inheritance <- inherits(x, class(y), which = TRUE) - !any(inheritance == 0) && length(setdiff(class(x), class(y))) > 0 -} - -#' Reports whether x is a theme object -#' @param x An object to test -#' @export -#' @keywords internal -is.theme <- function(x) inherits(x, "theme") - #' @export `$.theme` <- function(x, ...) { .subset2(x, ...) diff --git a/R/utilities-break.R b/R/utilities-break.R index 0ed711ad7a..11bc22019d 100644 --- a/R/utilities-break.R +++ b/R/utilities-break.R @@ -79,8 +79,8 @@ cut_width <- function(x, width, center = NULL, boundary = NULL, closed = "right" } boundary <- as.numeric(boundary) - # Determine bins - min_x <- find_origin(x_range, width, boundary) + # Determine bins, find origin + min_x <- boundary + floor((x_range[1] - boundary) / width) * width # Small correction factor so that we don't get an extra bin when, for # example, origin = 0, max(x) = 20, width = 10. max_x <- max(x, na.rm = TRUE) + (1 - 1e-08) * width @@ -89,12 +89,6 @@ cut_width <- function(x, width, center = NULL, boundary = NULL, closed = "right" cut(x, breaks, include.lowest = TRUE, right = (closed == "right"), ...) } -# Find the left side of left-most bin -find_origin <- function(x_range, width, boundary) { - shift <- floor((x_range[1] - boundary) / width) - boundary + shift * width -} - breaks <- function(x, equal, nbins = NULL, binwidth = NULL) { equal <- arg_match0(equal, c("numbers", "width")) if ((!is.null(nbins) && !is.null(binwidth)) || (is.null(nbins) && is.null(binwidth))) { diff --git a/R/utilities-matrix.R b/R/utilities-matrix.R deleted file mode 100644 index dd35e082ba..0000000000 --- a/R/utilities-matrix.R +++ /dev/null @@ -1,25 +0,0 @@ -# Col union -# Form the union of columns in a and b. If there are columns of the same name in both a and b, take the column from a. -# -# @param data frame a -# @param data frame b -# @keyword internal -cunion <- function(a, b) { - if (length(a) == 0) return(b) - if (length(b) == 0) return(a) - - cbind(a, b[setdiff(names(b), names(a))]) -} - -# Interleave (or zip) multiple units into one vector -interleave <- function(...) UseMethod("interleave") -#' @export -interleave.unit <- function(...) { - units <- lapply(list(...), as.list) - interleaved_list <- interleave.default(!!!units) - inject(unit.c(!!!interleaved_list)) -} -#' @export -interleave.default <- function(...) { - vec_interleave(...) -} diff --git a/R/utilities.R b/R/utilities.R index 56325e83d9..8772ed771b 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -84,16 +84,6 @@ clist <- function(l) { paste(paste(names(l), l, sep = " = ", collapse = ", "), sep = "") } -# Return unique columns -# This is used for figuring out which columns are constant within a group -# -# @keyword internal -uniquecols <- function(df) { - df <- df[1, sapply(df, is_unique), drop = FALSE] - rownames(df) <- seq_len(nrow(df)) - df -} - #' Convenience function to remove missing values from a data.frame #' #' Remove all non-complete rows, with a warning if `na.rm = FALSE`. @@ -200,12 +190,6 @@ waiver <- function() structure(list(), class = "waiver") is.waive <- function(x) inherits(x, "waiver") - -rescale01 <- function(x) { - rng <- range(x, na.rm = TRUE) - (x - rng[1]) / (rng[2] - rng[1]) -} - pal_binned <- function(palette) { function(x) { palette(length(x)) @@ -247,15 +231,6 @@ gg_dep <- function(version, msg) { invisible() } -has_name <- function(x) { - nms <- names(x) - if (is.null(nms)) { - return(rep(FALSE, length(x))) - } - - !is.na(nms) & nms != "" -} - # Use chartr() for safety since toupper() fails to convert i to I in Turkish locale lower_ascii <- "abcdefghijklmnopqrstuvwxyz" upper_ascii <- "ABCDEFGHIJKLMNOPQRSTUVWXYZ" @@ -273,7 +248,9 @@ toupper <- function(x) { # Convert a snake_case string to camelCase camelize <- function(x, first = FALSE) { x <- gsub("_(.)", "\\U\\1", x, perl = TRUE) - if (first) x <- firstUpper(x) + if (first) { + x <- paste0(to_upper_ascii(substring(x, 1, 1)), substring(x, 2)) + } x } @@ -284,10 +261,6 @@ snakeize <- function(x) { to_lower_ascii(x) } -firstUpper <- function(s) { - paste0(to_upper_ascii(substring(s, 1, 1)), substring(s, 2)) -} - snake_class <- function(x) { snakeize(class(x)[1]) } @@ -320,15 +293,6 @@ compact <- function(x) { is.formula <- function(x) inherits(x, "formula") -deparse2 <- function(x) { - y <- deparse(x, backtick = TRUE) - if (length(y) == 1) { - y - } else { - paste0(y[[1]], "...") - } -} - dispatch_args <- function(f, ...) { args <- list(...) formals <- formals(f) @@ -337,7 +301,6 @@ dispatch_args <- function(f, ...) { f } -is_missing_arg <- function(x) identical(x, quote(expr = )) # Get all arguments in a function as a list. Will fail if an ellipsis argument # named .ignore # @param ... passed on in case enclosing function uses ellipsis in argument list @@ -346,7 +309,8 @@ find_args <- function(...) { args <- names(formals(sys.function(sys.parent(1)))) vals <- mget(args, envir = env) - vals <- vals[!vapply(vals, is_missing_arg, logical(1))] + # Remove missing arguments + vals <- vals[!vapply(vals, identical, logical(1), y = quote(expr = ))] modify_list(vals, dots_list(..., `...` = NULL, .ignore_empty = "all")) } @@ -363,14 +327,6 @@ with_seed_null <- function(seed, code) { } } -seq_asc <- function(to, from) { - if (to > from) { - integer() - } else { - to:from - } -} - # Wrapping vctrs data_frame constructor with no name repair data_frame0 <- function(...) data_frame(..., .name_repair = "minimal") @@ -380,23 +336,19 @@ unique0 <- function(x, ...) if (is.null(x)) x else vec_unique(x, ...) # Code readability checking for uniqueness is_unique <- function(x) vec_unique_count(x) == 1L -is_scalar_numeric <- function(x) is_bare_numeric(x, n = 1L) - # Check inputs with tibble but allow column vectors (see #2609 and #2374) as_gg_data_frame <- function(x) { - x <- lapply(x, validate_column_vec) + x <- lapply(x, drop_column_vec) data_frame0(!!!x) } -validate_column_vec <- function(x) { - if (is_column_vec(x)) { + +drop_column_vec <- function(x) { + dims <- dim(x) + if (length(dims) == 2L && dims[[2]] == 1L) { dim(x) <- NULL } x } -is_column_vec <- function(x) { - dims <- dim(x) - length(dims) == 2L && dims[[2]] == 1L -} # Parse takes a vector of n lines and returns m expressions. # See https://github.com/tidyverse/ggplot2/issues/2864 for discussion. @@ -686,24 +638,6 @@ is_bang <- function(x) { }) } -is_triple_bang <- function(x) { - if (!is_bang(x)) { - return(FALSE) - } - - x <- x[[2]] - if (!is_bang(x)) { - return(FALSE) - } - - x <- x[[2]] - if (!is_bang(x)) { - return(FALSE) - } - - TRUE -} - # Restart handler for using vec_rbind with mix of types # Ordered is coerced to factor # If a character vector is present the other is converted to character diff --git a/man/ggproto.Rd b/man/ggproto.Rd index c00c2000f6..11e3af8093 100644 --- a/man/ggproto.Rd +++ b/man/ggproto.Rd @@ -3,14 +3,11 @@ \name{ggproto} \alias{ggproto} \alias{ggproto_parent} -\alias{is.ggproto} \title{Create a new ggproto object} \usage{ ggproto(`_class` = NULL, `_inherit` = NULL, ...) ggproto_parent(parent, self) - -is.ggproto(x) } \arguments{ \item{_class}{Class name to assign to the object. This is stored as the class @@ -24,8 +21,6 @@ inherit from any object.} functions that become methods of the class or regular objects.} \item{parent, self}{Access parent class \code{parent} of object \code{self}.} - -\item{x}{An object to test.} } \description{ Construct a new object with \code{ggproto()}, test with \code{is.ggproto()}, diff --git a/man/is.Coord.Rd b/man/is.Coord.Rd deleted file mode 100644 index 50b4520640..0000000000 --- a/man/is.Coord.Rd +++ /dev/null @@ -1,12 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/coord-.R -\name{is.Coord} -\alias{is.Coord} -\title{Is this object a coordinate system?} -\usage{ -is.Coord(x) -} -\description{ -Is this object a coordinate system? -} -\keyword{internal} diff --git a/man/is.facet.Rd b/man/is.facet.Rd deleted file mode 100644 index bd8fc7b5ba..0000000000 --- a/man/is.facet.Rd +++ /dev/null @@ -1,15 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/facet-.R -\name{is.facet} -\alias{is.facet} -\title{Is this object a faceting specification?} -\usage{ -is.facet(x) -} -\arguments{ -\item{x}{object to test} -} -\description{ -Is this object a faceting specification? -} -\keyword{internal} diff --git a/man/is.ggplot.Rd b/man/is.ggplot.Rd deleted file mode 100644 index 837bc9a919..0000000000 --- a/man/is.ggplot.Rd +++ /dev/null @@ -1,15 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/plot.R -\name{is.ggplot} -\alias{is.ggplot} -\title{Reports whether x is a ggplot object} -\usage{ -is.ggplot(x) -} -\arguments{ -\item{x}{An object to test} -} -\description{ -Reports whether x is a ggplot object -} -\keyword{internal} diff --git a/man/is.theme.Rd b/man/is.theme.Rd deleted file mode 100644 index c7930a2e96..0000000000 --- a/man/is.theme.Rd +++ /dev/null @@ -1,15 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/theme.R -\name{is.theme} -\alias{is.theme} -\title{Reports whether x is a theme object} -\usage{ -is.theme(x) -} -\arguments{ -\item{x}{An object to test} -} -\description{ -Reports whether x is a theme object -} -\keyword{internal} diff --git a/man/is_tests.Rd b/man/is_tests.Rd new file mode 100644 index 0000000000..62ded3db09 --- /dev/null +++ b/man/is_tests.Rd @@ -0,0 +1,63 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ggproto.R, R/aes.R, R/geom-.R, R/coord-.R, +% R/facet-.R, R/stat-.R, R/theme-elements.R, R/guide-.R, R/layer.R, +% R/guides-.R, R/margins.R, R/plot.R, R/position-.R, R/scale-.R, R/theme.R +\name{is.ggproto} +\alias{is.ggproto} +\alias{is.mapping} +\alias{is.geom} +\alias{is.coord} +\alias{is.Coord} +\alias{is.facet} +\alias{is.stat} +\alias{is.element} +\alias{is.guide} +\alias{is.layer} +\alias{is.guides} +\alias{is.margin} +\alias{is_tests} +\alias{is.ggplot} +\alias{is.position} +\alias{is.scale} +\alias{is.theme} +\title{Reports whether x is a type of object} +\usage{ +is.ggproto(x) + +is.mapping(x) + +is.geom(x) + +is.coord(x) + +is.Coord(x) # Deprecated + +is.facet(x) + +is.stat(x) + +is.element(x) + +is.guide(x) + +is.layer(x) + +is.guides(x) + +is.margin(x) + +is.ggplot(x) + +is.position(x) + +is.scale(x) + +is.theme(x) +} +\arguments{ +\item{x}{An object to test} +} +\description{ +Reports whether x is a type of object +} +\keyword{internal} diff --git a/tests/testthat/_snaps/compat-plyr.md b/tests/testthat/_snaps/compat-plyr.md deleted file mode 100644 index d31d586cc8..0000000000 --- a/tests/testthat/_snaps/compat-plyr.md +++ /dev/null @@ -1,16 +0,0 @@ -# input checks work in compat functions - - Can only remove rownames from and objects. - ---- - - `x` must be a factor or character vector, not an integer vector. - ---- - - Must be a character vector, call, or formula. - ---- - - `x` must be a vector, not a character vector. - diff --git a/tests/testthat/_snaps/margins.md b/tests/testthat/_snaps/margins.md deleted file mode 100644 index 3eefe771b7..0000000000 --- a/tests/testthat/_snaps/margins.md +++ /dev/null @@ -1,4 +0,0 @@ -# justify_grobs() checks input - - `grobs` must be an individual or list of objects, not the number 1. - diff --git a/tests/testthat/_snaps/utilities.md b/tests/testthat/_snaps/utilities.md index 4560379f1e..37138df4e9 100644 --- a/tests/testthat/_snaps/utilities.md +++ b/tests/testthat/_snaps/utilities.md @@ -50,10 +50,6 @@ Only one of `boundary` and `center` may be specified. -# interleave() checks the vector lengths - - Can't recycle `..1` (size 4) to match `..2` (size 0). - # summary method gives a nice summary Code diff --git a/tests/testthat/test-compat-plyr.R b/tests/testthat/test-compat-plyr.R deleted file mode 100644 index b8fd891ebf..0000000000 --- a/tests/testthat/test-compat-plyr.R +++ /dev/null @@ -1,6 +0,0 @@ -test_that("input checks work in compat functions", { - expect_snapshot_error(unrowname(1:6)) - expect_snapshot_error(revalue(1:7, c("5" = 2))) - expect_snapshot_error(as.quoted(1:7)) - expect_snapshot_error(round_any(letters)) -}) diff --git a/tests/testthat/test-facet-.R b/tests/testthat/test-facet-.R index 9e536798a8..5084737622 100644 --- a/tests/testthat/test-facet-.R +++ b/tests/testthat/test-facet-.R @@ -21,7 +21,7 @@ test_that("as_facets_list() coerces character vectors", { expect_identical(as_facets_list("foo"), list(foobar[1])) expect_identical(as_facets_list(c("foo", "bar")), list(foobar[1], foobar[2])) - expect_identical(wrap_as_facets_list(c("foo", "bar")), foobar) + expect_identical(compact_facets(c("foo", "bar")), foobar) }) test_that("as_facets_list() coerces lists", { @@ -47,12 +47,12 @@ test_that("facets reject aes()", { expect_error(facet_grid(aes(foo)), "Please use `vars()` to supply facet variables", fixed = TRUE) }) -test_that("wrap_as_facets_list() returns a quosures object with compacted", { - expect_identical(wrap_as_facets_list(vars(foo)), quos(foo = foo)) - expect_identical(wrap_as_facets_list(~foo + bar), quos(foo = foo, bar = bar)) +test_that("compact_facets() returns a quosures object with compacted", { + expect_identical(compact_facets(vars(foo)), quos(foo = foo)) + expect_identical(compact_facets(~foo + bar), quos(foo = foo, bar = bar)) f <- function(x) { - expect_identical(wrap_as_facets_list(vars(foo, {{ x }}, bar)), quos(foo = foo, bar = bar)) + expect_identical(compact_facets(vars(foo, {{ x }}, bar)), quos(foo = foo, bar = bar)) } f(NULL) @@ -71,12 +71,12 @@ test_that("grid_as_facets_list() returns a list of quosures objects with compact f() }) -test_that("wrap_as_facets_list() and grid_as_facets_list() accept empty specs", { - expect_identical(wrap_as_facets_list(NULL), quos()) - expect_identical(wrap_as_facets_list(list()), quos()) - expect_identical(wrap_as_facets_list(. ~ .), quos()) - expect_identical(wrap_as_facets_list(list(. ~ .)), quos()) - expect_identical(wrap_as_facets_list(list(NULL)), quos()) +test_that("compact_facets() and grid_as_facets_list() accept empty specs", { + expect_identical(compact_facets(NULL), quos()) + expect_identical(compact_facets(list()), quos()) + expect_identical(compact_facets(. ~ .), quos()) + expect_identical(compact_facets(list(. ~ .)), quos()) + expect_identical(compact_facets(list(NULL)), quos()) expect_identical(grid_as_facets_list(list(), NULL), list(rows = quos(), cols = quos())) expect_identical(grid_as_facets_list(. ~ ., NULL), list(rows = quos(), cols = quos())) diff --git a/tests/testthat/test-margins.R b/tests/testthat/test-margins.R deleted file mode 100644 index 522c457445..0000000000 --- a/tests/testthat/test-margins.R +++ /dev/null @@ -1,3 +0,0 @@ -test_that("justify_grobs() checks input", { - expect_snapshot_error(justify_grobs(1)) -}) diff --git a/tests/testthat/test-stat-bin2d.R b/tests/testthat/test-stat-bin2d.R index 31e9c819c6..54d95679c9 100644 --- a/tests/testthat/test-stat-bin2d.R +++ b/tests/testthat/test-stat-bin2d.R @@ -32,8 +32,8 @@ test_that("breaks override binwidth", { ) out <- get_layer_data(base) - expect_equal(out$xbin, cut(df$x, adjust_breaks(integer_breaks), include.lowest = TRUE, labels = FALSE)) - expect_equal(out$ybin, cut(df$y, adjust_breaks(half_breaks), include.lowest = TRUE, labels = FALSE)) + expect_equal(out$xbin, cut(df$x, bins(integer_breaks)$fuzzy, include.lowest = TRUE, labels = FALSE)) + expect_equal(out$ybin, cut(df$y, bins(half_breaks)$fuzzy, include.lowest = TRUE, labels = FALSE)) }) test_that("breaks are transformed by the scale", { diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index 315ca88ebc..a602eb22c7 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -132,10 +132,6 @@ test_that("cut_*() checks its input and output", { expect_snapshot_error(cut_width(1:10, 1, center = 0, boundary = 0.5)) }) -test_that("interleave() checks the vector lengths", { - expect_snapshot_error(interleave(1:4, numeric())) -}) - test_that("vec_rbind0 can combined ordered factors", { withr::local_options(lifecycle_verbosity = "warning") From 4fbc8575d80e54e1973ac58e979c2300aec21394 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 23 Sep 2024 14:01:15 +0200 Subject: [PATCH 135/264] Mask `stage()` at the expression level (#6110) * evaluation helper * use helper * generalise `substitute_aes()` * substitute expressions instead of wrangling data masks * add test * make a comment for the next person to trip over this * add news bullet --- NEWS.md | 2 ++ R/aes-evaluation.R | 36 ++++++++++++++++++++++++++++ R/aes.R | 7 ++++-- R/geom-.R | 14 ++++------- R/layer.R | 20 +++++----------- tests/testthat/test-aes-calculated.R | 25 +++++++++++++++++++ 6 files changed, 79 insertions(+), 25 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8d7f8760d0..f369879868 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug where the `ggplot2::`-prefix did not work with `stage()` + (@teunbrand, #6104). * New `get_labs()` function for retrieving completed plot labels (@teunbrand, #6008). * Built-in `theme_*()` functions now have `ink` and `paper` arguments to control diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index 8e47ebcd1e..30d0b3f501 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -358,3 +358,39 @@ make_labels <- function(mapping) { } Map(default_label, names(mapping), mapping) } + +eval_aesthetics <- function(aesthetics, data, mask = NULL) { + + env <- child_env(base_env()) + + # Here we mask functions, often to replace `stage()` with context appropriate + # functions `stage_calculated()`/`stage_scaled()`. + if (length(mask) > 0) { + aesthetics <- substitute_aes(aesthetics, mask_function, mask = mask) + } + + evaled <- lapply(aesthetics, eval_tidy, data = data, env = env) + names(evaled) <- names(aesthetics) + compact(rename_aes(evaled)) +} + +# `mask` is a list of functions where `names(mask)` indicate names of functions +# that need to be replaced, and `mask[[i]]` is the function to replace it +# with. +mask_function <- function(x, mask) { + if (!is.call(x)) { + return(x) + } + nms <- names(mask) + x[-1] <- lapply(x[-1], mask_function, mask = mask) + if (!is_call(x, nms)) { + return(x) + } + for (nm in nms) { + if (is_call(x, nm)) { + x[[1]] <- mask[[nm]] + return(x) + } + } +} + diff --git a/R/aes.R b/R/aes.R index d739289b0e..0829f64daf 100644 --- a/R/aes.R +++ b/R/aes.R @@ -198,9 +198,12 @@ rename_aes <- function(x) { } x } -substitute_aes <- function(x) { + +# `x` is assumed to be a strict list of quosures; +# it should have no non-quosure constants in it, even though `aes()` allows it. +substitute_aes <- function(x, fun = standardise_aes_symbols, ...) { x <- lapply(x, function(aesthetic) { - as_quosure(standardise_aes_symbols(quo_get_expr(aesthetic)), env = environment(aesthetic)) + as_quosure(fun(quo_get_expr(aesthetic), ...), env = environment(aesthetic)) }) class(x) <- "uneval" x diff --git a/R/geom-.R b/R/geom-.R index c5a1ab275d..bb409ba0cf 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -157,12 +157,10 @@ Geom <- ggproto("Geom", # This order means that they will have access to all default aesthetics if (length(modifiers) != 0) { # Set up evaluation environment - env <- child_env(baseenv(), after_scale = after_scale) - # Mask stage with stage_scaled so it returns the correct expression - stage_mask <- child_env(emptyenv(), stage = stage_scaled) - mask <- new_data_mask(as_environment(data, stage_mask), stage_mask) - mask$.data <- as_data_pronoun(mask) - modified_aes <- lapply(substitute_aes(modifiers), eval_tidy, mask, env) + modified_aes <- eval_aesthetics( + substitute_aes(modifiers), data, + mask = list(stage = stage_scaled) + ) # Check that all output are valid data nondata_modified <- check_nondata_cols(modified_aes) @@ -177,11 +175,9 @@ Geom <- ggproto("Geom", )) } - names(modified_aes) <- names(rename_aes(modifiers)) - modified_aes <- cleanup_mismatched_data(modified_aes, nrow(data), "after_scale") - modified_aes <- data_frame0(!!!compact(modified_aes)) + modified_aes <- data_frame0(!!!modified_aes) data <- data_frame0(!!!defaults(modified_aes, data)) } diff --git a/R/layer.R b/R/layer.R index 3fd89cf3f7..b10c230e1d 100644 --- a/R/layer.R +++ b/R/layer.R @@ -307,10 +307,7 @@ Layer <- ggproto("Layer", NULL, } # Evaluate aesthetics - env <- child_env(baseenv(), stage = stage) - evaled <- lapply(aesthetics, eval_tidy, data = data, env = env) - evaled <- compact(evaled) - + evaled <- eval_aesthetics(aesthetics, data) plot$scales$add_defaults(evaled, plot$plot_env) # Check for discouraged usage in mapping @@ -390,14 +387,10 @@ Layer <- ggproto("Layer", NULL, data_orig <- plot$scales$backtransform_df(data) # Add map stat output to aesthetics - env <- child_env(baseenv(), stat = stat, after_stat = after_stat) - stage_mask <- child_env(emptyenv(), stage = stage_calculated) - mask <- new_data_mask(as_environment(data_orig, stage_mask), stage_mask) - mask$.data <- as_data_pronoun(mask) - - new <- substitute_aes(new) - stat_data <- lapply(new, eval_tidy, mask, env) - + stat_data <- eval_aesthetics( + substitute_aes(new), data_orig, + mask = list(stage = stage_calculated) + ) # Check that all columns in aesthetic stats are valid data nondata_stat_cols <- check_nondata_cols(stat_data) if (length(nondata_stat_cols) > 0) { @@ -411,8 +404,7 @@ Layer <- ggproto("Layer", NULL, )) } - names(stat_data) <- names(new) - stat_data <- data_frame0(!!!compact(stat_data)) + stat_data <- data_frame0(!!!stat_data) # Add any new scales, if needed plot$scales$add_defaults(stat_data, plot$plot_env) diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index b453af02f5..3ac8e06dbe 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -99,3 +99,28 @@ test_that("A deprecated warning is issued when stat(var) or ..var.. is used", { p2 <- ggplot(NULL, aes(..bar..)) expect_snapshot_warning(b2 <- ggplot_build(p2)) }) + +test_that("functions can be masked", { + + foo <- function(x) x + 10 + bar <- function(x) x * 10 + + data <- data.frame(val = 10) + mapping <- aes(x = val, y = foo(20)) + + evaled <- eval_aesthetics(mapping, data = data, mask = list()) + expect_equal(evaled, list(x = 10, y = 30)) + + evaled <- eval_aesthetics(mapping, data = data, mask = list(foo = bar)) + expect_equal(evaled, list(x = 10, y = 200)) + + # Test namespace-prefixed evaluation (#6104) + mapping <- aes(x = val, y = ggplot2::stage(10, 20, 30)) + evaled <- eval_aesthetics(mapping, data = data, mask = list()) + expect_equal(evaled, list(x = 10, y = 10)) + evaled <- eval_aesthetics(mapping, data = data, mask = list(stage = stage_calculated)) + expect_equal(evaled, list(x = 10, y = 20)) + evaled <- eval_aesthetics(mapping, data = data, mask = list(stage = stage_scaled)) + expect_equal(evaled, list(x = 10, y = 30)) + +}) From ad97679f1290214baf7fdba743b47ae2b3983a97 Mon Sep 17 00:00:00 2001 From: Mikko Marttila <13412395+mikmart@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:17:48 +0100 Subject: [PATCH 136/264] Restore rather than recalculate scales (#6130) --- R/facet-wrap.R | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 4650d12dd8..114b3332d9 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -447,16 +447,8 @@ FacetWrap <- ggproto("FacetWrap", Facet, draw_panels = function(self, panels, layout, x_scales, y_scales, ranges, coord, data, theme, params) { if (inherits(coord, "CoordFlip")) { - if (params$free$x) { - layout$SCALE_X <- seq_len(nrow(layout)) - } else { - layout$SCALE_X <- 1L - } - if (params$free$y) { - layout$SCALE_Y <- seq_len(nrow(layout)) - } else { - layout$SCALE_Y <- 1L - } + # Switch the scales back + layout[c("SCALE_X", "SCALE_Y")] <- layout[c("SCALE_Y", "SCALE_X")] } panel_order <- order(layout$ROW, layout$COL) From ddd207e926cc1c1847dc661d9a099b8ec19c4010 Mon Sep 17 00:00:00 2001 From: June Choe <52832839+yjunechoe@users.noreply.github.com> Date: Fri, 11 Oct 2024 03:25:08 -0400 Subject: [PATCH 137/264] Add test for using `stage()` with a mapping specified for `start` only (#6131) * add test for using stage with a mapping to start only * clean up outdated comment * add to documentation --- R/aes-evaluation.R | 19 +++++++++++++------ man/aes_eval.Rd | 17 ++++++++++++----- tests/testthat/test-aes-calculated.R | 24 ++++++++++++++++++++++++ 3 files changed, 49 insertions(+), 11 deletions(-) diff --git a/R/aes-evaluation.R b/R/aes-evaluation.R index 30d0b3f501..e29d0c5d25 100644 --- a/R/aes-evaluation.R +++ b/R/aes-evaluation.R @@ -32,7 +32,7 @@ #' Below follows an overview of the three stages of evaluation and how aesthetic #' evaluation can be controlled. #' -#' ## Stage 1: direct input +#' ## Stage 1: direct input at the start #' The default is to map at the beginning, using the layer data provided by #' the user. If you want to map directly from the layer data you should not do #' anything special. This is the only stage where the original layer data can @@ -87,9 +87,11 @@ #' ``` #' #' ## Complex staging -#' If you want to map the same aesthetic multiple times, e.g. map `x` to a -#' data column for the stat, but remap it for the geom, you can use the -#' `stage()` function to collect multiple mappings. +#' Sometimes, you may want to map the same aesthetic multiple times, e.g. map +#' `x` to a data column at the start for the layer stat, but remap it later to +#' a variable from the stat transformation for the layer geom. The `stage()` +#' function allows you to control multiple mappings for the same aesthetic +#' across all three stages of evaluation. #' #' ```r #' # Use stage to modify the scaled fill @@ -97,7 +99,7 @@ #' geom_boxplot(aes(fill = stage(class, after_scale = alpha(fill, 0.4)))) #' #' # Using data for computing summary, but placing label elsewhere. -#' # Also, we're making our own computed variable to use for the label. +#' # Also, we're making our own computed variables to use for the label. #' ggplot(mpg, aes(class, displ)) + #' geom_violin() + #' stat_summary( @@ -110,6 +112,11 @@ #' ) #' ``` #' +#' Conceptually, `aes(x)` is equivalent to `aes(stage(start = x))`, and +#' `aes(after_stat(count))` is equivalent to `aes(stage(after_stat = count))`, +#' and so on. `stage()` is most useful when at least two of its arguments are +#' specified. +#' #' ## Theme access #' The `from_theme()` function can be used to acces the [`element_geom()`] #' fields of the `theme(geom)` argument. Using `aes(colour = from_theme(ink))` @@ -332,7 +339,7 @@ strip_stage <- function(expr) { } else if (is_call(uq_expr, "stage")) { uq_expr <- call_match(uq_expr, stage) # Prefer stat mapping if present, otherwise original mapping (fallback to - # scale mapping) but there should always be two arguments to stage() + # scale mapping) uq_expr$after_stat %||% uq_expr$start %||% uq_expr$after_scale } else { expr diff --git a/man/aes_eval.Rd b/man/aes_eval.Rd index 11b8d2f1bd..aaf4c55277 100644 --- a/man/aes_eval.Rd +++ b/man/aes_eval.Rd @@ -49,7 +49,7 @@ should be evaluated. \section{Staging}{ Below follows an overview of the three stages of evaluation and how aesthetic evaluation can be controlled. -\subsection{Stage 1: direct input}{ +\subsection{Stage 1: direct input at the start}{ The default is to map at the beginning, using the layer data provided by the user. If you want to map directly from the layer data you should not do @@ -108,16 +108,18 @@ ggplot(mpg, aes(cty, colour = factor(cyl))) + \subsection{Complex staging}{ -If you want to map the same aesthetic multiple times, e.g. map \code{x} to a -data column for the stat, but remap it for the geom, you can use the -\code{stage()} function to collect multiple mappings. +Sometimes, you may want to map the same aesthetic multiple times, e.g. map +\code{x} to a data column at the start for the layer stat, but remap it later to +a variable from the stat transformation for the layer geom. The \code{stage()} +function allows you to control multiple mappings for the same aesthetic +across all three stages of evaluation. \if{html}{\out{
}}\preformatted{# Use stage to modify the scaled fill ggplot(mpg, aes(class, hwy)) + geom_boxplot(aes(fill = stage(class, after_scale = alpha(fill, 0.4)))) # Using data for computing summary, but placing label elsewhere. -# Also, we're making our own computed variable to use for the label. +# Also, we're making our own computed variables to use for the label. ggplot(mpg, aes(class, displ)) + geom_violin() + stat_summary( @@ -129,6 +131,11 @@ ggplot(mpg, aes(class, displ)) + fun.data = ~ round(data.frame(mean = mean(.x), sd = sd(.x)), 2) ) }\if{html}{\out{
}} + +Conceptually, \code{aes(x)} is equivalent to \code{aes(stage(start = x))}, and +\code{aes(after_stat(count))} is equivalent to \code{aes(stage(after_stat = count))}, +and so on. \code{stage()} is most useful when at least two of its arguments are +specified. } \subsection{Theme access}{ diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index 3ac8e06dbe..9d5c49c68e 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -124,3 +124,27 @@ test_that("functions can be masked", { expect_equal(evaled, list(x = 10, y = 30)) }) + +test_that("stage allows aesthetics that are only mapped to start", { + + df <- data.frame(x = 1:2) + + start_unnamed <- aes(stage(x)) + expect_equal( + eval_aesthetics(start_unnamed, data = df), + list(x = 1:2) + ) + + start_named <- aes(stage(start = x)) + expect_equal( + eval_aesthetics(start_named, data = df), + list(x = 1:2) + ) + + start_nulls <- aes(stage(start = x, after_stat = NULL, after_scale = NULL)) + expect_equal( + eval_aesthetics(start_nulls, data = df), + list(x = 1:2) + ) + +}) From 5e62f0c3fea0d9a8e41697654277ec82ed82da95 Mon Sep 17 00:00:00 2001 From: nicholasdavies Date: Thu, 24 Oct 2024 15:03:58 +0100 Subject: [PATCH 138/264] Fixing misnamed panels for facet_wrap (#6082) (#6136) * Fixing misnamed panels for facet_wrap (#6082) See https://github.com/tidyverse/ggplot2/issues/6082 PR suggested by @teunbrand * Extra spaces crept in, removed --- R/facet-.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/facet-.R b/R/facet-.R index 8faafc1428..def19f221a 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -237,8 +237,8 @@ Facet <- ggproto("Facet", NULL, # Set panel names table$layout$name <- paste( "panel", - rep(seq_len(dim[2]), dim[1]), - rep(seq_len(dim[1]), each = dim[2]), + rep(seq_len(dim[2]), each = dim[1]), + rep(seq_len(dim[1]), dim[2]), sep = "-" ) From f12b73de2609603ff405360c73f1a5f38466af45 Mon Sep 17 00:00:00 2001 From: "Mattan S. Ben-Shachar" <35330040+mattansb@users.noreply.github.com> Date: Fri, 25 Oct 2024 14:33:22 +0300 Subject: [PATCH 139/264] Expand on docs/example for cases with non-equal-width bins in `stat_bin()` (#6151) * Docs/example for non-equal-width bins * Update R/geom-histogram.R Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * Update R/geom-histogram.R Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * move (count / width) note to details --------- Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> --- R/geom-histogram.R | 18 ++++++++++++++++++ man/geom_histogram.Rd | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/R/geom-histogram.R b/R/geom-histogram.R index dafc181f15..7bd832b611 100644 --- a/R/geom-histogram.R +++ b/R/geom-histogram.R @@ -17,6 +17,12 @@ #' one change at a time. You may need to look at a few options to uncover #' the full story behind your data. #' +#' By default, the _height_ of the bars represent the counts within each bin. +#' However, there are situations where this behavior might produce misleading +#' plots (e.g., when non-equal-width bins are used), in which case it might be +#' preferable to have the _area_ of the bars represent the counts (by setting +#' `aes(y = after_stat(count / width))`). See example below. +#' #' In addition to `geom_histogram()`, you can create a histogram plot by using #' `scale_x_binned()` with [geom_bar()]. This method by default plots tick marks #' in between each bar. @@ -63,6 +69,18 @@ #' ggplot(diamonds, aes(price, after_stat(density), colour = cut)) + #' geom_freqpoly(binwidth = 500) #' +#' +#' # When using the non-equal-width bins, we should set the area of the bars to +#' # represent the counts (not the height). +#' # Here we're using 10 equi-probable bins: +#' price_bins <- quantile(diamonds$price, probs = seq(0, 1, length = 11)) +#' +#' ggplot(diamonds, aes(price)) + +#' geom_histogram(breaks = price_bins, color = "black") # misleading (height = count) +#' +#' ggplot(diamonds, aes(price, after_stat(count / width))) + +#' geom_histogram(breaks = price_bins, color = "black") # area = count +#' #' if (require("ggplot2movies")) { #' # Often we don't want the height of the bar to represent the #' # count of observations, but the sum of some other variable. diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index 1f290dbcdc..a241aa2ba4 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -192,6 +192,12 @@ different number of bins. You can also experiment modifying the \code{binwidth} one change at a time. You may need to look at a few options to uncover the full story behind your data. +By default, the \emph{height} of the bars represent the counts within each bin. +However, there are situations where this behavior might produce misleading +plots (e.g., when non-equal-width bins are used), in which case it might be +preferable to have the \emph{area} of the bars represent the counts (by setting +\code{aes(y = after_stat(count / width))}). See example below. + In addition to \code{geom_histogram()}, you can create a histogram plot by using \code{scale_x_binned()} with \code{\link[=geom_bar]{geom_bar()}}. This method by default plots tick marks in between each bar. @@ -255,6 +261,18 @@ ggplot(diamonds, aes(price, colour = cut)) + ggplot(diamonds, aes(price, after_stat(density), colour = cut)) + geom_freqpoly(binwidth = 500) + +# When using the non-equal-width bins, we should set the area of the bars to +# represent the counts (not the height). +# Here we're using 10 equi-probable bins: +price_bins <- quantile(diamonds$price, probs = seq(0, 1, length = 11)) + +ggplot(diamonds, aes(price)) + + geom_histogram(breaks = price_bins, color = "black") # misleading (height = count) + +ggplot(diamonds, aes(price, after_stat(count / width))) + + geom_histogram(breaks = price_bins, color = "black") # area = count + if (require("ggplot2movies")) { # Often we don't want the height of the bar to represent the # count of observations, but the sum of some other variable. From 9c21cb575e7e2c91b21cb25a443c632fd6f41aa1 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:45:26 +0100 Subject: [PATCH 140/264] rename `is.element()` to `is.theme_element()` (#6160) --- NAMESPACE | 2 +- R/guide-.R | 2 +- R/plot-build.R | 2 +- R/theme-elements.R | 2 +- R/theme.R | 2 +- man/is_tests.Rd | 4 ++-- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 5737492a00..852cb97600 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -461,7 +461,6 @@ export(guides) export(has_flipped_aes) export(is.Coord) export(is.coord) -export(is.element) export(is.facet) export(is.geom) export(is.ggplot) @@ -475,6 +474,7 @@ export(is.position) export(is.scale) export(is.stat) export(is.theme) +export(is.theme_element) export(label_both) export(label_bquote) export(label_context) diff --git a/R/guide-.R b/R/guide-.R index dd63949cd2..fc002c33d2 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -381,7 +381,7 @@ Guide <- ggproto( # Renders tickmarks build_ticks = function(key, elements, params, position = params$position, length = elements$ticks_length) { - if (!is.element(elements)) { + if (!is.theme_element(elements)) { elements <- elements$ticks } if (!inherits(elements, "element_line")) { diff --git a/R/plot-build.R b/R/plot-build.R index c7e641c8e6..a624469b75 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -288,7 +288,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot_margin <- calc_element("plot.margin", theme) plot_table <- gtable_add_padding(plot_table, plot_margin) - if (is.element(theme$plot.background)) { + if (is.theme_element(theme$plot.background)) { plot_table <- gtable_add_grob(plot_table, element_render(theme, "plot.background"), t = 1, l = 1, b = -1, r = -1, name = "background", z = -Inf) diff --git a/R/theme-elements.R b/R/theme-elements.R index 7e5de2f777..fb3341bf49 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -204,7 +204,7 @@ element_geom <- function( #' @export #' @rdname is_tests -is.element <- function(x) inherits(x, "element") +is.theme_element <- function(x) inherits(x, "element") #' @export print.element <- function(x, ...) utils::str(x) diff --git a/R/theme.R b/R/theme.R index 2eedd300c5..2eecc13253 100644 --- a/R/theme.R +++ b/R/theme.R @@ -529,7 +529,7 @@ theme <- function(..., # If complete theme set all non-blank elements to inherit from blanks if (complete) { elements <- lapply(elements, function(el) { - if (is.element(el) && !inherits(el, "element_blank")) { + if (is.theme_element(el) && !inherits(el, "element_blank")) { el$inherit.blank <- TRUE } el diff --git a/man/is_tests.Rd b/man/is_tests.Rd index 62ded3db09..bcb7bf0683 100644 --- a/man/is_tests.Rd +++ b/man/is_tests.Rd @@ -10,7 +10,7 @@ \alias{is.Coord} \alias{is.facet} \alias{is.stat} -\alias{is.element} +\alias{is.theme_element} \alias{is.guide} \alias{is.layer} \alias{is.guides} @@ -36,7 +36,7 @@ is.facet(x) is.stat(x) -is.element(x) +is.theme_element(x) is.guide(x) From 0cbd4203f40c6c93e899eeaf431b5ad883128287 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:46:38 +0100 Subject: [PATCH 141/264] update `update_geom_defaults()` docs (#6158) --- R/geom-defaults.R | 12 +++++++++++- man/update_defaults.Rd | 12 +++++++++++- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/R/geom-defaults.R b/R/geom-defaults.R index b185990fbb..732f5ddb32 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -11,7 +11,17 @@ #' @keywords internal #' @note #' Please note that geom defaults can be set *en masse* via the `theme(geom)` -#' argument. +#' argument. The guidelines for when to use which function are as follows: +#' +#' * If you want to change defaults for all geoms in all plots, use +#' `theme_update(geom = element_geom(...))`. +#' * If you want to change defaults for all geoms in a single plot, use +#' `+ theme(geom = element_geom(...))`. +#' * If you want to change defaults for one geom in all plots, use +#' `update_geom_defaults()`. +#' * If you want to change settings for one geom in a single plot, use fixed +#' aesthetic parameters in a layer, like so: `geom_point(colour = "red")`. +#' #' @export #' @examples #' diff --git a/man/update_defaults.Rd b/man/update_defaults.Rd index 777182e24f..9620dde4e1 100644 --- a/man/update_defaults.Rd +++ b/man/update_defaults.Rd @@ -31,7 +31,17 @@ Functions to update or reset the default aesthetics of geoms and stats. } \note{ Please note that geom defaults can be set \emph{en masse} via the \code{theme(geom)} -argument. +argument. The guidelines for when to use which function are as follows: +\itemize{ +\item If you want to change defaults for all geoms in all plots, use +\code{theme_update(geom = element_geom(...))}. +\item If you want to change defaults for all geoms in a single plot, use +\code{+ theme(geom = element_geom(...))}. +\item If you want to change defaults for one geom in all plots, use +\code{update_geom_defaults()}. +\item If you want to change settings for one geom in a single plot, use fixed +aesthetic parameters in a layer, like so: \code{geom_point(colour = "red")}. +} } \examples{ From fe264141649fc66484aea86e448b3032b04abb2c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:48:50 +0100 Subject: [PATCH 142/264] import function instead of result (#6146) --- R/backports.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/backports.R b/R/backports.R index a3d5eb9465..7ccedc4296 100644 --- a/R/backports.R +++ b/R/backports.R @@ -67,6 +67,6 @@ on_load({ as.mask <- grid::as.mask } if ("linearGradient" %in% getNamespaceExports("grid")) { - linearGradient <- grid::linearGradient() + linearGradient <- grid::linearGradient } }) From b174986fbf9d6c2c7b0f0356a4dc98a21bf7de84 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:50:04 +0100 Subject: [PATCH 143/264] Fix binned scaled not accepting function-limits if there are transformations (#6145) * fix bug * add test * add news bullet --- NEWS.md | 2 ++ R/scale-.R | 2 +- tests/testthat/test-scale-binned.R | 10 ++++++++++ 3 files changed, 13 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index f369879868..540e662f0c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Fixed bug where binned scales wouldn't simultaneously accept transformations + and function-limits (@teunbrand, #6144). * Fixed bug where the `ggplot2::`-prefix did not work with `stage()` (@teunbrand, #6104). * New `get_labs()` function for retrieving completed plot labels diff --git a/R/scale-.R b/R/scale-.R index 878cc602b9..bb56743bdb 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -319,7 +319,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name = } transform <- as.transform(transform) - if (!is.null(limits)) { + if (!is.null(limits) && !is.function(limits)) { limits <- transform$transform(limits) } diff --git a/tests/testthat/test-scale-binned.R b/tests/testthat/test-scale-binned.R index 31e32e9eba..1f558b6c77 100644 --- a/tests/testthat/test-scale-binned.R +++ b/tests/testthat/test-scale-binned.R @@ -44,6 +44,16 @@ test_that("binned limits should not compute out-of-bounds breaks", { )) }) +test_that("binned scales can use limits and transformations simultaneously (#6144)", { + s <- scale_x_binned( + limits = function(x) x + 1, + trans = transform_log10() + ) + s$train(c(0, 1)) # c(1, 10) in untransformed space + out <- s$get_limits() + expect_equal(s$get_limits(), log10(c(2, 11))) +}) + test_that("binned scales can use NAs in limits", { scale <- scale_x_binned(limits = c(NA, 10)) scale$train(c(-20, 20)) From a47be596b501ce3915a34f9d924d2beda231ac42 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 30 Oct 2024 09:07:45 +0100 Subject: [PATCH 144/264] Upkeep 2024-10 (#6156) * record upkeep date * `usethis::use_mit_licence()` * fix broken urls * `usethis:::use_codecov_badge()` * `usethis::use_lifecycle()` * `usethis::use_tidy_logo()` & `pkgdown::build_favicons(overwrite = TRUE)` * Alt text for cheat sheet link * Use `knitr::convert_chunk_header(type = "yaml")` (#6149) * Use `expect_snapshot(error = TRUE)` instead of `expect_error()` (#6150) * replace `expect_error()` by `expect_snapshot(error = TRUE)` * censor machine dependent paths in snapshots * commit snapshots * skip gnarly snapshots * Bump R version * `usethis::use_tidy_description()` * distribute `test-guides.R` * convert chunk headers * regenerate snapshots after moving guides * adapt to gtable 0.3.6 * use 'core developer team' as copyright holder * replace `expect_warning()` * fix non portable file path check * Hmisc 5.2-0 requires R >= 4.2.0 --- .github/workflows/R-CMD-check.yaml | 2 +- DESCRIPTION | 5 +- LICENSE.md | 2 +- R/stat-ellipse.R | 2 +- README.Rmd | 15 +- README.md | 8 +- man/figures/lifecycle-deprecated.svg | 22 +- man/figures/lifecycle-experimental.svg | 22 +- man/figures/lifecycle-stable.svg | 30 +- man/figures/lifecycle-superseded.svg | 22 +- man/figures/logo.png | Bin 24183 -> 24069 bytes man/stat_ellipse.Rd | 2 +- pkgdown/favicon/apple-touch-icon.png | Bin 15859 -> 11877 bytes pkgdown/favicon/favicon-48x48.png | Bin 0 -> 2046 bytes pkgdown/favicon/favicon.ico | Bin 15086 -> 15086 bytes pkgdown/favicon/favicon.svg | 3 + pkgdown/favicon/site.webmanifest | 21 + pkgdown/favicon/web-app-manifest-192x192.png | Bin 0 -> 13222 bytes pkgdown/favicon/web-app-manifest-512x512.png | Bin 0 -> 72477 bytes tests/testthat/_snaps/aes-calculated.md | 8 + tests/testthat/_snaps/aes-setting.md | 36 + tests/testthat/_snaps/aes.md | 40 + tests/testthat/_snaps/coord-.md | 16 + tests/testthat/_snaps/coord-transform.md | 8 + tests/testthat/_snaps/empty-data.md | 27 + tests/testthat/_snaps/facet-.md | 33 + tests/testthat/_snaps/facet-labels.md | 21 + tests/testthat/_snaps/fortify.md | 150 ++++ tests/testthat/_snaps/geom-bar.md | 4 + tests/testthat/_snaps/geom-boxplot.md | 15 + tests/testthat/_snaps/geom-col.md | 8 + tests/testthat/_snaps/geom-dotplot.md | 8 + tests/testthat/_snaps/geom-path.md | 12 + tests/testthat/_snaps/geom-rect.md | 9 + tests/testthat/_snaps/geom-rug.md | 4 + tests/testthat/_snaps/geom-sf.md | 12 + tests/testthat/_snaps/geom-smooth.md | 4 + tests/testthat/_snaps/geom-text.md | 16 + tests/testthat/_snaps/ggsave.md | 69 ++ tests/testthat/_snaps/guide-.md | 11 + tests/testthat/_snaps/guide-axis.md | 19 + .../align-facet-labels-facets-horizontal.svg | 0 .../align-facet-labels-facets-vertical.svg | 0 .../axis-guides-basic.svg | 41 - .../axis-guides-check-overlap.svg | 41 - .../axis-guides-negative-rotation.svg | 41 - .../axis-guides-positive-rotation.svg | 41 - ...axis-guides-text-dodged-into-rows-cols.svg | 41 - ...axis-guides-vertical-negative-rotation.svg | 41 - .../axis-guides-vertical-rotation.svg | 41 - .../axis-guides-with-capped-ends.svg | 0 .../guide-axis/axis-guides-zero-breaks.svg | 26 + .../axis-guides-zero-rotation.svg | 41 - .../guide-axis-customization.svg | 0 ...de-axis-theta-in-cartesian-coordinates.svg | 0 ...xis-theta-with-angle-adapting-to-theta.svg | 0 .../guide-titles-with-coord-trans.svg | 0 .../guides-specified-in-guides.svg | 0 .../guides-with-minor-ticks.svg | 0 .../logtick-axes-with-customisation.svg | 0 .../position-guide-titles.svg | 0 .../{guides => guide-axis}/stacked-axes.svg | 0 .../stacked-radial-axes.svg | 0 .../thick-axis-lines.svg | 0 tests/testthat/_snaps/guide-colorbar.md | 14 + .../combined-colour-and-fill-aesthetics.svg} | 2 +- .../customized-colorbar.svg | 0 ...e-to-red-colorbar-white-ticks-no-frame.svg | 0 .../enlarged-guides.svg | 0 .../horizontal-legend-direction.svg | 0 .../left-aligned-legend-key.svg | 0 .../legend-byrow-true.svg | 0 .../legend-with-widely-spaced-keys.svg | 0 .../vertical-legend-direction.svg | 0 tests/testthat/_snaps/guides.md | 47 +- .../_snaps/guides/axis-guides-zero-breaks.svg | 67 -- tests/testthat/_snaps/labels.md | 16 + tests/testthat/_snaps/layer.md | 44 + tests/testthat/_snaps/performance.md | 9 + tests/testthat/_snaps/position_dodge.md | 11 + tests/testthat/_snaps/scale-date.md | 10 + tests/testthat/_snaps/scale-discrete.md | 60 ++ tests/testthat/_snaps/scale-gradient.md | 4 + tests/testthat/_snaps/scale-manual.md | 16 + tests/testthat/_snaps/scales-breaks-labels.md | 133 +++ tests/testthat/_snaps/scales.md | 28 + tests/testthat/_snaps/stat-bin.md | 20 + tests/testthat/_snaps/stat-contour.md | 14 + tests/testthat/_snaps/stat-density.md | 8 + tests/testthat/_snaps/stat-ecdf.md | 18 + tests/testthat/_snaps/stat-function.md | 5 + tests/testthat/_snaps/stat-ydensity.md | 9 + tests/testthat/_snaps/stats.md | 29 + tests/testthat/_snaps/theme.md | 24 + tests/testthat/_snaps/utilities-checks.md | 28 + tests/testthat/_snaps/utilities.md | 4 + tests/testthat/test-aes-calculated.R | 10 +- tests/testthat/test-aes-setting.R | 8 +- tests/testthat/test-aes.R | 27 +- tests/testthat/test-coord-.R | 4 +- tests/testthat/test-coord-transform.R | 4 +- tests/testthat/test-empty-data.R | 16 +- tests/testthat/test-facet-.R | 12 +- tests/testthat/test-facet-labels.R | 6 +- tests/testthat/test-fortify.R | 33 +- tests/testthat/test-geom-bar.R | 6 +- tests/testthat/test-geom-boxplot.R | 18 +- tests/testthat/test-geom-col.R | 11 +- tests/testthat/test-geom-dotplot.R | 6 +- tests/testthat/test-geom-path.R | 9 +- tests/testthat/test-geom-rect.R | 5 +- tests/testthat/test-geom-rug.R | 6 +- tests/testthat/test-geom-sf.R | 17 +- tests/testthat/test-geom-smooth.R | 2 +- tests/testthat/test-geom-text.R | 9 +- tests/testthat/test-geom-violin.R | 2 +- tests/testthat/test-ggsave.R | 30 +- tests/testthat/test-guide-.R | 49 ++ tests/testthat/test-guide-axis.R | 399 +++++++++ tests/testthat/test-guide-colorbar.R | 100 +++ tests/testthat/test-guide-legend.R | 213 +++++ tests/testthat/test-guides.R | 768 +----------------- tests/testthat/test-labels.R | 8 +- tests/testthat/test-layer.R | 24 +- tests/testthat/test-performance.R | 2 +- tests/testthat/test-position_dodge.R | 2 +- tests/testthat/test-qplot.R | 2 +- tests/testthat/test-scale-date.R | 12 +- tests/testthat/test-scale-discrete.R | 18 +- tests/testthat/test-scale-expansion.R | 2 +- tests/testthat/test-scale-gradient.R | 5 +- tests/testthat/test-scale-manual.R | 5 +- tests/testthat/test-scales-breaks-labels.R | 54 +- tests/testthat/test-scales.R | 38 +- tests/testthat/test-stat-bin.R | 4 +- tests/testthat/test-stat-contour.R | 9 +- tests/testthat/test-stat-density.R | 7 +- tests/testthat/test-stat-ecdf.R | 15 +- tests/testthat/test-stat-function.R | 2 +- tests/testthat/test-stat-ydensity.R | 10 +- tests/testthat/test-stats.R | 11 +- tests/testthat/test-theme.R | 9 +- tests/testthat/test-utilities-checks.R | 14 +- tests/testthat/test-utilities.R | 19 +- vignettes/articles/faq-annotation.Rmd | 3 +- vignettes/articles/faq-axes.Rmd | 21 +- vignettes/articles/faq-bars.Rmd | 3 +- vignettes/articles/faq-customising.Rmd | 6 +- vignettes/articles/faq-faceting.Rmd | 9 +- vignettes/articles/faq-reordering.Rmd | 3 +- vignettes/extending-ggplot2.Rmd | 24 +- vignettes/ggplot2-in-packages.Rmd | 18 +- vignettes/ggplot2-specs.Rmd | 16 +- vignettes/ggplot2.Rmd | 38 +- vignettes/profiling.Rmd | 8 +- 155 files changed, 2320 insertions(+), 1531 deletions(-) create mode 100644 pkgdown/favicon/favicon-48x48.png create mode 100644 pkgdown/favicon/favicon.svg create mode 100644 pkgdown/favicon/site.webmanifest create mode 100644 pkgdown/favicon/web-app-manifest-192x192.png create mode 100644 pkgdown/favicon/web-app-manifest-512x512.png create mode 100644 tests/testthat/_snaps/aes-setting.md create mode 100644 tests/testthat/_snaps/empty-data.md create mode 100644 tests/testthat/_snaps/facet-labels.md create mode 100644 tests/testthat/_snaps/geom-bar.md create mode 100644 tests/testthat/_snaps/geom-col.md create mode 100644 tests/testthat/_snaps/geom-rect.md create mode 100644 tests/testthat/_snaps/geom-smooth.md create mode 100644 tests/testthat/_snaps/guide-.md create mode 100644 tests/testthat/_snaps/guide-axis.md rename tests/testthat/_snaps/{guides => guide-axis}/align-facet-labels-facets-horizontal.svg (100%) rename tests/testthat/_snaps/{guides => guide-axis}/align-facet-labels-facets-vertical.svg (100%) rename tests/testthat/_snaps/{guides => guide-axis}/axis-guides-basic.svg (52%) rename tests/testthat/_snaps/{guides => 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guide-colorbar/combined-colour-and-fill-aesthetics.svg} (98%) rename tests/testthat/_snaps/{guides => guide-colorbar}/customized-colorbar.svg (100%) rename tests/testthat/_snaps/{guides => guide-colorbar}/white-to-red-colorbar-white-ticks-no-frame.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/enlarged-guides.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/horizontal-legend-direction.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/left-aligned-legend-key.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/legend-byrow-true.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/legend-with-widely-spaced-keys.svg (100%) rename tests/testthat/_snaps/{guides => guide-legend}/vertical-legend-direction.svg (100%) delete mode 100644 tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg create mode 100644 tests/testthat/_snaps/performance.md create mode 100644 tests/testthat/_snaps/position_dodge.md create mode 100644 tests/testthat/_snaps/scale-date.md create mode 100644 tests/testthat/_snaps/scale-gradient.md create mode 100644 tests/testthat/_snaps/scales-breaks-labels.md create mode 100644 tests/testthat/_snaps/stat-contour.md create mode 100644 tests/testthat/_snaps/stat-function.md create mode 100644 tests/testthat/_snaps/utilities-checks.md create mode 100644 tests/testthat/test-guide-.R create mode 100644 tests/testthat/test-guide-axis.R create mode 100644 tests/testthat/test-guide-colorbar.R create mode 100644 tests/testthat/test-guide-legend.R diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2e6d40ab70..430ac87c5d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -63,7 +63,7 @@ jobs: cache-version: 3 extra-packages: > any::rcmdcheck, - Hmisc=?ignore-before-r=4.1.0, + Hmisc=?ignore-before-r=4.2.0, quantreg=?ignore-before-r=4.3.0 needs: check diff --git a/DESCRIPTION b/DESCRIPTION index ff587e4b88..77755980b7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ggplot2 -Version: 3.5.1.9000 Title: Create Elegant Data Visualisations Using the Grammar of Graphics +Version: 3.5.1.9000 Authors@R: c( person("Hadley", "Wickham", , "hadley@posit.co", role = "aut", comment = c(ORCID = "0000-0003-4757-117X")), @@ -30,7 +30,7 @@ License: MIT + file LICENSE URL: https://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2 BugReports: https://github.com/tidyverse/ggplot2/issues Depends: - R (>= 3.5) + R (>= 4.0) Imports: cli, grDevices, @@ -75,6 +75,7 @@ VignetteBuilder: knitr Config/Needs/website: ggtext, tidyr, forcats, tidyverse/tidytemplate Config/testthat/edition: 3 +Config/usethis/last-upkeep: 2024-10-24 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) diff --git a/LICENSE.md b/LICENSE.md index 0a8a19674c..ce73598634 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ # MIT License -Copyright (c) 2020 ggplot2 authors +Copyright (c) 2024 ggplot2 core developer team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/R/stat-ellipse.R b/R/stat-ellipse.R index 152b27d280..7404e9eed6 100644 --- a/R/stat-ellipse.R +++ b/R/stat-ellipse.R @@ -5,7 +5,7 @@ #' #' @references John Fox and Sanford Weisberg (2011). An \R Companion to #' Applied Regression, Second Edition. Thousand Oaks CA: Sage. URL: -#' \url{https://socialsciences.mcmaster.ca/jfox/Books/Companion/} +#' \url{https://www.john-fox.ca/Companion/} #' @references Michael Friendly. Georges Monette. John Fox. "Elliptical Insights: Understanding Statistical Methods through Elliptical Geometry." #' Statist. Sci. 28 (1) 1 - 39, February 2013. URL: \url{https://projecteuclid.org/journals/statistical-science/volume-28/issue-1/Elliptical-Insights-Understanding-Statistical-Methods-through-Elliptical-Geometry/10.1214/12-STS402.full} #' diff --git a/README.Rmd b/README.Rmd index 337aa50b45..f546e5dc22 100644 --- a/README.Rmd +++ b/README.Rmd @@ -4,7 +4,8 @@ output: github_document -```{r, echo = FALSE} +```{r} +#| echo: false knitr::opts_chunk$set( collapse = TRUE, comment = "#>", @@ -12,12 +13,12 @@ knitr::opts_chunk$set( ) ``` -# ggplot2 +# ggplot2 ggplot2 website [![R-CMD-check](https://github.com/tidyverse/ggplot2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidyverse/ggplot2/actions/workflows/R-CMD-check.yaml) -[![Codecov test coverage](https://codecov.io/gh/tidyverse/ggplot2/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/ggplot2?branch=main) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ggplot2)](https://cran.r-project.org/package=ggplot2) +[![Codecov test coverage](https://codecov.io/gh/tidyverse/ggplot2/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/ggplot2) ## Overview @@ -26,7 +27,8 @@ ggplot2 is a system for declaratively creating graphics, based on [The Grammar o ## Installation -```{r, eval = FALSE} +```{r} +#| eval: false # The easiest way to get ggplot2 is to install the whole tidyverse: install.packages("tidyverse") @@ -40,13 +42,14 @@ pak::pak("tidyverse/ggplot2") ## Cheatsheet - +ggplot2 cheatsheet ## Usage It's hard to succinctly describe how ggplot2 works because it embodies a deep philosophy of visualisation. However, in most cases you start with `ggplot()`, supply a dataset and aesthetic mapping (with `aes()`). You then add on layers (like `geom_point()` or `geom_histogram()`), scales (like `scale_colour_brewer()`), faceting specifications (like `facet_wrap()`) and coordinate systems (like `coord_flip()`). -```{r example} +```{r} +#| label: example #| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars coloured by 7 'types' of car. The displacement and miles #| per gallon are inversely correlated." diff --git a/README.md b/README.md index 71f0060465..7fa139829b 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,14 @@ -# ggplot2 +# ggplot2 ggplot2 website [![R-CMD-check](https://github.com/tidyverse/ggplot2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidyverse/ggplot2/actions/workflows/R-CMD-check.yaml) -[![Codecov test -coverage](https://codecov.io/gh/tidyverse/ggplot2/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/ggplot2?branch=main) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ggplot2)](https://cran.r-project.org/package=ggplot2) +[![Codecov test +coverage](https://codecov.io/gh/tidyverse/ggplot2/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/ggplot2) ## Overview @@ -35,7 +35,7 @@ pak::pak("tidyverse/ggplot2") ## Cheatsheet - +ggplot2 cheatsheet ## Usage diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg index 4baaee01cd..b61c57c3f9 100644 --- a/man/figures/lifecycle-deprecated.svg +++ b/man/figures/lifecycle-deprecated.svg @@ -1 +1,21 @@ -lifecyclelifecycledeprecateddeprecated \ No newline at end of file + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg index d1d060e923..5d88fc2c65 100644 --- a/man/figures/lifecycle-experimental.svg +++ b/man/figures/lifecycle-experimental.svg @@ -1 +1,21 @@ -lifecyclelifecycleexperimentalexperimental \ No newline at end of file + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg index e015dc8110..9bf21e76bc 100644 --- a/man/figures/lifecycle-stable.svg +++ b/man/figures/lifecycle-stable.svg @@ -1 +1,29 @@ -lifecyclelifecyclestablestable \ No newline at end of file + + lifecycle: stable + + + + + + + + + + + + + + + + lifecycle + + + + stable + + + diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg index 75f24f5534..db8d757f70 100644 --- a/man/figures/lifecycle-superseded.svg +++ b/man/figures/lifecycle-superseded.svg @@ -1 +1,21 @@ - lifecyclelifecyclesupersededsuperseded \ No newline at end of file + + lifecycle: superseded + + + + + + + + + + + + + + + lifecycle + + superseded + + diff --git a/man/figures/logo.png b/man/figures/logo.png index 719583f61960cb16c0e19c5099583354af8eeba7..8007389c72657a700637d15b5d39e3ab808a8542 100644 GIT binary patch delta 30 mcmeyqhp}}J;{=t7CN5krxFk5#`PXh=b!lT$YV2gsI6VNsU<^Y5 delta 140 zcmZqO!}xs<;{+96mUKs7M+SzC{oH>NStlyGb3JEfXBW|6-nQ!I#-h~Nc-0cuh?11V zl2ohYqEsNoU}RuqtZM*7<{<{=Rz?O^#-`c^237_JlO8K=W?*1IXvob^$xN%nt>N*$ LS^Sf)#2NwsF>NaG diff --git a/man/stat_ellipse.Rd b/man/stat_ellipse.Rd index 138bda2e65..4bc30ef863 100644 --- a/man/stat_ellipse.Rd +++ b/man/stat_ellipse.Rd @@ -151,7 +151,7 @@ ggplot(faithful, aes(waiting, eruptions, fill = eruptions > 3)) + \references{ John Fox and Sanford Weisberg (2011). An \R Companion to Applied Regression, Second Edition. Thousand Oaks CA: Sage. URL: -\url{https://socialsciences.mcmaster.ca/jfox/Books/Companion/} +\url{https://www.john-fox.ca/Companion/} Michael Friendly. Georges Monette. John Fox. "Elliptical Insights: Understanding Statistical Methods through Elliptical Geometry." Statist. Sci. 28 (1) 1 - 39, February 2013. URL: \url{https://projecteuclid.org/journals/statistical-science/volume-28/issue-1/Elliptical-Insights-Understanding-Statistical-Methods-through-Elliptical-Geometry/10.1214/12-STS402.full} diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png index c78bb690e52f2b5c588b19414cd1d3ccae2d31a7..74c6511d61f81ece0a87bde2f477734f6bc97d1b 100644 GIT binary patch literal 11877 zcmW-nby!qQ8^(75MOsl1Bo$bsyFpgEJC~NOrIBV)0qJgpr3G2KyE|4oC6-2{yS{zD zy{_5w*O@ajXU_9HbKk!(H5FL`+&8!Y0DwSVPD%rPt@*D#dy4)S8-2=+zTh~^>AL{{ zcrX8JKtOsX82~^FkeB+X<&}Bx11D9hclr|hq=YMsiz^~K{i=_zkHaaRk^VaN^-fun z80Y&hFihs~)h~Gen&IzopM{G&HFU<*?+uo=h|^Znw@jka4|PmUgPP8*UuT*8=Ho}X zUmj%r+s#Td7}r!CKhvm(PCsVd%nB8a4GtbFEQF75-&Udoy&?Ny3dQn}eXEvjf=1mE z?cG1EzDC*OpUX5#QZ(!mH1@=`5a(9yD=W<|sJ`vZ?d`|+llN!gy6dFb!8ltrn99-Rx1} z6pJle5O~!BJpnByK5cs{cRGKAItQj0v5VB=y8{h7>?Dmzwd-rYHWRPOy`)4^Er-U& z#=sc}(FEksnJx}92)5)p%*JgyK|fz@9rKEmbf_on<*2XUmd2;UDM&l{GpvVx%~S7! 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zNi<-IL$mya2He>*sP&p`vj+Rb<312X9*o6{QL#3mSumW~aem1N?16S3p&ZZC3jHR# zHP%?ZcL6z7l)N8wB&E>Wl=7t`x1w{yX}zW&;QiUYes#vBB#TMq7G_T1T9a@(W?(F}F3%EFj)ruBpW(%fuf>3;+AepN27ZOwR>d@a$;2c+ z%@+CKDj52HfPK=20)W~!?#OM{EwTa1DBhyGx0ErVJk-WW zKuo*h3V=_=QS8Cxr&{J=H$}M-RH-$0Hpg#I>F8q7z0K$z{tI3!z+>RysipL811{`* zudy(++-#AroXogpzkt;;a$EkKYHC9`Rf^%xrf_Gy5z|f8)z$yxhKLpvTK}z_!2d_s zVf|V3;ye*Baunski$f6NfvYN(ve{D+rZuqkY@SX$7OP6t^7_WUI{pT5(nvyYC)lzD zqaz#0BSWr;t>5BS1Guvvfw_3_vu?l=J!FASbZ8SAhFFvya&?i*4Ef`Ku*3t#q#`5Q zcl6S_Y>yzMU`ysu?r;o_!*FQcWD!XYSOeLCEzsa|>)*ros_w(4in_yTjOd8u;HR5n q1}4#HRt&brR>B8mjrK=4QmFB*M^a@d`a1X~HRO512iNQtn(=?yKojr) literal 0 HcmV?d00001 diff --git a/tests/testthat/_snaps/aes-calculated.md b/tests/testthat/_snaps/aes-calculated.md index 629d2007d5..cd3424516b 100644 --- a/tests/testthat/_snaps/aes-calculated.md +++ b/tests/testthat/_snaps/aes-calculated.md @@ -6,6 +6,14 @@ Duplicated aesthetics after name standardisation: colour +# calculated aesthetics throw warnings when lengths mismatch + + Failed to apply `after_stat()` for the following aesthetic: colour. + +--- + + Failed to apply `after_scale()` for the following aesthetic: colour. + # A deprecated warning is issued when stat(var) or ..var.. is used `stat(foo)` was deprecated in ggplot2 3.4.0. diff --git a/tests/testthat/_snaps/aes-setting.md b/tests/testthat/_snaps/aes-setting.md new file mode 100644 index 0000000000..b0ba47a52a --- /dev/null +++ b/tests/testthat/_snaps/aes-setting.md @@ -0,0 +1,36 @@ +# aesthetic parameters match length of data + + Code + set_colours(rep("red", 2)) + Condition + Error in `geom_point()`: + ! Problem while setting up geom aesthetics. + i Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (5). + x Fix the following mappings: `colour`. + +--- + + Code + set_colours(rep("red", 3)) + Condition + Error in `geom_point()`: + ! Problem while setting up geom aesthetics. + i Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (5). + x Fix the following mappings: `colour`. + +--- + + Code + set_colours(rep("red", 4)) + Condition + Error in `geom_point()`: + ! Problem while setting up geom aesthetics. + i Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (5). + x Fix the following mappings: `colour`. + diff --git a/tests/testthat/_snaps/aes.md b/tests/testthat/_snaps/aes.md index 7f7f3ddc89..4a891eacbe 100644 --- a/tests/testthat/_snaps/aes.md +++ b/tests/testthat/_snaps/aes.md @@ -1,3 +1,43 @@ +# accessing an undefined variable results in an error + + Code + get_layer_data(p) + Condition + Error in `geom_point()`: + ! Problem while computing aesthetics. + i Error occurred in the 1st layer. + Caused by error: + ! object 'foo' not found + +# aes standardises aesthetic names + + Duplicated aesthetics after name standardisation: colour + +# warn_for_aes_extract_usage() warns for discouraged uses of $ and [[ within aes() + + Use of `df$x` is discouraged. + i Use `x` instead. + +--- + + Use of `df[["x"]]` is discouraged. + i Use `.data[["x"]]` instead. + +--- + + Use of `df$x` is discouraged. + i Use `x` instead. + +# warn_for_aes_extract_usage() does not evaluate function calls + + Use of `df$x` is discouraged. + i Use `x` instead. + +# Warnings are issued when plots use discouraged extract usage within aes() + + Use of `df$x` is discouraged. + i Use `x` instead. + # aes evaluation fails with unknown input Unknown input: diff --git a/tests/testthat/_snaps/coord-.md b/tests/testthat/_snaps/coord-.md index c4f74d626c..acf9ad78c6 100644 --- a/tests/testthat/_snaps/coord-.md +++ b/tests/testthat/_snaps/coord-.md @@ -18,3 +18,19 @@ `coord()` has not implemented a `range()` method. +# check coord limits errors only on bad inputs + + Code + check_coord_limits(xlim(1, 2)) + Condition + Error: + ! `xlim(1, 2)` must be a vector of length 2, not a object. + +--- + + Code + check_coord_limits(1:3) + Condition + Error: + ! `1:3` must be a vector of length 2, not an integer vector of length 3. + diff --git a/tests/testthat/_snaps/coord-transform.md b/tests/testthat/_snaps/coord-transform.md index def35a0f27..2aaa3c156f 100644 --- a/tests/testthat/_snaps/coord-transform.md +++ b/tests/testthat/_snaps/coord-transform.md @@ -1,3 +1,11 @@ +# warnings are generated when coord_trans() results in new infinite values + + Transformation introduced infinite values in y-axis + +--- + + Transformation introduced infinite values in x-axis + # coord_trans() throws error when limits are badly specified `xlim` must be a vector of length 2, not a object. diff --git a/tests/testthat/_snaps/empty-data.md b/tests/testthat/_snaps/empty-data.md new file mode 100644 index 0000000000..9889c48a91 --- /dev/null +++ b/tests/testthat/_snaps/empty-data.md @@ -0,0 +1,27 @@ +# layers with empty data are silently omitted with facet_wrap + + Code + get_layer_data(d) + Condition + Error in `combine_vars()`: + ! Faceting variables must have at least one value. + +# layers with empty data are silently omitted with facet_grid + + Code + get_layer_data(d) + Condition + Error in `combine_vars()`: + ! Faceting variables must have at least one value. + +# Should error when totally empty data frame because there's no x and y + + Code + get_layer_data(d) + Condition + Error in `geom_point()`: + ! Problem while computing aesthetics. + i Error occurred in the 2nd layer. + Caused by error: + ! object 'wt' not found + diff --git a/tests/testthat/_snaps/facet-.md b/tests/testthat/_snaps/facet-.md index 2efa86bc64..17d76b1f86 100644 --- a/tests/testthat/_snaps/facet-.md +++ b/tests/testthat/_snaps/facet-.md @@ -1,3 +1,19 @@ +# facets reject aes() + + Code + facet_wrap(aes(foo)) + Condition + Error in `validate_facets()`: + ! Please use `vars()` to supply facet variables. + +--- + + Code + facet_grid(aes(foo)) + Condition + Error in `validate_facets()`: + ! Please use `vars()` to supply facet variables. + # facet_grid() fails if passed both a formula and a vars() `rows` must be `NULL` or a `vars()` list if `cols` is a `vars()` list. @@ -30,6 +46,14 @@ x Plot is missing `letter` Layer is missing `letter` +# at least one combination must exist in combine_vars() + + Code + combine_vars(list(df), vars = vars(letter = letter)) + Condition + Error in `combine_vars()`: + ! Faceting variables must have at least one value. + # combine_vars() generates the correct combinations At least one layer must contain all faceting variables: `b` and `c` @@ -40,6 +64,15 @@ Faceting variables must have at least one value. +# eval_facet() is tolerant for missing columns (#2963) + + Code + eval_facet(quo(no_such_variable * x), data_frame(foo = 1), possible_columns = c( + "x")) + Condition + Error: + ! object 'no_such_variable' not found + # validate_facets() provide meaningful errors Please use `vars()` to supply facet variables. diff --git a/tests/testthat/_snaps/facet-labels.md b/tests/testthat/_snaps/facet-labels.md new file mode 100644 index 0000000000..6cdd9c1ad0 --- /dev/null +++ b/tests/testthat/_snaps/facet-labels.md @@ -0,0 +1,21 @@ +# labeller() dispatches labellers + + Code + ggplotGrob(p3) + Condition + Error in `resolve_labeller()`: + ! Cannot supply both `rows` and `cols` to `facet_wrap()`. + +--- + + Code + ggplotGrob(p5) + Condition + Error in `labeller()`: + ! Conflict between `.cols` and `cyl`. + +# old school labellers still work + + The `labeller` API has been updated. Labellers taking `variable` and `value` arguments are now deprecated. + i See labellers documentation. + diff --git a/tests/testthat/_snaps/fortify.md b/tests/testthat/_snaps/fortify.md index 81c3decea5..2034f092fb 100644 --- a/tests/testthat/_snaps/fortify.md +++ b/tests/testthat/_snaps/fortify.md @@ -3,3 +3,153 @@ `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`, not a object. i Did you accidentally pass `aes()` to the `data` argument? +# fortify.default can handle healthy data-frame-like objects + + Code + fortify(X) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` must return an of length 2. + +--- + + Code + fortify(array(1:60, 5:3)) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` must return an of length 2. + +--- + + Code + fortify(cbind(X, Y, Z, deparse.level = 0)) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `colnames(data)` must return a of length `ncol(data)`. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `dim.foo()`: + ! oops! + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` must return an of length 2. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` must return an of length 2. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` can't have `NA`s or negative values. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `dim(data)` can't have `NA`s or negative values. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `dimnames(x)[[2L]]`: + ! subscript out of bounds + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `colnames(data)` must return a of length `ncol(data)`. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.prevalidate_data_frame_like_object()`: + ! `colnames(data)` must return a of length `ncol(data)`. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `as.data.frame.foo()`: + ! oops! + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.postvalidate_data_frame_like_object()`: + ! `as.data.frame(data)` must return a . + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.postvalidate_data_frame_like_object()`: + ! `as.data.frame(data)` must preserve dimensions. + +--- + + Code + fortify(object) + Condition + Error in `fortify()`: + ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. + Caused by error in `.postvalidate_data_frame_like_object()`: + ! `as.data.frame(data)` must preserve column names. + diff --git a/tests/testthat/_snaps/geom-bar.md b/tests/testthat/_snaps/geom-bar.md new file mode 100644 index 0000000000..0afff44c16 --- /dev/null +++ b/tests/testthat/_snaps/geom-bar.md @@ -0,0 +1,4 @@ +# geom_bar removes bars with parts outside the plot limits + + Removed 1 row containing missing values or values outside the scale range (`geom_bar()`). + diff --git a/tests/testthat/_snaps/geom-boxplot.md b/tests/testthat/_snaps/geom-boxplot.md index d50a9db5e9..10e75bb438 100644 --- a/tests/testthat/_snaps/geom-boxplot.md +++ b/tests/testthat/_snaps/geom-boxplot.md @@ -1,3 +1,18 @@ +# geom_boxplot for continuous x gives warning if more than one x (#992) + + Continuous x aesthetic + i did you forget `aes(group = ...)`? + +--- + + Continuous x aesthetic + i did you forget `aes(group = ...)`? + +--- + + Continuous x aesthetic + i did you forget `aes(group = ...)`? + # boxplots with a group size >1 error Can only draw one boxplot per group. diff --git a/tests/testthat/_snaps/geom-col.md b/tests/testthat/_snaps/geom-col.md new file mode 100644 index 0000000000..1dfce430b0 --- /dev/null +++ b/tests/testthat/_snaps/geom-col.md @@ -0,0 +1,8 @@ +# geom_col removes columns with parts outside the plot limits + + Removed 3 rows containing missing values or values outside the scale range (`geom_col()`). + +--- + + Removed 1 row containing missing values or values outside the scale range (`geom_col()`). + diff --git a/tests/testthat/_snaps/geom-dotplot.md b/tests/testthat/_snaps/geom-dotplot.md index ba2fa8558c..a559276853 100644 --- a/tests/testthat/_snaps/geom-dotplot.md +++ b/tests/testthat/_snaps/geom-dotplot.md @@ -14,3 +14,11 @@ Caused by error in `compute_group()`: ! `weight` must be nonnegative integers, not a double vector. +# geom_dotplot draws correctly + + Removed 2 rows containing missing values or values outside the scale range (`stat_bindot()`). + +--- + + Removed 2 rows containing missing values or values outside the scale range (`stat_bindot()`). + diff --git a/tests/testthat/_snaps/geom-path.md b/tests/testthat/_snaps/geom-path.md index 6516134f98..9396883a78 100644 --- a/tests/testthat/_snaps/geom-path.md +++ b/tests/testthat/_snaps/geom-path.md @@ -5,3 +5,15 @@ Caused by error in `draw_panel()`: ! `geom_path()` can't have varying colour, linewidth, and/or alpha along the line when linetype isn't solid. +# stairstep() exists with error when an invalid `direction` is given + + Code + stairstep(df, direction = "invalid") + Condition + Error in `stairstep()`: + ! `direction` must be one of "hv", "vh", or "mid", not "invalid". + +# NA linetype is dropped with warning + + Removed 2 rows containing missing values or values outside the scale range (`geom_path()`). + diff --git a/tests/testthat/_snaps/geom-rect.md b/tests/testthat/_snaps/geom-rect.md new file mode 100644 index 0000000000..8c04cbbb21 --- /dev/null +++ b/tests/testthat/_snaps/geom-rect.md @@ -0,0 +1,9 @@ +# geom_rect can derive corners + + Code + GeomRect$setup_data(test, NULL) + Condition + Error in `resolve_rect()`: + ! `geom_rect()` requires two of the following aesthetics: xmin, xmax, x, or width. + i Currently, x is present. + diff --git a/tests/testthat/_snaps/geom-rug.md b/tests/testthat/_snaps/geom-rug.md index 06e4ad195b..c9e2157860 100644 --- a/tests/testthat/_snaps/geom-rug.md +++ b/tests/testthat/_snaps/geom-rug.md @@ -5,3 +5,7 @@ Caused by error in `draw_panel()`: ! `length` must be a object, not the number 0.01. +# geom_rug() warns about missing values when na.rm = FALSE + + Removed 2 rows containing missing values or values outside the scale range (`geom_rug()`). + diff --git a/tests/testthat/_snaps/geom-sf.md b/tests/testthat/_snaps/geom-sf.md index 1cc4fbb7d1..2d5217dd4f 100644 --- a/tests/testthat/_snaps/geom-sf.md +++ b/tests/testthat/_snaps/geom-sf.md @@ -1,3 +1,15 @@ +# geom_sf() removes rows containing missing aes + + Removed 1 row containing missing values or values outside the scale range (`geom_sf()`). + +--- + + Removed 1 row containing missing values or values outside the scale range (`geom_sf()`). + +--- + + Removed 1 row containing missing values or values outside the scale range (`geom_sf()`). + # errors are correctly triggered Problem while converting geom to grob. diff --git a/tests/testthat/_snaps/geom-smooth.md b/tests/testthat/_snaps/geom-smooth.md new file mode 100644 index 0000000000..aaffd02403 --- /dev/null +++ b/tests/testthat/_snaps/geom-smooth.md @@ -0,0 +1,4 @@ +# geom_smooth() works when one group fails + + span too small. fewer data values than degrees of freedom. + diff --git a/tests/testthat/_snaps/geom-text.md b/tests/testthat/_snaps/geom-text.md index c9d11b2bc7..e86cc9c905 100644 --- a/tests/testthat/_snaps/geom-text.md +++ b/tests/testthat/_snaps/geom-text.md @@ -3,3 +3,19 @@ Both `position` and `nudge_x`/`nudge_y` are supplied. i Only use one approach to alter the position. +# geom_text() drops missing angles + + Removed 1 row containing missing values or values outside the scale range (`geom_text()`). + +# geom_text() rejects exotic units + + Code + ggplotGrob(p + geom_text(size = 10, size.unit = "npc")) + Condition + Error in `geom_text()`: + ! Problem while converting geom to grob. + i Error occurred in the 1st layer. + Caused by error in `resolve_text_unit()`: + ! `unit` must be one of "mm", "pt", "cm", "in", or "pc", not "npc". + i Did you mean "pc"? + diff --git a/tests/testthat/_snaps/ggsave.md b/tests/testthat/_snaps/ggsave.md index 8a16fc672b..372d324b95 100644 --- a/tests/testthat/_snaps/ggsave.md +++ b/tests/testthat/_snaps/ggsave.md @@ -1,7 +1,76 @@ +# ggsave can create directories + + Code + ggsave(path, p) + Condition + Error in `ggsave()`: + ! Cannot find directory 'PATH' + i Please supply an existing directory or use `create.dir = TRUE`. + +# ggsave warns about empty or multiple filenames + + Code + x <- suppressMessages(ggsave(c(file1, file2), plot)) + Condition + Warning in `ggsave()`: + `filename` must have length 1, not 2. + ! Only the first,'PATH', will be used. + +--- + + Code + ggsave(character(), plot) + Condition + Error in `ggsave()`: + ! `filename` must be a single string, not an empty character vector. + +# ggsave fails informatively for no-extension filenames + + Code + ggsave(tempfile(), plot) + Condition + Error in `ggsave()`: + ! Can't save to PATH + i Either supply `filename` with a file extension or supply `device`. + +# warned about large plot unless limitsize = FALSE + + Code + plot_dim(c(50, 50)) + Condition + Error: + ! Dimensions exceed 50 inches (`height` and `width` are specified in inches not pixels). + i If you're sure you want a plot that big, use `limitsize = FALSE`. + +--- + + Code + plot_dim(c(15000, 15000), units = "px") + Condition + Error: + ! Dimensions exceed 50 inches (`height` and `width` are specified in pixels). + i If you're sure you want a plot that big, use `limitsize = FALSE`. + # unknown device triggers error `device` must be a string, function or `NULL`, not the number 1. +--- + + Code + plot_dev("xyz") + Condition + Error: + ! Unknown graphics device "xyz" + +--- + + Code + plot_dev(NULL, "test.xyz") + Condition + Error: + ! Unknown graphics device "xyz" + # invalid single-string DPI values throw an error `dpi` must be one of "screen", "print", or "retina", not "abc". diff --git a/tests/testthat/_snaps/guide-.md b/tests/testthat/_snaps/guide-.md new file mode 100644 index 0000000000..600e56f797 --- /dev/null +++ b/tests/testthat/_snaps/guide-.md @@ -0,0 +1,11 @@ +# dots are checked when making guides + + Ignoring unknown argument to `guide_axis()`: `foo`. + +--- + + Arguments in `...` must be used. + x Problematic argument: + * foo = "bar" + i Did you misspell an argument name? + diff --git a/tests/testthat/_snaps/guide-axis.md b/tests/testthat/_snaps/guide-axis.md new file mode 100644 index 0000000000..97bb6b8fca --- /dev/null +++ b/tests/testthat/_snaps/guide-axis.md @@ -0,0 +1,19 @@ +# a warning is generated when guides are drawn at a location that doesn't make sense + + Position guide is perpendicular to the intended axis. + i Did you mean to specify a different guide `position`? + +# a warning is generated when more than one position guide is drawn at a location + + `guide_axis()`: Discarding guide on merge. + i Do you have more than one guide with the same `position`? + +# Using non-position guides for position scales results in an informative error + + `guide_legend()` cannot be used for x, xmin, xmax, or xend. + i Use any non position aesthetic instead. + +# guide_axis_logticks calculates appropriate ticks + + The `prescale.base` argument will override the scale's log-10 transformation in log-tick positioning. + diff --git a/tests/testthat/_snaps/guides/align-facet-labels-facets-horizontal.svg b/tests/testthat/_snaps/guide-axis/align-facet-labels-facets-horizontal.svg similarity index 100% rename from tests/testthat/_snaps/guides/align-facet-labels-facets-horizontal.svg rename to tests/testthat/_snaps/guide-axis/align-facet-labels-facets-horizontal.svg diff --git a/tests/testthat/_snaps/guides/align-facet-labels-facets-vertical.svg b/tests/testthat/_snaps/guide-axis/align-facet-labels-facets-vertical.svg similarity index 100% rename from tests/testthat/_snaps/guides/align-facet-labels-facets-vertical.svg rename to tests/testthat/_snaps/guide-axis/align-facet-labels-facets-vertical.svg diff --git a/tests/testthat/_snaps/guides/axis-guides-basic.svg b/tests/testthat/_snaps/guide-axis/axis-guides-basic.svg similarity index 52% rename from tests/testthat/_snaps/guides/axis-guides-basic.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-basic.svg index ae2a74c24d..32f3b568eb 100644 --- a/tests/testthat/_snaps/guides/axis-guides-basic.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-basic.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-check-overlap.svg b/tests/testthat/_snaps/guide-axis/axis-guides-check-overlap.svg similarity index 83% rename from tests/testthat/_snaps/guides/axis-guides-check-overlap.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-check-overlap.svg index cf2312f98c..ad9d4f2f71 100644 --- a/tests/testthat/_snaps/guides/axis-guides-check-overlap.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-check-overlap.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg b/tests/testthat/_snaps/guide-axis/axis-guides-negative-rotation.svg similarity index 76% rename from tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-negative-rotation.svg index 8902fa04cd..8bb60d982b 100644 --- a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-negative-rotation.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-positive-rotation.svg b/tests/testthat/_snaps/guide-axis/axis-guides-positive-rotation.svg similarity index 76% rename from tests/testthat/_snaps/guides/axis-guides-positive-rotation.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-positive-rotation.svg index e1cd91eb77..61084a3df1 100644 --- a/tests/testthat/_snaps/guides/axis-guides-positive-rotation.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-positive-rotation.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-text-dodged-into-rows-cols.svg b/tests/testthat/_snaps/guide-axis/axis-guides-text-dodged-into-rows-cols.svg similarity index 76% rename from tests/testthat/_snaps/guides/axis-guides-text-dodged-into-rows-cols.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-text-dodged-into-rows-cols.svg index 79e94af549..0af3c6bcc1 100644 --- a/tests/testthat/_snaps/guides/axis-guides-text-dodged-into-rows-cols.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-text-dodged-into-rows-cols.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg b/tests/testthat/_snaps/guide-axis/axis-guides-vertical-negative-rotation.svg similarity index 77% rename from tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-vertical-negative-rotation.svg index 1d83ebc1e2..06d782e9c8 100644 --- a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-vertical-negative-rotation.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-vertical-rotation.svg b/tests/testthat/_snaps/guide-axis/axis-guides-vertical-rotation.svg similarity index 77% rename from tests/testthat/_snaps/guides/axis-guides-vertical-rotation.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-vertical-rotation.svg index f379bb7797..76adc31334 100644 --- a/tests/testthat/_snaps/guides/axis-guides-vertical-rotation.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-vertical-rotation.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/axis-guides-with-capped-ends.svg b/tests/testthat/_snaps/guide-axis/axis-guides-with-capped-ends.svg similarity index 100% rename from tests/testthat/_snaps/guides/axis-guides-with-capped-ends.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-with-capped-ends.svg diff --git a/tests/testthat/_snaps/guide-axis/axis-guides-zero-breaks.svg b/tests/testthat/_snaps/guide-axis/axis-guides-zero-breaks.svg new file mode 100644 index 0000000000..a89bf8e8f1 --- /dev/null +++ b/tests/testthat/_snaps/guide-axis/axis-guides-zero-breaks.svg @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/guides/axis-guides-zero-rotation.svg b/tests/testthat/_snaps/guide-axis/axis-guides-zero-rotation.svg similarity index 75% rename from tests/testthat/_snaps/guides/axis-guides-zero-rotation.svg rename to tests/testthat/_snaps/guide-axis/axis-guides-zero-rotation.svg index bb81af4971..8d5dad8f65 100644 --- a/tests/testthat/_snaps/guides/axis-guides-zero-rotation.svg +++ b/tests/testthat/_snaps/guide-axis/axis-guides-zero-rotation.svg @@ -18,47 +18,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/guides/guide-axis-customization.svg b/tests/testthat/_snaps/guide-axis/guide-axis-customization.svg similarity index 100% rename from tests/testthat/_snaps/guides/guide-axis-customization.svg rename to tests/testthat/_snaps/guide-axis/guide-axis-customization.svg diff --git a/tests/testthat/_snaps/guides/guide-axis-theta-in-cartesian-coordinates.svg b/tests/testthat/_snaps/guide-axis/guide-axis-theta-in-cartesian-coordinates.svg similarity index 100% rename from tests/testthat/_snaps/guides/guide-axis-theta-in-cartesian-coordinates.svg rename to tests/testthat/_snaps/guide-axis/guide-axis-theta-in-cartesian-coordinates.svg diff --git a/tests/testthat/_snaps/guides/guide-axis-theta-with-angle-adapting-to-theta.svg b/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg similarity index 100% rename from tests/testthat/_snaps/guides/guide-axis-theta-with-angle-adapting-to-theta.svg rename to tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg diff --git a/tests/testthat/_snaps/guides/guide-titles-with-coord-trans.svg b/tests/testthat/_snaps/guide-axis/guide-titles-with-coord-trans.svg similarity index 100% rename from tests/testthat/_snaps/guides/guide-titles-with-coord-trans.svg rename to tests/testthat/_snaps/guide-axis/guide-titles-with-coord-trans.svg diff --git a/tests/testthat/_snaps/guides/guides-specified-in-guides.svg b/tests/testthat/_snaps/guide-axis/guides-specified-in-guides.svg similarity index 100% rename from tests/testthat/_snaps/guides/guides-specified-in-guides.svg rename to tests/testthat/_snaps/guide-axis/guides-specified-in-guides.svg diff --git a/tests/testthat/_snaps/guides/guides-with-minor-ticks.svg b/tests/testthat/_snaps/guide-axis/guides-with-minor-ticks.svg similarity index 100% rename from tests/testthat/_snaps/guides/guides-with-minor-ticks.svg rename to tests/testthat/_snaps/guide-axis/guides-with-minor-ticks.svg diff --git a/tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg b/tests/testthat/_snaps/guide-axis/logtick-axes-with-customisation.svg similarity index 100% rename from tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg rename to tests/testthat/_snaps/guide-axis/logtick-axes-with-customisation.svg diff --git a/tests/testthat/_snaps/guides/position-guide-titles.svg b/tests/testthat/_snaps/guide-axis/position-guide-titles.svg similarity index 100% rename from tests/testthat/_snaps/guides/position-guide-titles.svg rename to tests/testthat/_snaps/guide-axis/position-guide-titles.svg diff --git a/tests/testthat/_snaps/guides/stacked-axes.svg b/tests/testthat/_snaps/guide-axis/stacked-axes.svg similarity index 100% rename from tests/testthat/_snaps/guides/stacked-axes.svg rename to tests/testthat/_snaps/guide-axis/stacked-axes.svg diff --git a/tests/testthat/_snaps/guides/stacked-radial-axes.svg b/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg similarity index 100% rename from tests/testthat/_snaps/guides/stacked-radial-axes.svg rename to tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg diff --git a/tests/testthat/_snaps/guides/thick-axis-lines.svg b/tests/testthat/_snaps/guide-axis/thick-axis-lines.svg similarity index 100% rename from tests/testthat/_snaps/guides/thick-axis-lines.svg rename to tests/testthat/_snaps/guide-axis/thick-axis-lines.svg diff --git a/tests/testthat/_snaps/guide-colorbar.md b/tests/testthat/_snaps/guide-colorbar.md new file mode 100644 index 0000000000..95818b07a1 --- /dev/null +++ b/tests/testthat/_snaps/guide-colorbar.md @@ -0,0 +1,14 @@ +# colorsteps and bins checks the breaks format + + Breaks are not formatted correctly for a bin legend. + i Use `(, ]` format to indicate bins. + +--- + + Breaks are not formatted correctly for a bin legend. + i Use `(, ]` format to indicate bins. + +# guide_colourbar warns about discrete scales + + `guide_colourbar()` needs continuous scales. + diff --git a/tests/testthat/_snaps/guides/one-combined-colorbar-for-colour-and-fill-aesthetics.svg b/tests/testthat/_snaps/guide-colorbar/combined-colour-and-fill-aesthetics.svg similarity index 98% rename from tests/testthat/_snaps/guides/one-combined-colorbar-for-colour-and-fill-aesthetics.svg rename to tests/testthat/_snaps/guide-colorbar/combined-colour-and-fill-aesthetics.svg index 9d656ece9f..75f9b641d3 100644 --- a/tests/testthat/_snaps/guides/one-combined-colorbar-for-colour-and-fill-aesthetics.svg +++ b/tests/testthat/_snaps/guide-colorbar/combined-colour-and-fill-aesthetics.svg @@ -79,6 +79,6 @@ 5 6 7 -one combined colorbar for colour and fill aesthetics +combined colour and fill aesthetics diff --git a/tests/testthat/_snaps/guides/customized-colorbar.svg b/tests/testthat/_snaps/guide-colorbar/customized-colorbar.svg similarity index 100% rename from tests/testthat/_snaps/guides/customized-colorbar.svg rename to tests/testthat/_snaps/guide-colorbar/customized-colorbar.svg diff --git a/tests/testthat/_snaps/guides/white-to-red-colorbar-white-ticks-no-frame.svg b/tests/testthat/_snaps/guide-colorbar/white-to-red-colorbar-white-ticks-no-frame.svg similarity index 100% rename from tests/testthat/_snaps/guides/white-to-red-colorbar-white-ticks-no-frame.svg rename to tests/testthat/_snaps/guide-colorbar/white-to-red-colorbar-white-ticks-no-frame.svg diff --git a/tests/testthat/_snaps/guides/enlarged-guides.svg b/tests/testthat/_snaps/guide-legend/enlarged-guides.svg similarity index 100% rename from tests/testthat/_snaps/guides/enlarged-guides.svg rename to tests/testthat/_snaps/guide-legend/enlarged-guides.svg diff --git a/tests/testthat/_snaps/guides/horizontal-legend-direction.svg b/tests/testthat/_snaps/guide-legend/horizontal-legend-direction.svg similarity index 100% rename from tests/testthat/_snaps/guides/horizontal-legend-direction.svg rename to tests/testthat/_snaps/guide-legend/horizontal-legend-direction.svg diff --git a/tests/testthat/_snaps/guides/left-aligned-legend-key.svg b/tests/testthat/_snaps/guide-legend/left-aligned-legend-key.svg similarity index 100% rename from tests/testthat/_snaps/guides/left-aligned-legend-key.svg rename to tests/testthat/_snaps/guide-legend/left-aligned-legend-key.svg diff --git a/tests/testthat/_snaps/guides/legend-byrow-true.svg b/tests/testthat/_snaps/guide-legend/legend-byrow-true.svg similarity index 100% rename from tests/testthat/_snaps/guides/legend-byrow-true.svg rename to tests/testthat/_snaps/guide-legend/legend-byrow-true.svg diff --git a/tests/testthat/_snaps/guides/legend-with-widely-spaced-keys.svg b/tests/testthat/_snaps/guide-legend/legend-with-widely-spaced-keys.svg similarity index 100% rename from tests/testthat/_snaps/guides/legend-with-widely-spaced-keys.svg rename to tests/testthat/_snaps/guide-legend/legend-with-widely-spaced-keys.svg diff --git a/tests/testthat/_snaps/guides/vertical-legend-direction.svg b/tests/testthat/_snaps/guide-legend/vertical-legend-direction.svg similarity index 100% rename from tests/testthat/_snaps/guides/vertical-legend-direction.svg rename to tests/testthat/_snaps/guide-legend/vertical-legend-direction.svg diff --git a/tests/testthat/_snaps/guides.md b/tests/testthat/_snaps/guides.md index be7c84d7f3..a47fba746b 100644 --- a/tests/testthat/_snaps/guides.md +++ b/tests/testthat/_snaps/guides.md @@ -1,19 +1,3 @@ -# dots are checked when making guides - - Ignoring unknown argument to `guide_axis()`: `foo`. - ---- - - Arguments in `...` must be used. - x Problematic argument: - * foo = "bar" - i Did you misspell an argument name? - -# Using non-position guides for position scales results in an informative error - - `guide_legend()` cannot be used for x, xmin, xmax, or xend. - i Use any non position aesthetic instead. - # guide specifications are properly checked Unknown guide: test @@ -53,19 +37,21 @@ `nrow` * `ncol` needs to be larger than the number of breaks (5). -# colorsteps and bins checks the breaks format +# get_guide_data retrieves keys appropriately - Breaks are not formatted correctly for a bin legend. - i Use `(, ]` format to indicate bins. + Code + get_guide_data(b, 1) + Condition + Error in `get_guide_data()`: + ! `aesthetic` must be a single string, not the number 1. --- - Breaks are not formatted correctly for a bin legend. - i Use `(, ]` format to indicate bins. - -# guide_axis_logticks calculates appropriate ticks - - The `prescale.base` argument will override the scale's log-10 transformation in log-tick positioning. + Code + get_guide_data(b, "x", panel = "a") + Condition + Error in `get_guide_data()`: + ! `panel` must be a whole number, not the string "a". # binning scales understand the different combinations of limits, breaks, labels, and show.limits @@ -77,10 +63,15 @@ `show.limits` is ignored when `labels` are given as a character vector. i Either add the limits to `breaks` or provide a function for `labels`. -# a warning is generated when guides( = FALSE) is specified +# guides() warns if unnamed guides are provided + + Guides provided to `guides()` must be named. + i All guides are unnamed. + +--- - The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in ggplot2 3.3.4. - i Please use "none" instead. + Guides provided to `guides()` must be named. + i The 2nd guide is unnamed. # old S3 guides can be implemented diff --git a/tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg b/tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg deleted file mode 100644 index 2ef933e31b..0000000000 --- a/tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg +++ /dev/null @@ -1,67 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index 49efe59a72..80b541e2e4 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -25,3 +25,19 @@ `plot.tag.position` must be one of "topleft", "top", "topright", "left", "right", "bottomleft", "bottom", or "bottomright", not "foobar". +--- + + Code + ggplotGrob(p + theme(plot.tag.position = c(0, 0.5, 1))) + Condition + Error in `theme()`: + ! A `plot.tag.position` theme setting must have length 2. + +--- + + Code + ggplotGrob(p + theme(plot.tag.position = c(0, 0), plot.tag.location = "margin")) + Condition + Error in `theme()`: + ! A `plot.tag.position` cannot be used with `"margin"` as `plot.tag.location`. + diff --git a/tests/testthat/_snaps/layer.md b/tests/testthat/_snaps/layer.md index d95e11bed6..70573a3d7c 100644 --- a/tests/testthat/_snaps/layer.md +++ b/tests/testthat/_snaps/layer.md @@ -27,6 +27,18 @@ `x` must be either a string or a object, not an environment. +# unknown params create warning + + Ignoring unknown parameters: `blah` + +# unknown aesthetics create warning + + Ignoring unknown aesthetics: blah + +# empty aesthetics create warning + + Ignoring empty aesthetics: `fill` and `shape`. + # invalid aesthetics throws errors Problem while computing aesthetics. @@ -47,6 +59,28 @@ x `fill = after_stat(data)` i Did you map your stat in the wrong layer? +# missing aesthetics trigger informative error + + Code + ggplot_build(ggplot(df) + geom_line()) + Condition + Error in `geom_line()`: + ! Problem while setting up geom. + i Error occurred in the 1st layer. + Caused by error in `compute_geom_1()`: + ! `geom_line()` requires the following missing aesthetics: x and y. + +--- + + Code + ggplot_build(ggplot(df) + geom_col()) + Condition + Error in `geom_col()`: + ! Problem while setting up geom. + i Error occurred in the 1st layer. + Caused by error in `compute_geom_1()`: + ! `geom_col()` requires the following missing aesthetics: x and y. + # function aesthetics are wrapped with after_stat() Problem while computing aesthetics. @@ -89,6 +123,16 @@ All aesthetics have length 1, but the data has 32 rows. i Please consider using `annotate()` or provide this layer with data containing a single row. +# layer names can be resolved + + Code + p + l + l + Condition + Error in `new_layer_names()`: + ! Names must be unique. + x These names are duplicated: + * "foobar" at locations 3 and 4. + # layer_data returns a data.frame `layer_data()` must return a . diff --git a/tests/testthat/_snaps/performance.md b/tests/testthat/_snaps/performance.md new file mode 100644 index 0000000000..153fde6c57 --- /dev/null +++ b/tests/testthat/_snaps/performance.md @@ -0,0 +1,9 @@ +# modifyList is masked + + Code + modifyList(testlist, testappend) + Condition + Error in `modifyList()`: + ! Please use `modify_list()` instead of `modifyList()` for better performance. + i See the vignette ggplot2 internal programming guidelines for details. + diff --git a/tests/testthat/_snaps/position_dodge.md b/tests/testthat/_snaps/position_dodge.md new file mode 100644 index 0000000000..044f2b4392 --- /dev/null +++ b/tests/testthat/_snaps/position_dodge.md @@ -0,0 +1,11 @@ +# position_dodge warns about missing required aesthetics + + Code + ggplot_build(p) + Condition + Error: + ! Problem while computing position. + i Error occurred in the 1st layer. + Caused by error in `setup_params()`: + ! `position_dodge()` requires the following missing aesthetics: x or xmin. + diff --git a/tests/testthat/_snaps/scale-date.md b/tests/testthat/_snaps/scale-date.md new file mode 100644 index 0000000000..9717f0f785 --- /dev/null +++ b/tests/testthat/_snaps/scale-date.md @@ -0,0 +1,10 @@ +# date(time) scales throw warnings when input is numeric + + A value was passed to a Date scale. + i The value was converted to a object. + +--- + + A value was passed to a Datetime scale. + i The value was converted to a object. + diff --git a/tests/testthat/_snaps/scale-discrete.md b/tests/testthat/_snaps/scale-discrete.md index c668bceba9..a3251c4c4e 100644 --- a/tests/testthat/_snaps/scale-discrete.md +++ b/tests/testthat/_snaps/scale-discrete.md @@ -1,3 +1,39 @@ +# Scale is checked in default colour scale + + Code + scale_colour_discrete(type = scale_colour_gradient) + Condition + Error in `scale_colour_discrete()`: + ! The `type` argument must return a discrete scale for the colour aesthetic. + x The provided scale is continuous. + +--- + + Code + scale_fill_discrete(type = scale_fill_gradient) + Condition + Error in `scale_fill_discrete()`: + ! The `type` argument must return a discrete scale for the fill aesthetic. + x The provided scale is continuous. + +--- + + Code + scale_colour_discrete(type = scale_fill_hue) + Condition + Error in `scale_colour_discrete()`: + ! The `type` argument must return a continuous scale for the colour aesthetic. + x The provided scale works with the following aesthetics: fill. + +--- + + Code + scale_fill_discrete(type = scale_colour_hue) + Condition + Error in `scale_fill_discrete()`: + ! The `type` argument must return a continuous scale for the fill aesthetic. + x The provided scale works with the following aesthetics: colour. + # Aesthetics with no continuous interpretation fails when called A continuous variable cannot be mapped to the linetype aesthetic. @@ -8,3 +44,27 @@ A continuous variable cannot be mapped to the shape aesthetic. i Choose a different aesthetic or use `scale_shape_binned()`. +# mapped_discrete vectors behaves as predicted + + Code + mapped_discrete(letters) + Condition + Error in `mapped_discrete()`: + ! Can't convert `x` to . + +# invalid palettes trigger errors + + Code + ggplot_build(p + scale_x_discrete(palette = function(x) LETTERS[1:3])) + Condition + Error in `scale_x_discrete()`: + ! The `palette` function must return a vector. + +--- + + Code + ggplot_build(p + scale_x_discrete(palette = function(x) 1:2)) + Condition + Error in `scale_x_discrete()`: + ! The `palette` function must return at least 3 values. + diff --git a/tests/testthat/_snaps/scale-gradient.md b/tests/testthat/_snaps/scale-gradient.md new file mode 100644 index 0000000000..ebb18a84e7 --- /dev/null +++ b/tests/testthat/_snaps/scale-gradient.md @@ -0,0 +1,4 @@ +# midpoints are transformed + + log-10 transformation introduced infinite values in `midpoint`. + diff --git a/tests/testthat/_snaps/scale-manual.md b/tests/testthat/_snaps/scale-manual.md index faf69a7899..70c2fa4dfd 100644 --- a/tests/testthat/_snaps/scale-manual.md +++ b/tests/testthat/_snaps/scale-manual.md @@ -2,3 +2,19 @@ No shared levels found between `names(values)` of the manual scale and the data's colour values. +# insufficient values raise an error + + Code + ggplot_build(p + scale_colour_manual(values = "black")) + Condition + Error in `palette()`: + ! Insufficient values in manual scale. 2 needed but only 1 provided. + +# fewer values (#3451) + + Code + s2$map(c("4", "6", "8")) + Condition + Error in `palette()`: + ! Insufficient values in manual scale. 3 needed but only 2 provided. + diff --git a/tests/testthat/_snaps/scales-breaks-labels.md b/tests/testthat/_snaps/scales-breaks-labels.md new file mode 100644 index 0000000000..e3b5f28532 --- /dev/null +++ b/tests/testthat/_snaps/scales-breaks-labels.md @@ -0,0 +1,133 @@ +# labels match breaks + + Code + scale_x_discrete(breaks = 1:3, labels = 1:2) + Condition + Error in `scale_x_discrete()`: + ! `breaks` and `labels` must have the same length. + +--- + + Code + scale_x_continuous(breaks = 1:3, labels = 1:2) + Condition + Error in `scale_x_continuous()`: + ! `breaks` and `labels` must have the same length. + +# passing continuous limits to a discrete scale generates a warning + + Continuous limits supplied to discrete scale. + i Did you mean `limits = factor(...)` or `scale_*_continuous()`? + +# suppressing breaks, minor_breask, and labels works + + Code + scale_x_date(breaks = NA, limits = lims)$get_breaks() + Condition + Error in `scale_x_date()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + scale_x_date(labels = NA, limits = lims)$get_labels() + Condition + Error in `scale_x_date()`: + ! Invalid `labels` specification. Use `NULL`, not `NA`. + +--- + + Code + scale_x_date(minor_breaks = NA, limits = lims)$get_breaks_minor() + Condition + Error in `scale_x_date()`: + ! Invalid `minor_breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + scale_x_datetime(breaks = NA, limits = lims)$get_breaks() + Condition + Error in `scale_x_datetime()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + scale_x_datetime(labels = NA, limits = lims)$get_labels() + Condition + Error in `scale_x_datetime()`: + ! Invalid `labels` specification. Use `NULL`, not `NA`. + +--- + + Code + scale_x_datetime(minor_breaks = NA, limits = lims)$get_breaks_minor() + Condition + Error in `scale_x_datetime()`: + ! Invalid `minor_breaks` specification. Use `NULL`, not `NA`. + +# scale_breaks with explicit NA options (deprecated) + + Code + sxc$get_breaks() + Condition + Error in `scale_x_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + sxc$get_breaks_minor() + Condition + Error in `scale_x_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + syc$get_breaks() + Condition + Error in `scale_y_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + syc$get_breaks_minor() + Condition + Error in `scale_y_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + sac$get_breaks() + Condition + Error in `scale_alpha_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + ssc$get_breaks() + Condition + Error in `scale_size_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + sfc$get_breaks() + Condition + Error in `scale_fill_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + +--- + + Code + scc$get_breaks() + Condition + Error in `scale_colour_continuous()`: + ! Invalid `breaks` specification. Use `NULL`, not `NA`. + diff --git a/tests/testthat/_snaps/scales.md b/tests/testthat/_snaps/scales.md index 61754a645a..40298a1836 100644 --- a/tests/testthat/_snaps/scales.md +++ b/tests/testthat/_snaps/scales.md @@ -1,3 +1,31 @@ +# oob affects position values + + Removed 1 row containing missing values or values outside the scale range (`geom_bar()`). + +--- + + Removed 3 rows containing missing values or values outside the scale range (`geom_bar()`). + +# scales warn when transforms introduces non-finite values + + log-10 transformation introduced infinite values. + +# size and alpha scales throw appropriate warnings for factors + + Using size for a discrete variable is not advised. + +--- + + Using alpha for a discrete variable is not advised. + +--- + + Using linewidth for a discrete variable is not advised. + +# shape scale throws appropriate warnings for factors + + Using shapes for an ordinal variable is not advised + # scale_apply preserves class and attributes `scale_id` must not contain any "NA". diff --git a/tests/testthat/_snaps/stat-bin.md b/tests/testthat/_snaps/stat-bin.md index dd7a8127bf..f92e737d94 100644 --- a/tests/testthat/_snaps/stat-bin.md +++ b/tests/testthat/_snaps/stat-bin.md @@ -53,6 +53,26 @@ Caused by error in `bin_breaks_bins()`: ! `bins` must be a whole number larger than or equal to 1, not the number -4. +# setting boundary and center + + Code + comp_bin(df, boundary = 5, center = 0) + Condition + Error in `stat_bin()`: + ! Problem while computing stat. + i Error occurred in the 1st layer. + Caused by error in `setup_params()`: + ! Only one of `boundary` and `center` may be specified in `stat_bin()`. + +# bin errors at high bin counts + + Code + bin_breaks_width(c(1, 2e+06), 1) + Condition + Error in `bin_breaks_width()`: + ! The number of histogram bins must be less than 1,000,000. + i Did you make `binwidth` too small? + # stat_count throws error when both x and y aesthetic present Problem while computing stat. diff --git a/tests/testthat/_snaps/stat-contour.md b/tests/testthat/_snaps/stat-contour.md new file mode 100644 index 0000000000..d20d5aee72 --- /dev/null +++ b/tests/testthat/_snaps/stat-contour.md @@ -0,0 +1,14 @@ +# a warning is issued when there is more than one z per x+y + + Contour data has duplicated x, y coordinates. + i 1 duplicated row have been dropped. + +# contouring sparse data results in a warning + + `stat_contour()`: Zero contours were generated + +# stat_contour() removes duplicated coordinates + + Contour data has duplicated x, y coordinates. + i 4 duplicated rows have been dropped. + diff --git a/tests/testthat/_snaps/stat-density.md b/tests/testthat/_snaps/stat-density.md index 17cbca4b7d..94902bca55 100644 --- a/tests/testthat/_snaps/stat-density.md +++ b/tests/testthat/_snaps/stat-density.md @@ -1,3 +1,7 @@ +# stat_density handles data outside of `bounds` + + Some data points are outside of `bounds`. Removing them. + # stat_density works in both directions Problem while computing stat. @@ -5,6 +9,10 @@ Caused by error in `setup_params()`: ! `stat_density()` requires an x or y aesthetic. +# compute_density returns useful df and throws warning when <2 values + + Groups with fewer than two data points have been dropped. + # precompute_bandwidth() errors appropriately `bw` must be one of "nrd0", "nrd", "ucv", "bcv", "sj", "sj-ste", or "sj-dpi", not "foobar". diff --git a/tests/testthat/_snaps/stat-ecdf.md b/tests/testthat/_snaps/stat-ecdf.md index e4da4c47f9..92edd3193f 100644 --- a/tests/testthat/_snaps/stat-ecdf.md +++ b/tests/testthat/_snaps/stat-ecdf.md @@ -5,3 +5,21 @@ Caused by error in `setup_params()`: ! `stat_ecdf()` requires an x or y aesthetic. +# weighted ecdf warns about weird weights + + The weight aesthetic does not support non-finite or `NA` values. + i These weights were replaced by "0". + +--- + + The sum of the weight aesthetic is close to "0". + i Computed eCDF might be unstable. + +--- + + Code + wecdf(1:10, rep(c(-1, 1), 5)) + Condition + Error in `wecdf()`: + ! Cannot compute eCDF when the weight aesthetic sums up to "0". + diff --git a/tests/testthat/_snaps/stat-function.md b/tests/testthat/_snaps/stat-function.md new file mode 100644 index 0000000000..329b6cc8de --- /dev/null +++ b/tests/testthat/_snaps/stat-function.md @@ -0,0 +1,5 @@ +# Warn when drawing multiple copies of the same function + + Multiple drawing groups in `geom_function()` + i Did you use the correct group, colour, or fill aesthetics? + diff --git a/tests/testthat/_snaps/stat-ydensity.md b/tests/testthat/_snaps/stat-ydensity.md index 1511b0b462..f72f4ebd57 100644 --- a/tests/testthat/_snaps/stat-ydensity.md +++ b/tests/testthat/_snaps/stat-ydensity.md @@ -6,3 +6,12 @@ `test` is not a valid bandwidth rule. +# `drop = FALSE` preserves groups with 1 observations + + Groups with fewer than two datapoints have been dropped. + i Set `drop = FALSE` to consider such groups for position adjustment purposes. + +--- + + Cannot compute density for groups with fewer than two datapoints. + diff --git a/tests/testthat/_snaps/stats.md b/tests/testthat/_snaps/stats.md index 92a4296185..f5b46f9669 100644 --- a/tests/testthat/_snaps/stats.md +++ b/tests/testthat/_snaps/stats.md @@ -1,6 +1,35 @@ +# plot succeeds even if some computation fails + + Computation failed in `stat_summary()`. + Caused by error in `fun()`: + ! Failed computation + +# error message is thrown when aesthetics are missing + + Code + ggplot_build(p) + Condition + Error in `stat_sum()`: + ! Problem while computing stat. + i Error occurred in the 1st layer. + Caused by error in `compute_layer()`: + ! `stat_sum()` requires the following missing aesthetics: x and y. + # erroneously dropped aesthetics are found and issue a warning + The following aesthetics were dropped during statistical transformation: fill. + i This can happen when ggplot fails to infer the correct grouping structure in the data. + i Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? + +--- + The following aesthetics were dropped during statistical transformation: colour and fill. i This can happen when ggplot fails to infer the correct grouping structure in the data. i Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? +--- + + The following aesthetics were dropped during statistical transformation: colour. + i This can happen when ggplot fails to infer the correct grouping structure in the data. + i Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? + diff --git a/tests/testthat/_snaps/theme.md b/tests/testthat/_snaps/theme.md index 259a887c1a..fa7237d37d 100644 --- a/tests/testthat/_snaps/theme.md +++ b/tests/testthat/_snaps/theme.md @@ -1,3 +1,19 @@ +# modifying theme element properties with + operator works + + Code + theme_grey() + "asdf" + Condition + Error: + ! Can't add `"asdf"` to a theme object. + +# replacing theme elements with %+replace% operator works + + Code + theme_grey() + "asdf" + Condition + Error: + ! Can't add `"asdf"` to a theme object. + # theme validation happens at build stage The `text` theme element must be a object. @@ -40,6 +56,14 @@ The `blablabla` theme element must be a object. +# elements can be merged + + Code + merge_element(text_base, rect_base) + Condition + Error in `merge_element()`: + ! Only elements of the same class can be merged. + # Theme elements are checked during build `plot.title.position` must be one of "panel" or "plot", not "test". diff --git a/tests/testthat/_snaps/utilities-checks.md b/tests/testthat/_snaps/utilities-checks.md new file mode 100644 index 0000000000..e356c2f701 --- /dev/null +++ b/tests/testthat/_snaps/utilities-checks.md @@ -0,0 +1,28 @@ +# check_device checks R versions correctly + + R 4.0.0 does not support gradients. + +--- + + R 4.1.0 does not support gradients. + +--- + + R 4.2.0 does not support glyphs. + +# check_device finds device capabilities + + The pdf device does not support clipping paths. + +--- + + Unable to check the capabilities of the foobar device. + +# check_device finds ragg capabilities + + The agg_tiff device does not support compositing. + +# check_device finds svglite capabilities + + The devSVG device does not support compositing. + diff --git a/tests/testthat/_snaps/utilities.md b/tests/testthat/_snaps/utilities.md index 37138df4e9..4ccf6d67d1 100644 --- a/tests/testthat/_snaps/utilities.md +++ b/tests/testthat/_snaps/utilities.md @@ -18,6 +18,10 @@ `na.rm` must be `TRUE` or `FALSE`, not an integer vector. +# characters survive remove_missing + + Removed 1 row containing non-finite outside the scale range. + # tolower() and toupper() has been masked Please use `to_lower_ascii()`, which works fine in all locales. diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index 9d5c49c68e..ac77df4c48 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -76,18 +76,16 @@ test_that("calculated aesthetics throw warnings when lengths mismatch", { p <- ggplot(df, aes(x, x)) - expect_warning( + expect_snapshot_warning( ggplot_build( p + geom_point(aes(colour = after_stat(c("A", "B", "C")))) - ), - "Failed to apply" + ) ) - expect_warning( + expect_snapshot_warning( ggplot_build( p + geom_point(aes(colour = after_scale(c("red", "green", "blue")))) - ), - "Failed to apply" + ) ) }) diff --git a/tests/testthat/test-aes-setting.R b/tests/testthat/test-aes-setting.R index 422032017f..2071921c03 100644 --- a/tests/testthat/test-aes-setting.R +++ b/tests/testthat/test-aes-setting.R @@ -7,9 +7,9 @@ test_that("aesthetic parameters match length of data", { } set_colours("red") - expect_error(set_colours(rep("red", 2)), "must be either length 1") - expect_error(set_colours(rep("red", 3)), "must be either length 1") - expect_error(set_colours(rep("red", 4)), "must be either length 1") + expect_snapshot(set_colours(rep("red", 2)), error = TRUE) + expect_snapshot(set_colours(rep("red", 3)), error = TRUE) + expect_snapshot(set_colours(rep("red", 4)), error = TRUE) set_colours(rep("red", 5)) }) @@ -31,7 +31,7 @@ test_that("legend filters out aesthetics not of length 1", { # Ideally would test something in the legend data structure, but # that's not easily accessible currently. - expect_error(ggplot_gtable(ggplot_build(p)), NA) + expect_no_error(ggplot_gtable(ggplot_build(p))) }) test_that("alpha affects only fill colour of solid geoms", { diff --git a/tests/testthat/test-aes.R b/tests/testthat/test-aes.R index 1cb333fcac..a42b4a3ae1 100644 --- a/tests/testthat/test-aes.R +++ b/tests/testthat/test-aes.R @@ -48,8 +48,10 @@ test_that("aes evaluated in environment where plot created", { df <- data_frame(x = 1, y = 1) p <- ggplot(df, aes(foo, y)) + geom_point() - # Accessing an undefined variable should result in error - expect_error(get_layer_data(p), "'foo' not found") + test_that("accessing an undefined variable results in an error", { + skip_if(getRversion() <= "4.4.0") + expect_snapshot(get_layer_data(p), error = TRUE) + }) # Once it's defined we should get it back foo <- 0 @@ -114,29 +116,26 @@ test_that("aes standardises aesthetic names", { expect_identical(aes(color_point = x), aes(colour_point = x)) # warning when standardisation creates duplicates - expect_warning(aes(color = x, colour = y), "Duplicated aesthetics") + expect_snapshot_warning(aes(color = x, colour = y)) }) test_that("warn_for_aes_extract_usage() warns for discouraged uses of $ and [[ within aes()", { df <- data_frame(x = 1:5, nested_df = data_frame(x = 6:10)) - expect_warning( - warn_for_aes_extract_usage(aes(df$x), df), - "Use of `df\\$x` is discouraged" + expect_snapshot_warning( + warn_for_aes_extract_usage(aes(df$x), df) ) - expect_warning( - warn_for_aes_extract_usage(aes(df[["x"]]), df), - 'Use of `df\\[\\["x"\\]\\]` is discouraged' + expect_snapshot_warning( + warn_for_aes_extract_usage(aes(df[["x"]]), df) ) # Check that rownames are ignored (#5392) df2 <- df rownames(df2) <- LETTERS[seq_len(nrow(df))] - expect_warning( - warn_for_aes_extract_usage(aes(df$x), df2), - "Use of `df\\$x` is discouraged" + expect_snapshot_warning( + warn_for_aes_extract_usage(aes(df$x), df2) ) }) @@ -144,7 +143,7 @@ test_that("warn_for_aes_extract_usage() does not evaluate function calls", { df <- data_frame(x = 1:5, nested_df = data_frame(x = 6:10)) returns_df <- function() df - expect_warning(warn_for_aes_extract_usage(aes(df$x), df)) + expect_snapshot_warning(warn_for_aes_extract_usage(aes(df$x), df)) expect_silent(warn_for_aes_extract_usage(aes(returns_df()$x), df)) }) @@ -163,7 +162,7 @@ test_that("warn_for_aes_extract_usage() does not warn for valid uses of $ and [[ test_that("Warnings are issued when plots use discouraged extract usage within aes()", { df <- data_frame(x = 1:3, y = 1:3) p <- ggplot(df, aes(df$x, y)) + geom_point() - expect_warning(ggplot_build(p), "Use of `df\\$x` is discouraged") + expect_snapshot_warning(ggplot_build(p)) }) test_that("aes evaluation fails with unknown input", { diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index f1e910c807..b0cef2de26 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -47,10 +47,10 @@ test_that("check coord limits errors only on bad inputs", { expect_null(check_coord_limits(c(1,2))) # Should raise error if Scale object is passed - expect_error(check_coord_limits(xlim(1,2))) + expect_snapshot(check_coord_limits(xlim(1,2)), error = TRUE) # Should raise error if vector of wrong length is passed - expect_error(check_coord_limits(1:3)) + expect_snapshot(check_coord_limits(1:3), error = TRUE) }) test_that("coords append a column to the layout correctly", { diff --git a/tests/testthat/test-coord-transform.R b/tests/testthat/test-coord-transform.R index abb05a3cae..f3dd4a6b00 100644 --- a/tests/testthat/test-coord-transform.R +++ b/tests/testthat/test-coord-transform.R @@ -10,8 +10,8 @@ test_that("warnings are generated when coord_trans() results in new infinite val # TODO: These multiple warnings should be summarized nicely. Until this gets # fixed, this test ignores all the following errors than the first one. suppressWarnings({ - expect_warning(ggplot_gtable(ggplot_build(p)), "Transformation introduced infinite values in y-axis") - expect_warning(ggplot_gtable(ggplot_build(p2)), "Transformation introduced infinite values in x-axis") + expect_snapshot_warning(ggplot_gtable(ggplot_build(p))) + expect_snapshot_warning(ggplot_gtable(ggplot_build(p2))) }) }) diff --git a/tests/testthat/test-empty-data.R b/tests/testthat/test-empty-data.R index bdcc02003c..e6fe24ce38 100644 --- a/tests/testthat/test-empty-data.R +++ b/tests/testthat/test-empty-data.R @@ -34,7 +34,7 @@ test_that("layers with empty data are silently omitted with facet_wrap", { d <- ggplot(df0, aes(mpg, wt)) + geom_point() + facet_wrap(~cyl) - expect_error(get_layer_data(d), "must have at least one value") + expect_snapshot(get_layer_data(d), error = TRUE) d <- d + geom_point(data = mtcars) expect_equal(nrow(get_layer_data(d, 1)), 0) @@ -45,7 +45,7 @@ test_that("layers with empty data are silently omitted with facet_grid", { d <- ggplot(df0, aes(mpg, wt)) + geom_point() + facet_grid(am ~ cyl) - expect_error(get_layer_data(d), "must have at least one value") + expect_snapshot(get_layer_data(d), error = TRUE) d <- d + geom_point(data = mtcars) expect_equal(nrow(get_layer_data(d, 1)), 0) @@ -53,11 +53,13 @@ test_that("layers with empty data are silently omitted with facet_grid", { }) test_that("empty data overrides plot defaults", { - # Should error when totally empty data frame because there's no x and y - d <- ggplot(mtcars, aes(mpg, wt)) + - geom_point() + - geom_point(data = data_frame()) - expect_error(get_layer_data(d), "not found") + test_that("Should error when totally empty data frame because there's no x and y", { + skip_if(getRversion() <= "4.4.0") + d <- ggplot(mtcars, aes(mpg, wt)) + + geom_point() + + geom_point(data = data_frame()) + expect_snapshot(get_layer_data(d), error = TRUE) + }) # No extra points when x and y vars don't exist but are set d <- ggplot(mtcars, aes(mpg, wt)) + diff --git a/tests/testthat/test-facet-.R b/tests/testthat/test-facet-.R index 5084737622..11e86247ca 100644 --- a/tests/testthat/test-facet-.R +++ b/tests/testthat/test-facet-.R @@ -43,8 +43,8 @@ test_that("as_facets_list() coerces quosures objectss", { }) test_that("facets reject aes()", { - expect_error(facet_wrap(aes(foo)), "Please use `vars()` to supply facet variables", fixed = TRUE) - expect_error(facet_grid(aes(foo)), "Please use `vars()` to supply facet variables", fixed = TRUE) + expect_snapshot(facet_wrap(aes(foo)), error = TRUE) + expect_snapshot(facet_grid(aes(foo)), error = TRUE) }) test_that("compact_facets() returns a quosures object with compacted", { @@ -353,9 +353,9 @@ test_that("at least one layer must contain all facet variables in combine_vars() test_that("at least one combination must exist in combine_vars()", { df <- data_frame(letter = character(0)) - expect_error( + expect_snapshot( combine_vars(list(df), vars = vars(letter = letter)), - "Faceting variables must have at least one value" + error = TRUE ) }) @@ -463,9 +463,9 @@ test_that("eval_facet() is tolerant for missing columns (#2963)", { ) # If the expression contains any non-existent variable, it fails - expect_error( + expect_snapshot( eval_facet(quo(no_such_variable * x), data_frame(foo = 1), possible_columns = c("x")), - "object 'no_such_variable' not found" + error = TRUE ) }) diff --git a/tests/testthat/test-facet-labels.R b/tests/testthat/test-facet-labels.R index c8613bc978..b0b014cd2e 100644 --- a/tests/testthat/test-facet-labels.R +++ b/tests/testthat/test-facet-labels.R @@ -86,7 +86,7 @@ test_that("labeller() dispatches labellers", { # facet_wrap() shouldn't get both rows and cols p3 <- p + facet_wrap(~cyl, labeller = labeller( .cols = label_both, .rows = label_both)) - expect_error(ggplotGrob(p3)) + expect_snapshot(ggplotGrob(p3), error = TRUE) # facet_grid() can get both rows and cols p4 <- p + facet_grid(am ~ cyl, labeller = labeller( @@ -98,7 +98,7 @@ test_that("labeller() dispatches labellers", { # margin-wide labeller p5 <- p + facet_wrap(~cyl, labeller = labeller( .rows = label_both, cyl = label_value)) - expect_error(ggplotGrob(p5)) + expect_snapshot(ggplotGrob(p5), error = TRUE) # Variables can be attributed labellers p6 <- p + facet_grid(am + cyl ~ ., labeller = labeller( @@ -135,7 +135,7 @@ test_that("old school labellers still work", { paste0("var = ", as.character(value)) } - expect_warning(p <- + expect_snapshot_warning(p <- ggplot(mtcars, aes(disp, drat)) + geom_point() + facet_grid(~cyl, labeller = my_labeller)) diff --git a/tests/testthat/test-fortify.R b/tests/testthat/test-fortify.R index 3a48c76ba0..e98edad549 100644 --- a/tests/testthat/test-fortify.R +++ b/tests/testthat/test-fortify.R @@ -67,12 +67,12 @@ test_that("fortify.default can handle healthy data-frame-like objects", { # Not even data-frame-like - expect_error(fortify(X)) - expect_error(fortify(array(1:60, 5:3))) + expect_snapshot(fortify(X), error = TRUE) + expect_snapshot(fortify(array(1:60, 5:3)), error = TRUE) # Unhealthy data-frame-like (matrix with no colnames) - expect_error(fortify(cbind(X, Y, Z, deparse.level=0))) + expect_snapshot(fortify(cbind(X, Y, Z, deparse.level=0)), error = TRUE) # Healthy data-frame-like (matrix with colnames) @@ -100,25 +100,27 @@ test_that("fortify.default can handle healthy data-frame-like objects", { # Rejected by fortify.default() because of unhealthy dim() behavior + skip_if(getRversion() <= "4.4.0") + dim.foo <- function(x) stop("oops!") registerS3method("dim", "foo", dim.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) dim.foo <- function(x) c(length(x), 2) registerS3method("dim", "foo", dim.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) dim.foo <- function(x) 5:2 registerS3method("dim", "foo", dim.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) dim.foo <- function(x) c(length(x), NA_integer_) registerS3method("dim", "foo", dim.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) dim.foo <- function(x) c(length(x), -5L) registerS3method("dim", "foo", dim.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) # Repair dim() @@ -129,18 +131,18 @@ test_that("fortify.default can handle healthy data-frame-like objects", { dimnames.foo <- function(x) list() # this breaks colnames() registerS3method("dimnames", "foo", dimnames.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) dimnames.foo <- function(x) list(format(seq_along(x)), toupper) registerS3method("dimnames", "foo", dimnames.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) # Rejected by fortify.default() because behaviors of dim() and colnames() # don't align dimnames.foo <- function(x) list(NULL, c("X1", "X2", "X3")) registerS3method("dimnames", "foo", dimnames.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) # Repair colnames() @@ -151,20 +153,21 @@ test_that("fortify.default can handle healthy data-frame-like objects", { as.data.frame.foo <- function(x, row.names = NULL, ...) stop("oops!") registerS3method("as.data.frame", "foo", as.data.frame.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) as.data.frame.foo <- function(x, row.names = NULL, ...) "whatever" registerS3method("as.data.frame", "foo", as.data.frame.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) as.data.frame.foo <- function(x, row.names = NULL, ...) data.frame() registerS3method("as.data.frame", "foo", as.data.frame.foo) - expect_error(fortify(object)) + + expect_snapshot(fortify(object), error = TRUE) as.data.frame.foo <- function(x, row.names = NULL, ...) { key <- if (is.null(names(x))) rownames(x) else names(x) data.frame(oops=key, value=unname(unclass(x))) } registerS3method("as.data.frame", "foo", as.data.frame.foo) - expect_error(fortify(object)) + expect_snapshot(fortify(object), error = TRUE) }) diff --git a/tests/testthat/test-geom-bar.R b/tests/testthat/test-geom-bar.R index 28d2430c09..4fb34ef4e6 100644 --- a/tests/testthat/test-geom-bar.R +++ b/tests/testthat/test-geom-bar.R @@ -3,10 +3,8 @@ test_that("geom_bar removes bars with parts outside the plot limits", { p <- ggplot(dat, aes(x)) + geom_bar() - expect_warning( # warning created at render stage - ggplotGrob(p + ylim(0, 2.5)), - "Removed 1 row containing missing values or values outside the scale range" - ) + # warning created at render stage + expect_snapshot_warning(ggplotGrob(p + ylim(0, 2.5))) }) test_that("geom_bar works in both directions", { diff --git a/tests/testthat/test-geom-boxplot.R b/tests/testthat/test-geom-boxplot.R index 195a3d9ade..dabcb6ddeb 100644 --- a/tests/testthat/test-geom-boxplot.R +++ b/tests/testthat/test-geom-boxplot.R @@ -42,15 +42,15 @@ test_that("geom_boxplot for continuous x gives warning if more than one x (#992) ggplot_build(ggplot(dat, aes) + geom_boxplot(aes) + extra) } - expect_warning(bplot(aes(x, y)), "Continuous x aesthetic") - expect_warning(bplot(aes(x, y), facet_wrap(~x)), "Continuous x aesthetic") - expect_warning(bplot(aes(Sys.Date() + x, y)), "Continuous x aesthetic") - - expect_warning(bplot(aes(x, group = x, y)), NA) - expect_warning(bplot(aes(1, y)), NA) - expect_warning(bplot(aes(factor(x), y)), NA) - expect_warning(bplot(aes(x == 1, y)), NA) - expect_warning(bplot(aes(as.character(x), y)), NA) + expect_snapshot_warning(bplot(aes(x, y))) + expect_snapshot_warning(bplot(aes(x, y), facet_wrap(~x))) + expect_snapshot_warning(bplot(aes(Sys.Date() + x, y))) + + expect_silent(bplot(aes(x, group = x, y))) + expect_silent(bplot(aes(1, y))) + expect_silent(bplot(aes(factor(x), y))) + expect_silent(bplot(aes(x == 1, y))) + expect_silent(bplot(aes(as.character(x), y))) }) test_that("can use US spelling of colour", { diff --git a/tests/testthat/test-geom-col.R b/tests/testthat/test-geom-col.R index 5849ea0bcc..32840fbd9e 100644 --- a/tests/testthat/test-geom-col.R +++ b/tests/testthat/test-geom-col.R @@ -3,14 +3,9 @@ test_that("geom_col removes columns with parts outside the plot limits", { p <- ggplot(dat, aes(x, x)) + geom_col() - expect_warning( # warning created at render stage - ggplotGrob(p + ylim(0.5, 4)), - "Removed 3 rows containing missing values or values outside the scale range" - ) - expect_warning( # warning created at render stage - ggplotGrob(p + ylim(0, 2.5)), - "Removed 1 row containing missing values or values outside the scale range" - ) + # warnings created at render stage + expect_snapshot_warning(ggplotGrob(p + ylim(0.5, 4))) + expect_snapshot_warning(ggplotGrob(p + ylim(0, 2.5))) }) test_that("geom_col works in both directions", { diff --git a/tests/testthat/test-geom-dotplot.R b/tests/testthat/test-geom-dotplot.R index 648c52f926..f7159bdd80 100644 --- a/tests/testthat/test-geom-dotplot.R +++ b/tests/testthat/test-geom-dotplot.R @@ -230,10 +230,12 @@ test_that("geom_dotplot draws correctly", { dat2 <- dat dat2$x[c(1, 10)] <- NA - expect_warning(expect_doppelganger("2 NA values, dot-density binning, binwidth = .4", + expect_snapshot_warning(expect_doppelganger( + "2 NA values, dot-density binning, binwidth = .4", ggplot(dat2, aes(x)) + geom_dotplot(binwidth = 0.4) )) - expect_warning(expect_doppelganger("2 NA values, bin along y, stack center", + expect_snapshot_warning(expect_doppelganger( + "2 NA values, bin along y, stack center", ggplot(dat2, aes(0, x)) + geom_dotplot(binwidth = 0.4, binaxis = "y", stackdir = "center") )) }) diff --git a/tests/testthat/test-geom-path.R b/tests/testthat/test-geom-path.R index 3255a2f4cb..161508459a 100644 --- a/tests/testthat/test-geom-path.R +++ b/tests/testthat/test-geom-path.R @@ -35,7 +35,7 @@ test_that("stairstep() does not error with too few observations", { test_that("stairstep() exists with error when an invalid `direction` is given", { df <- data_frame(x = 1:3, y = 1:3) - expect_error(stairstep(df, direction="invalid")) + expect_snapshot(stairstep(df, direction = "invalid"), error = TRUE) }) test_that("stairstep() output is correct for direction = 'vh'", { @@ -90,11 +90,8 @@ test_that("geom_path draws correctly", { test_that("NA linetype is dropped with warning", { df <- data_frame(x = 1:2, y = 1:2, z = "a") - expect_warning( - expect_doppelganger( + expect_snapshot_warning(expect_doppelganger( "NA linetype", ggplot(df, aes(x, y)) + geom_path(linetype = NA) - ), - "containing missing values or values outside the scale range" - ) + )) }) diff --git a/tests/testthat/test-geom-rect.R b/tests/testthat/test-geom-rect.R index a0d90899f8..204df65ef2 100644 --- a/tests/testthat/test-geom-rect.R +++ b/tests/testthat/test-geom-rect.R @@ -29,8 +29,5 @@ test_that("geom_rect can derive corners", { expect_equal(full[, corners], test[, corners]) test <- full[, c("x", "y")] - expect_error( - GeomRect$setup_data(test, NULL), - "requires two of the following aesthetics" - ) + expect_snapshot(GeomRect$setup_data(test, NULL), error = TRUE) }) diff --git a/tests/testthat/test-geom-rug.R b/tests/testthat/test-geom-rug.R index 7539a494a6..108d030ca0 100644 --- a/tests/testthat/test-geom-rug.R +++ b/tests/testthat/test-geom-rug.R @@ -50,11 +50,7 @@ test_that( p1 <- ggplot(df2, aes(x = x)) + geom_rug() p2 <- ggplot(df2, aes(x = x)) + geom_rug(na.rm = TRUE) - expect_warning( - ggplotGrob(p1), - paste0("Removed ", n_missing, " rows containing missing values or values outside the scale range") - ) - + expect_snapshot_warning(ggplotGrob(p1)) expect_no_warning(ggplotGrob(p2)) } ) diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index e52a13e917..e0db498a2b 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -93,19 +93,16 @@ test_that("geom_sf() removes rows containing missing aes", { ) p <- ggplot(pts) - expect_warning( - expect_identical(grob_xy_length(p + geom_sf(aes(size = size))), c(1L, 1L)), - "Removed 1 row containing missing values or values outside the scale range" + expect_snapshot_warning( + expect_identical(grob_xy_length(p + geom_sf(aes(size = size))), c(1L, 1L)) ) - expect_warning( - expect_identical(grob_xy_length(p + geom_sf(aes(shape = shape))), c(1L, 1L)), - "Removed 1 row containing missing values or values outside the scale range" + expect_snapshot_warning( + expect_identical(grob_xy_length(p + geom_sf(aes(shape = shape))), c(1L, 1L)) ) # default colour scale maps a colour even to a NA, so identity scale is needed to see if NA is removed - expect_warning( + expect_snapshot_warning( expect_identical(grob_xy_length(p + geom_sf(aes(colour = colour)) + scale_colour_identity()), - c(1L, 1L)), - "Removed 1 row containing missing values or values outside the scale range" + c(1L, 1L)) ) }) @@ -177,7 +174,7 @@ test_that("geom_sf draws correctly", { # Perform minimal tests pts <- sf::st_sf(a = 1:2, geometry = sf::st_sfc(sf::st_point(0:1), sf::st_point(1:2))) plot <- ggplot() + geom_sf(data = pts) - expect_error(regexp = NA, ggplot_build(plot)) + expect_no_error(ggplot_build(plot)) expect_doppelganger("North Carolina county boundaries", ggplot() + geom_sf(data = nc) + coord_sf(datum = 4326) diff --git a/tests/testthat/test-geom-smooth.R b/tests/testthat/test-geom-smooth.R index 42c82108c7..270bf3760f 100644 --- a/tests/testthat/test-geom-smooth.R +++ b/tests/testthat/test-geom-smooth.R @@ -92,7 +92,7 @@ test_that("geom_smooth() works when one group fails", { geom_smooth(method = "loess", formula = y ~ x) suppressWarnings( - expect_warning(ld <- get_layer_data(p), "Failed to fit group 1") + expect_snapshot_warning(ld <- get_layer_data(p)) ) expect_equal(unique(ld$group), 2) expect_gte(nrow(ld), 2) diff --git a/tests/testthat/test-geom-text.R b/tests/testthat/test-geom-text.R index ca5b495968..a6fe3359d9 100644 --- a/tests/testthat/test-geom-text.R +++ b/tests/testthat/test-geom-text.R @@ -12,10 +12,7 @@ test_that("geom_text() drops missing angles", { ) df$angle <- NA - expect_warning( - geom$geom$handle_na(df, geom$geom_params), - "Removed 1 row" - ) + expect_snapshot_warning(geom$geom$handle_na(df, geom$geom_params)) }) test_that("geom_text() accepts mm and pt size units", { @@ -30,9 +27,9 @@ test_that("geom_text() accepts mm and pt size units", { test_that("geom_text() rejects exotic units", { p <- ggplot(data_frame0(x = 1, y = 1, label = "A"), aes(x, y, label = label)) - expect_error( + expect_snapshot( ggplotGrob(p + geom_text(size = 10, size.unit = "npc")), - "must be one of" + error = TRUE ) }) diff --git a/tests/testthat/test-geom-violin.R b/tests/testthat/test-geom-violin.R index 7d73c04e94..a93a534b40 100644 --- a/tests/testthat/test-geom-violin.R +++ b/tests/testthat/test-geom-violin.R @@ -72,7 +72,7 @@ test_that("quantiles do not issue warning", { p <- ggplot(data, aes(x = x, y = y)) + geom_violin(draw_quantiles = 0.5) - expect_warning(plot(p), regexp = NA) + expect_silent(plot(p)) }) diff --git a/tests/testthat/test-ggsave.R b/tests/testthat/test-ggsave.R index a5d7a5283c..4180eadc98 100644 --- a/tests/testthat/test-ggsave.R +++ b/tests/testthat/test-ggsave.R @@ -16,7 +16,10 @@ test_that("ggsave can create directories", { p <- ggplot(mpg, aes(displ, hwy)) + geom_point() - expect_error(ggsave(path, p)) + expect_snapshot( + ggsave(path, p), error = TRUE, + transform = function(x) gsub("directory '.*'\\.$", "directory 'PATH'", x) + ) expect_false(dir.exists(dirname(path))) # 2 messages: 1 for saving and 1 informing about directory creation @@ -77,23 +80,20 @@ test_that("ggsave warns about empty or multiple filenames", { plot <- ggplot(mtcars, aes(disp, mpg)) + geom_point() withr::with_tempfile(c("file1", "file2"), fileext = ".png", { - expect_warning( - suppressMessages(ggsave(c(file1, file2), plot)), - "`filename` must have length 1" + expect_snapshot( + x <- suppressMessages(ggsave(c(file1, file2), plot)), + transform = function(x) gsub(" \\'.*\\.png\\'", "'PATH'", x) ) }) - expect_error( - ggsave(character(), plot), - "`filename` must be a single string" - ) + expect_snapshot(ggsave(character(), plot), error = TRUE) }) test_that("ggsave fails informatively for no-extension filenames", { plot <- ggplot(mtcars, aes(disp, mpg)) + geom_point() - expect_error( - ggsave(tempfile(), plot), - "Can't save to" + expect_snapshot( + ggsave(tempfile(), plot), error = TRUE, + transform = function(x) gsub("to .*\\.$", "to PATH", x) ) }) @@ -112,9 +112,9 @@ test_that("uses 7x7 if no graphics device open", { }) test_that("warned about large plot unless limitsize = FALSE", { - expect_error(plot_dim(c(50, 50)), "exceed 50 inches") + expect_snapshot(plot_dim(c(50, 50)), error = TRUE) expect_equal(plot_dim(c(50, 50), limitsize = FALSE), c(50, 50)) - expect_error(plot_dim(c(15000, 15000), units = "px"), "in pixels).") + expect_snapshot(plot_dim(c(15000, 15000), units = "px"), error = TRUE) }) test_that("scale multiplies height & width", { @@ -126,8 +126,8 @@ test_that("scale multiplies height & width", { test_that("unknown device triggers error", { expect_snapshot_error(plot_dev(1)) - expect_error(plot_dev("xyz"), "Unknown graphics device") - expect_error(plot_dev(NULL, "test.xyz"), "Unknown graphics device") + expect_snapshot(plot_dev("xyz"), error = TRUE) + expect_snapshot(plot_dev(NULL, "test.xyz"), error = TRUE) }) diff --git a/tests/testthat/test-guide-.R b/tests/testthat/test-guide-.R new file mode 100644 index 0000000000..4f66920c3e --- /dev/null +++ b/tests/testthat/test-guide-.R @@ -0,0 +1,49 @@ +skip_on_cran() + +test_that("plotting does not induce state changes in guides", { + + guides <- guides( + x = guide_axis(title = "X-axis"), + colour = guide_colourbar(title = "Colourbar"), + shape = guide_legend(title = "Legend"), + size = guide_bins(title = "Bins") + ) + + p <- ggplot(mpg, aes(displ, hwy, colour = cty, shape = factor(cyl), + size = cyl)) + + geom_point() + + guides + + snapshot <- serialize(as.list(p$guides), NULL) + + grob <- ggplotGrob(p) + + expect_identical(as.list(p$guides), unserialize(snapshot)) +}) + +test_that("adding guides doesn't change plot state", { + + p1 <- ggplot(mtcars, aes(disp, mpg)) + + expect_length(p1$guides$guides, 0) + + p2 <- p1 + guides(y = guide_axis(angle = 45)) + + expect_length(p1$guides$guides, 0) + expect_length(p2$guides$guides, 1) + + p3 <- p2 + guides(y = guide_axis(angle = 90)) + + expect_length(p3$guides$guides, 1) + expect_equal(p3$guides$guides[[1]]$params$angle, 90) + expect_equal(p2$guides$guides[[1]]$params$angle, 45) +}) + +test_that("dots are checked when making guides", { + expect_snapshot_warning( + new_guide(foo = "bar", super = GuideAxis) + ) + expect_snapshot_warning( + guide_legend(foo = "bar") + ) +}) diff --git a/tests/testthat/test-guide-axis.R b/tests/testthat/test-guide-axis.R new file mode 100644 index 0000000000..5e2010d1c5 --- /dev/null +++ b/tests/testthat/test-guide-axis.R @@ -0,0 +1,399 @@ +skip_on_cran() # This test suite is long-running (on cran) and is skipped + +test_that("axis_label_overlap_priority always returns the correct number of elements", { + expect_identical(axis_label_priority(0), numeric(0)) + expect_setequal(axis_label_priority(1), seq_len(1)) + expect_setequal(axis_label_priority(5), seq_len(5)) + expect_setequal(axis_label_priority(10), seq_len(10)) + expect_setequal(axis_label_priority(100), seq_len(100)) +}) + +test_that("a warning is generated when guides are drawn at a location that doesn't make sense", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + scale_y_continuous(guide = guide_axis(position = "top")) + expect_snapshot_warning(ggplot_build(plot)) +}) + +test_that("a warning is not generated when a guide is specified with duplicate breaks", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + scale_y_continuous(breaks = c(20, 20)) + built <- expect_silent(ggplot_build(plot)) + expect_silent(ggplot_gtable(built)) +}) + +test_that("a warning is generated when more than one position guide is drawn at a location", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + guides( + y = guide_axis(position = "left"), + y.sec = guide_axis(position = "left") + ) + built <- expect_silent(ggplot_build(plot)) + + expect_snapshot_warning(ggplot_gtable(built)) +}) + +test_that("a warning is not generated when properly changing the position of a guide_axis()", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + guides( + y = guide_axis(position = "right") + ) + built <- expect_silent(ggplot_build(plot)) + expect_silent(ggplot_gtable(built)) +}) + +test_that("Using non-position guides for position scales results in an informative error", { + p <- ggplot(mpg, aes(cty, hwy)) + + geom_point() + + scale_x_continuous(guide = guide_legend()) + expect_snapshot_warning(ggplot_build(p)) +}) + +test_that("guide_axis_logticks calculates appropriate ticks", { + + test_scale <- function(transform = transform_identity(), limits = c(NA, NA)) { + scale <- scale_x_continuous(transform = transform) + scale$train(scale$transform(limits)) + view_scale_primary(scale) + } + + train_guide <- function(guide, scale) { + params <- guide$params + params$position <- "bottom" + guide$train(params, scale, "x") + } + + guide <- guide_axis_logticks(negative.small = 10) + outcome <- c((1:10)*10, (2:10)*100) + + # Test the classic log10 transformation + scale <- test_scale(transform_log10(), c(10, 1000)) + key <- train_guide(guide, scale)$logkey + + expect_equal(sort(key$x), log10(outcome)) + expect_equal(key$.type, rep(c(1,2,3), c(3, 2, 14))) + + # Test compound transformation + scale <- test_scale(transform_compose(transform_log10(), transform_reverse()), c(10, 1000)) + key <- train_guide(guide, scale)$logkey + + expect_equal(sort(key$x), -log10(rev(outcome))) + + # Test transformation with negatives + scale <- test_scale(transform_pseudo_log(), c(-1000, 1000)) + key <- train_guide(guide, scale)$logkey + + unlog <- sort(transform_pseudo_log()$inverse(key$x)) + expect_equal(unlog, c(-rev(outcome), 0, outcome)) + expect_equal(key$.type, rep(c(1,2,3), c(7, 4, 28))) + + # Test expanded argument + scale <- test_scale(transform_log10(), c(20, 900)) + scale$continuous_range <- c(1, 3) + + guide <- guide_axis_logticks(expanded = TRUE) + key <- train_guide(guide, scale)$logkey + + expect_equal(sort(key$x), log10(outcome)) + + guide <- guide_axis_logticks(expanded = FALSE) + key <- train_guide(guide, scale)$logkey + + expect_equal(sort(key$x), log10(outcome[-c(1, length(outcome))])) + + # Test with prescaled input + guide <- guide_axis_logticks(prescale.base = 2) + scale <- test_scale(limits = log2(c(10, 1000))) + + key <- train_guide(guide, scale)$logkey + expect_equal(sort(key$x), log2(outcome)) + + # Should warn when scale also has transformation + scale <- test_scale(transform_log10(), limits = c(10, 1000)) + expect_snapshot_warning(train_guide(guide, scale)$logkey) +}) + +# Visual tests ------------------------------------------------------------ + +test_that("axis guides are drawn correctly", { + theme_test_axis <- theme_test() + theme(axis.line = element_line(linewidth = 0.5)) + test_draw_axis <- function(n_breaks = 3, + break_positions = seq_len(n_breaks) / (n_breaks + 1), + labels = as.character, + positions = c("top", "right", "bottom", "left"), + theme = theme_test_axis, + ...) { + + break_labels <- labels(seq_along(break_positions)) + + # create the axes + axes <- lapply(positions, function(position) { + draw_axis(break_positions, break_labels, axis_position = position, theme = theme, ...) + }) + axes_grob <- gTree(children = do.call(gList, axes)) + + # arrange them so there's some padding on each side + gt <- gtable( + widths = unit(c(0.05, 0.9, 0.05), "npc"), + heights = unit(c(0.05, 0.9, 0.05), "npc") + ) + gt <- gtable_add_grob(gt, list(axes_grob), 2, 2, clip = "off") + plot(gt) + } + + # basic + expect_doppelganger("axis guides basic", function() test_draw_axis()) + expect_doppelganger("axis guides, zero breaks", function() test_draw_axis(n_breaks = 0)) + + # overlapping text + expect_doppelganger( + "axis guides, check overlap", + function() test_draw_axis(20, labels = function(b) comma(b * 1e9), check.overlap = TRUE) + ) + + # rotated text + expect_doppelganger( + "axis guides, zero rotation", + function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 0) + ) + + expect_doppelganger( + "axis guides, positive rotation", + function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 45) + ) + + expect_doppelganger( + "axis guides, negative rotation", + function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = -45) + ) + + expect_doppelganger( + "axis guides, vertical rotation", + function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 90) + ) + + expect_doppelganger( + "axis guides, vertical negative rotation", + function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = -90) + ) + + # dodged text + expect_doppelganger( + "axis guides, text dodged into rows/cols", + function() test_draw_axis(10, labels = function(b) comma(b * 1e9), n.dodge = 2) + ) +}) + +test_that("axis guides are drawn correctly in plots", { + expect_doppelganger("align facet labels, facets horizontal", + ggplot(mpg, aes(hwy, reorder(model, hwy))) + + geom_point() + + facet_grid(manufacturer ~ ., scales = "free", space = "free") + + theme_test() + + theme(strip.text.y = element_text(angle = 0)) + ) + expect_doppelganger("align facet labels, facets vertical", + ggplot(mpg, aes(reorder(model, hwy), hwy)) + + geom_point() + + facet_grid(. ~ manufacturer, scales = "free", space = "free") + + theme_test() + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) + ) + expect_doppelganger("thick axis lines", + ggplot(mtcars, aes(wt, mpg)) + + geom_point() + + theme_test() + + theme(axis.line = element_line(linewidth = 5, lineend = "square")) + ) +}) + +test_that("axis guides can be customized", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + scale_y_continuous( + sec.axis = dup_axis(guide = guide_axis(n.dodge = 2)), + guide = guide_axis(n.dodge = 2) + ) + + scale_x_discrete(guide = guide_axis(n.dodge = 2)) + + expect_doppelganger("guide_axis() customization", plot) +}) + +test_that("guides can be specified in guides()", { + plot <- ggplot(mpg, aes(class, hwy)) + + geom_point() + + guides( + x = guide_axis(n.dodge = 2), + y = guide_axis(n.dodge = 2), + x.sec = guide_axis(n.dodge = 2), + y.sec = guide_axis(n.dodge = 2) + ) + + expect_doppelganger("guides specified in guides()", plot) +}) + +test_that("guides have the final say in x and y", { + df <- data_frame(x = 1, y = 1) + plot <- ggplot(df, aes(x, y)) + + geom_point() + + guides( + x = guide_none(title = "x (primary)"), + y = guide_none(title = "y (primary)"), + x.sec = guide_none(title = "x (secondary)"), + y.sec = guide_none(title = "y (secondary)") + ) + + expect_doppelganger("position guide titles", plot) +}) + +test_that("Axis titles won't be blown away by coord_*()", { + df <- data_frame(x = 1, y = 1) + plot <- ggplot(df, aes(x, y)) + + geom_point() + + guides( + x = guide_axis(title = "x (primary)"), + y = guide_axis(title = "y (primary)"), + x.sec = guide_axis(title = "x (secondary)"), + y.sec = guide_axis(title = "y (secondary)") + ) + + expect_doppelganger("guide titles with coord_trans()", plot + coord_trans()) + # TODO + # expect_doppelganger("guide titles with coord_polar()", plot + coord_polar()) + # TODO + # expect_doppelganger("guide titles with coord_sf()", plot + coord_sf()) +}) + +test_that("guide_axis() draws minor ticks correctly", { + p <- ggplot(mtcars, aes(wt, disp)) + + geom_point() + + theme(axis.ticks.length = unit(1, "cm"), + axis.ticks.x.bottom = element_line(linetype = 2), + axis.ticks.length.x.top = unit(-0.5, "cm"), + axis.minor.ticks.x.bottom = element_line(colour = "red"), + axis.minor.ticks.length.y.left = unit(-0.5, "cm"), + axis.minor.ticks.length.x.top = unit(-0.5, "cm"), + axis.minor.ticks.length.x.bottom = unit(0.75, "cm"), + axis.minor.ticks.length.y.right = unit(5, "cm")) + + scale_x_continuous(labels = label_math()) + + guides( + # Test for styling and style inheritance + x = guide_axis(minor.ticks = TRUE), + # # Test for opposed lengths + y = guide_axis(minor.ticks = TRUE), + # # Test for flipped lenghts + x.sec = guide_axis(minor.ticks = TRUE), + # # Test that minor.length doesn't influence spacing when no minor ticks are drawn + y.sec = guide_axis(minor.ticks = FALSE) + ) + expect_doppelganger("guides with minor ticks", p) +}) + +test_that("axis guides can be capped", { + p <- ggplot(mtcars, aes(hp, disp)) + + geom_point() + + theme(axis.line = element_line()) + + guides( + x = guide_axis(cap = "both"), + y = guide_axis(cap = "upper"), + y.sec = guide_axis(cap = "lower"), + x.sec = guide_axis(cap = "none") + ) + expect_doppelganger("axis guides with capped ends", p) +}) + +test_that("guide_axis_stack stacks axes", { + + left <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "left") + right <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "right") + bottom <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "bottom") + top <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "top") + + p <- ggplot(mtcars, aes(hp, disp)) + + geom_point() + + theme(axis.line = element_line()) + + guides(x = bottom, x.sec = top, y = left, y.sec = right) + expect_doppelganger("stacked axes", p) + + bottom <- guide_axis_stack("axis_theta", guide_axis_theta(cap = "both")) + top <- guide_axis_stack("axis_theta", guide_axis_theta(cap = "both")) + + p <- ggplot(mtcars, aes(hp, disp)) + + geom_point() + + theme(axis.line = element_line()) + + coord_radial(start = 0.25 * pi, end = 1.75 * pi, inner.radius = 0.5) + + guides(theta = top, theta.sec = bottom, r = left, r.sec = right) + expect_doppelganger("stacked radial axes", p) + +}) + +test_that("logticks look as they should", { + + p <- ggplot(data.frame(x = c(-100, 100), y = c(10, 1000)), aes(x, y)) + + geom_point() + + scale_y_continuous( + transform = transform_compose(transform_log10(), transform_reverse()), + expand = expansion(add = 0.5) + ) + + scale_x_continuous( + breaks = c(-100, -10, -1, 0, 1, 10, 100) + ) + + coord_trans(x = transform_pseudo_log()) + + theme_test() + + theme(axis.line = element_line(colour = "black"), + panel.border = element_blank(), + axis.ticks.length.x.top = unit(-2.75, "pt")) + + guides( + x = guide_axis_logticks( + title = "Pseudo-logticks with 1 as smallest tick", + negative.small = 1 + ), + y = guide_axis_logticks( + title = "Inverted logticks with swapped tick lengths", + long = 0.75, short = 2.25 + ), + x.sec = guide_axis_logticks( + negative.small = 0.1, + title = "Negative length pseudo-logticks with 0.1 as smallest tick" + ), + y.sec = guide_axis_logticks( + expanded = FALSE, cap = "both", + title = "Capped and not-expanded inverted logticks" + ) + ) + expect_doppelganger("logtick axes with customisation", p) +}) + +test_that("guide_axis_theta sets relative angle", { + + p <- ggplot(mtcars, aes(disp, mpg)) + + geom_point() + + scale_x_continuous(breaks = breaks_width(25)) + + coord_radial(inner.radius = 0.5) + + guides( + theta = guide_axis_theta(angle = 0, cap = "none"), + theta.sec = guide_axis_theta(angle = 90, cap = "both") + ) + + theme(axis.line = element_line(colour = "black")) + + expect_doppelganger("guide_axis_theta with angle adapting to theta", p) +}) + +test_that("guide_axis_theta can be used in cartesian coordinates", { + + p <- ggplot(mtcars, aes(disp, mpg)) + + geom_point() + + guides(x = "axis_theta", y = "axis_theta", + x.sec = "axis_theta", y.sec = "axis_theta") + + theme( + axis.line.x.bottom = element_line(colour = "tomato"), + axis.line.x.top = element_line(colour = "limegreen"), + axis.line.y.left = element_line(colour = "dodgerblue"), + axis.line.y.right = element_line(colour = "orchid") + ) + + expect_doppelganger("guide_axis_theta in cartesian coordinates", p) +}) diff --git a/tests/testthat/test-guide-colorbar.R b/tests/testthat/test-guide-colorbar.R new file mode 100644 index 0000000000..9f44adb371 --- /dev/null +++ b/tests/testthat/test-guide-colorbar.R @@ -0,0 +1,100 @@ +skip_on_cran() # This test suite is long-running (on cran) and is skipped + +test_that("colourbar trains without labels", { + g <- guide_colorbar() + sc <- scale_colour_continuous(limits = c(0, 4), labels = NULL) + + out <- g$train(scale = sc) + expect_named(out$key, c("colour", ".value")) +}) + +test_that("Colorbar respects show.legend in layer", { + df <- data_frame(x = 1:3, y = 1) + p <- ggplot(df, aes(x = x, y = y, color = x)) + + geom_point(size = 20, shape = 21, show.legend = FALSE) + expect_length(ggplot_build(p)$plot$guides$guides, 0L) + p <- ggplot(df, aes(x = x, y = y, color = x)) + + geom_point(size = 20, shape = 21, show.legend = TRUE) + expect_length(ggplot_build(p)$plot$guides$guides, 1L) +}) + +test_that("colorsteps and bins checks the breaks format", { + p <- ggplot(mtcars) + + geom_point(aes(mpg, disp, colour = paste("A", gear))) + + guides(colour = "colorsteps") + expect_snapshot_error(suppressWarnings(ggplotGrob(p))) + p <- ggplot(mtcars) + + geom_point(aes(mpg, disp, colour = paste("A", gear))) + + guides(colour = "bins") + expect_snapshot_error(suppressWarnings(ggplotGrob(p))) +}) + +test_that("guide_colourbar merging preserves both aesthetics", { + # See issue 5324 + + scale1 <- scale_colour_viridis_c() + scale1$train(c(0, 2)) + + scale2 <- scale_fill_viridis_c() + scale2$train(c(0, 2)) + + g <- guide_colourbar() + p <- g$params + + p1 <- g$train(p, scale1, "colour") + p2 <- g$train(p, scale2, "fill") + + merged <- g$merge(p1, g, p2) + + expect_true(all(c("colour", "fill") %in% names(merged$params$key))) +}) + + +test_that("guide_colourbar warns about discrete scales", { + + g <- guide_colourbar() + s <- scale_colour_discrete() + s$train(LETTERS[1:3]) + + expect_snapshot_warning(g <- g$train(g$params, s, "colour")) + expect_null(g) + +}) + +test_that("colorbar can be styled", { + df <- data_frame(x = c(0, 1, 2)) + p <- ggplot(df, aes(x, x, color = x)) + geom_point() + + expect_doppelganger( + "white-to-red colorbar, white ticks, no frame", + p + scale_color_gradient(low = 'white', high = 'red') + ) + + expect_doppelganger( + "customized colorbar", + p + scale_color_gradient( + low = 'white', high = 'red', + guide = guide_colorbar( + theme = theme( + legend.frame = element_rect(colour = "green", linewidth = 1.5 / .pt), + legend.ticks = element_line("black", linewidth = 2.5 / .pt), + legend.ticks.length = unit(0.4, "npc") + ), alpha = 0.75 + ) + ) + labs(subtitle = "white-to-red semitransparent colorbar, long thick black ticks, green frame") + ) +}) + +test_that("guides can handle multiple aesthetics for one scale", { + df <- data_frame(x = c(1, 2, 3), + y = c(6, 5, 7)) + + p <- ggplot(df, aes(x, y, color = x, fill = y)) + + geom_point(shape = 21, size = 3, stroke = 2) + + scale_colour_viridis_c( + name = "value", + option = "B", aesthetics = c("colour", "fill") + ) + + expect_doppelganger("combined colour and fill aesthetics", p) +}) diff --git a/tests/testthat/test-guide-legend.R b/tests/testthat/test-guide-legend.R new file mode 100644 index 0000000000..ff79bd7aa7 --- /dev/null +++ b/tests/testthat/test-guide-legend.R @@ -0,0 +1,213 @@ +skip_on_cran() + +test_that("show.legend handles named vectors", { + n_legends <- function(p) { + g <- ggplotGrob(p) + gb <- grep("guide-box", g$layout$name) + n <- vapply(g$grobs[gb], function(x) { + if (is.zero(x)) return(0) + length(x$grobs) - 1 + }, numeric(1)) + sum(n) + } + + df <- data_frame(x = 1:3, y = 20:22) + p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + + geom_point(size = 20) + expect_equal(n_legends(p), 2) + + p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + + geom_point(size = 20, show.legend = c(color = FALSE)) + expect_equal(n_legends(p), 1) + + p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + + geom_point(size = 20, show.legend = c(color = FALSE, shape = FALSE)) + expect_equal(n_legends(p), 0) + + # c.f.https://github.com/tidyverse/ggplot2/issues/3461 + p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + + geom_point(size = 20, show.legend = c(shape = FALSE, color = TRUE)) + expect_equal(n_legends(p), 1) +}) + +test_that("guide merging for guide_legend() works as expected", { + + merge_test_guides <- function(scale1, scale2) { + scale1$guide <- guide_legend(direction = "vertical") + scale2$guide <- guide_legend(direction = "vertical") + scales <- scales_list() + scales$add(scale1) + scales$add(scale2) + scales <- scales$scales + + aesthetics <- lapply(scales, `[[`, "aesthetics") + scales <- rep.int(scales, lengths(aesthetics)) + aesthetics <- unlist(aesthetics, FALSE, FALSE) + + guides <- guides_list(NULL) + guides <- guides$setup(scales, aesthetics) + guides$train(scales, labs()) + guides$merge() + guides$params + } + + different_limits <- merge_test_guides( + scale_colour_discrete(limits = c("a", "b", "c", "d")), + scale_linetype_discrete(limits = c("a", "b", "c")) + ) + expect_length(different_limits, 2) + + same_limits <- merge_test_guides( + scale_colour_discrete(limits = c("a", "b", "c")), + scale_linetype_discrete(limits = c("a", "b", "c")) + ) + expect_length(same_limits, 1) + expect_equal(same_limits[[1]]$key$.label, c("a", "b", "c")) + + same_labels_different_limits <- merge_test_guides( + scale_colour_discrete(limits = c("a", "b", "c")), + scale_linetype_discrete(limits = c("one", "two", "three"), labels = c("a", "b", "c")) + ) + expect_length(same_labels_different_limits, 1) + expect_equal(same_labels_different_limits[[1]]$key$.label, c("a", "b", "c")) + + same_labels_different_scale <- merge_test_guides( + scale_colour_continuous(limits = c(0, 4), breaks = 1:3, labels = c("a", "b", "c")), + scale_linetype_discrete(limits = c("a", "b", "c")) + ) + expect_length(same_labels_different_scale, 1) + expect_equal(same_labels_different_scale[[1]]$key$.label, c("a", "b", "c")) + + repeated_identical_labels <- merge_test_guides( + scale_colour_discrete(limits = c("one", "two", "three"), labels = c("label1", "label1", "label2")), + scale_linetype_discrete(limits = c("1", "2", "3"), labels = c("label1", "label1", "label2")) + ) + expect_length(repeated_identical_labels, 1) + expect_equal(repeated_identical_labels[[1]]$key$.label, c("label1", "label1", "label2")) +}) + +test_that("size = NA doesn't throw rendering errors", { + df <- data.frame( + x = c(1, 2), + group = c("a","b") + ) + p <- ggplot(df, aes(x = x, y = 0, colour = group)) + + geom_point(size = NA, na.rm = TRUE) + + expect_silent(plot(p)) +}) + +test_that("legend reverse argument reverses the key", { + + scale <- scale_colour_discrete() + scale$train(LETTERS[1:4]) + + guides <- guides_list(NULL) + guides <- guides$setup(list(scale), "colour") + + guides$params[[1]]$reverse <- FALSE + guides$train(list(scale), labels = labs()) + fwd <- guides$get_params(1)$key + + guides$params[[1]]$reverse <- TRUE + guides$train(list(scale), labels = labs()) + rev <- guides$get_params(1)$key + + expect_equal(fwd$colour, rev(rev$colour)) +}) + +test_that("legends can be forced to display unrelated geoms", { + + df <- data.frame(x = 1:2) + + p <- ggplot(df, aes(x, x)) + + geom_tile(fill = "red", show.legend = TRUE) + + scale_colour_discrete( + limits = c("A", "B") + ) + + b <- ggplot_build(p) + legend <- b$plot$guides$params[[1]] + + expect_equal( + legend$decor[[1]]$data$fill, + c("red", "red") + ) +}) + + +# Visual tests ------------------------------------------------------------ + +test_that("legend directions are set correctly", { + + p <- ggplot(mtcars, aes(disp, mpg, shape = factor(cyl), colour = drat)) + + geom_point() + + theme_test() + + expect_doppelganger( + "vertical legend direction", + p + theme(legend.direction = "vertical") + ) + + expect_doppelganger( + "horizontal legend direction", + p + theme(legend.direction = "horizontal") + ) +}) + +test_that("guide_legend uses key.spacing correctly", { + p <- ggplot(mtcars, aes(disp, mpg, colour = factor(carb))) + + geom_point() + + guides(colour = guide_legend(ncol = 2)) + + theme_test() + + theme( + legend.key.spacing.x = unit(2, "lines"), + legend.key.spacing.y = unit(1, "lines") + ) + + expect_doppelganger("legend with widely spaced keys", p) +}) + +test_that("absent titles don't take up space", { + + p <- ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + + geom_point() + + theme( + legend.title = element_blank(), + legend.margin = margin(), + legend.position = "top", + legend.justification = "left", + legend.key = element_rect(colour = "black"), + axis.line = element_line(colour = "black") + ) + + expect_doppelganger("left aligned legend key", p) +}) + +test_that("size and linewidth affect key size", { + df <- data_frame(x = c(0, 1, 2)) + p <- ggplot(df, aes(x, x)) + + geom_point(aes(size = x)) + + geom_line(aes(linewidth = 2 - x)) + + scale_size_continuous(range = c(1, 12)) + + scale_linewidth_continuous(range = c(1, 20)) + + expect_doppelganger("enlarged guides", p) +}) + +test_that("legend.byrow works in `guide_legend()`", { + + df <- data.frame(x = 1:6, f = LETTERS[1:6]) + + p <- ggplot(df, aes(x, x, colour = f)) + + geom_point() + + scale_colour_discrete( + guide = guide_legend( + ncol = 3, + theme = theme(legend.byrow = TRUE) + ) + ) + + expect_doppelganger("legend.byrow = TRUE", p) +}) + diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 23df1f75e2..5904676541 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -1,146 +1,5 @@ skip_on_cran() # This test suite is long-running (on cran) and is skipped -test_that("plotting does not induce state changes in guides", { - - guides <- guides( - x = guide_axis(title = "X-axis"), - colour = guide_colourbar(title = "Colourbar"), - shape = guide_legend(title = "Legend"), - size = guide_bins(title = "Bins") - ) - - p <- ggplot(mpg, aes(displ, hwy, colour = cty, shape = factor(cyl), - size = cyl)) + - geom_point() + - guides - - snapshot <- serialize(as.list(p$guides), NULL) - - grob <- ggplotGrob(p) - - expect_identical(as.list(p$guides), unserialize(snapshot)) -}) - -test_that("adding guides doesn't change plot state", { - - p1 <- ggplot(mtcars, aes(disp, mpg)) - - expect_length(p1$guides$guides, 0) - - p2 <- p1 + guides(y = guide_axis(angle = 45)) - - expect_length(p1$guides$guides, 0) - expect_length(p2$guides$guides, 1) - - p3 <- p2 + guides(y = guide_axis(angle = 90)) - - expect_length(p3$guides$guides, 1) - expect_equal(p3$guides$guides[[1]]$params$angle, 90) - expect_equal(p2$guides$guides[[1]]$params$angle, 45) -}) - -test_that("colourbar trains without labels", { - g <- guide_colorbar() - sc <- scale_colour_continuous(limits = c(0, 4), labels = NULL) - - out <- g$train(scale = sc) - expect_named(out$key, c("colour", ".value")) -}) - -test_that("Colorbar respects show.legend in layer", { - df <- data_frame(x = 1:3, y = 1) - p <- ggplot(df, aes(x = x, y = y, color = x)) + - geom_point(size = 20, shape = 21, show.legend = FALSE) - expect_length(ggplot_build(p)$plot$guides$guides, 0L) - p <- ggplot(df, aes(x = x, y = y, color = x)) + - geom_point(size = 20, shape = 21, show.legend = TRUE) - expect_length(ggplot_build(p)$plot$guides$guides, 1L) -}) - -test_that("show.legend handles named vectors", { - n_legends <- function(p) { - g <- ggplotGrob(p) - gb <- grep("guide-box", g$layout$name) - n <- vapply(g$grobs[gb], function(x) { - if (is.zero(x)) return(0) - length(x$grobs) - 1 - }, numeric(1)) - sum(n) - } - - df <- data_frame(x = 1:3, y = 20:22) - p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + - geom_point(size = 20) - expect_equal(n_legends(p), 2) - - p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + - geom_point(size = 20, show.legend = c(color = FALSE)) - expect_equal(n_legends(p), 1) - - p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + - geom_point(size = 20, show.legend = c(color = FALSE, shape = FALSE)) - expect_equal(n_legends(p), 0) - - # c.f.https://github.com/tidyverse/ggplot2/issues/3461 - p <- ggplot(df, aes(x = x, y = y, color = x, shape = factor(y))) + - geom_point(size = 20, show.legend = c(shape = FALSE, color = TRUE)) - expect_equal(n_legends(p), 1) -}) - -test_that("dots are checked when making guides", { - expect_snapshot_warning( - new_guide(foo = "bar", super = GuideAxis) - ) - expect_snapshot_warning( - guide_legend(foo = "bar") - ) -}) - -test_that("axis_label_overlap_priority always returns the correct number of elements", { - expect_identical(axis_label_priority(0), numeric(0)) - expect_setequal(axis_label_priority(1), seq_len(1)) - expect_setequal(axis_label_priority(5), seq_len(5)) - expect_setequal(axis_label_priority(10), seq_len(10)) - expect_setequal(axis_label_priority(100), seq_len(100)) -}) - -test_that("a warning is generated when guides are drawn at a location that doesn't make sense", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - scale_y_continuous(guide = guide_axis(position = "top")) - expect_warning(ggplot_build(plot), "Position guide is perpendicular") -}) - -test_that("a warning is not generated when a guide is specified with duplicate breaks", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - scale_y_continuous(breaks = c(20, 20)) - built <- expect_silent(ggplot_build(plot)) - expect_silent(ggplot_gtable(built)) -}) - -test_that("a warning is generated when more than one position guide is drawn at a location", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - guides( - y = guide_axis(position = "left"), - y.sec = guide_axis(position = "left") - ) - built <- expect_silent(ggplot_build(plot)) - - expect_warning(ggplot_gtable(built), "Discarding guide") -}) - -test_that("a warning is not generated when properly changing the position of a guide_axis()", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - guides( - y = guide_axis(position = "right") - ) - built <- expect_silent(ggplot_build(plot)) - expect_silent(ggplot_gtable(built)) -}) - test_that("guide_none() can be used in non-position scales", { p <- ggplot(mpg, aes(cty, hwy, colour = class)) + geom_point() + @@ -158,80 +17,6 @@ test_that("guide_none() can be used in non-position scales", { expect_length(guides$guides, 0) }) -test_that("Using non-position guides for position scales results in an informative error", { - p <- ggplot(mpg, aes(cty, hwy)) + - geom_point() + - scale_x_continuous(guide = guide_legend()) - expect_snapshot_warning(ggplot_build(p)) -}) - -test_that("guide merging for guide_legend() works as expected", { - - merge_test_guides <- function(scale1, scale2) { - scale1$guide <- guide_legend(direction = "vertical") - scale2$guide <- guide_legend(direction = "vertical") - scales <- scales_list() - scales$add(scale1) - scales$add(scale2) - scales <- scales$scales - - aesthetics <- lapply(scales, `[[`, "aesthetics") - scales <- rep.int(scales, lengths(aesthetics)) - aesthetics <- unlist(aesthetics, FALSE, FALSE) - - guides <- guides_list(NULL) - guides <- guides$setup(scales, aesthetics) - guides$train(scales, labs()) - guides$merge() - guides$params - } - - different_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c", "d")), - scale_linetype_discrete(limits = c("a", "b", "c")) - ) - expect_length(different_limits, 2) - - same_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c")), - scale_linetype_discrete(limits = c("a", "b", "c")) - ) - expect_length(same_limits, 1) - expect_equal(same_limits[[1]]$key$.label, c("a", "b", "c")) - - same_labels_different_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c")), - scale_linetype_discrete(limits = c("one", "two", "three"), labels = c("a", "b", "c")) - ) - expect_length(same_labels_different_limits, 1) - expect_equal(same_labels_different_limits[[1]]$key$.label, c("a", "b", "c")) - - same_labels_different_scale <- merge_test_guides( - scale_colour_continuous(limits = c(0, 4), breaks = 1:3, labels = c("a", "b", "c")), - scale_linetype_discrete(limits = c("a", "b", "c")) - ) - expect_length(same_labels_different_scale, 1) - expect_equal(same_labels_different_scale[[1]]$key$.label, c("a", "b", "c")) - - repeated_identical_labels <- merge_test_guides( - scale_colour_discrete(limits = c("one", "two", "three"), labels = c("label1", "label1", "label2")), - scale_linetype_discrete(limits = c("1", "2", "3"), labels = c("label1", "label1", "label2")) - ) - expect_length(repeated_identical_labels, 1) - expect_equal(repeated_identical_labels[[1]]$key$.label, c("label1", "label1", "label2")) -}) - -test_that("size = NA doesn't throw rendering errors", { - df <- data.frame( - x = c(1, 2), - group = c("a","b") - ) - p <- ggplot(df, aes(x = x, y = 0, colour = group)) + - geom_point(size = NA, na.rm = TRUE) - - expect_silent(plot(p)) -}) - test_that("guide specifications are properly checked", { expect_snapshot_error(validate_guide("test")) expect_snapshot_error(validate_guide(1)) @@ -266,36 +51,6 @@ test_that("guide specifications are properly checked", { expect_snapshot_error(ggplotGrob(p)) }) -test_that("colorsteps and bins checks the breaks format", { - p <- ggplot(mtcars) + - geom_point(aes(mpg, disp, colour = paste("A", gear))) + - guides(colour = "colorsteps") - expect_snapshot_error(suppressWarnings(ggplotGrob(p))) - p <- ggplot(mtcars) + - geom_point(aes(mpg, disp, colour = paste("A", gear))) + - guides(colour = "bins") - expect_snapshot_error(suppressWarnings(ggplotGrob(p))) -}) - -test_that("legend reverse argument reverses the key", { - - scale <- scale_colour_discrete() - scale$train(LETTERS[1:4]) - - guides <- guides_list(NULL) - guides <- guides$setup(list(scale), "colour") - - guides$params[[1]]$reverse <- FALSE - guides$train(list(scale), labels = labs()) - fwd <- guides$get_params(1)$key - - guides$params[[1]]$reverse <- TRUE - guides$train(list(scale), labels = labs()) - rev <- guides$get_params(1)$key - - expect_equal(fwd$colour, rev(rev$colour)) -}) - test_that("guide_coloursteps and guide_bins return ordered breaks", { scale <- scale_colour_viridis_c(breaks = c(2, 3, 1)) scale$train(c(0, 4)) @@ -334,27 +89,6 @@ test_that("guide_coloursteps can parse (un)even steps from discrete scales", { expect_equal(decor$max - decor$min, c(0.3, 0.2, 0.5)) }) - -test_that("guide_colourbar merging preserves both aesthetics", { - # See issue 5324 - - scale1 <- scale_colour_viridis_c() - scale1$train(c(0, 2)) - - scale2 <- scale_fill_viridis_c() - scale2$train(c(0, 2)) - - g <- guide_colourbar() - p <- g$params - - p1 <- g$train(p, scale1, "colour") - p2 <- g$train(p, scale2, "fill") - - merged <- g$merge(p1, g, p2) - - expect_true(all(c("colour", "fill") %in% names(merged$params$key))) -}) - test_that("get_guide_data retrieves keys appropriately", { p <- ggplot(mtcars, aes(mpg, disp, colour = drat, size = drat, fill = wt)) + @@ -381,8 +115,8 @@ test_that("get_guide_data retrieves keys appropriately", { # Non-existent panels expect_null(get_guide_data(b, "x", panel = 4)) - expect_error(get_guide_data(b, 1), "must be a single string") - expect_error(get_guide_data(b, "x", panel = "a"), "must be a whole number") + expect_snapshot(get_guide_data(b, 1), error = TRUE) + expect_snapshot(get_guide_data(b, "x", panel = "a"), error = TRUE) }) test_that("get_guide_data retrieves keys from exotic coords", { @@ -404,111 +138,6 @@ test_that("get_guide_data retrieves keys from exotic coords", { expect_equal(test$theta.labels, c("15", "20", "25", "30")) }) -test_that("guide_colourbar warns about discrete scales", { - - g <- guide_colourbar() - s <- scale_colour_discrete() - s$train(LETTERS[1:3]) - - expect_warning(g <- g$train(g$params, s, "colour"), "needs continuous scales") - expect_null(g) - -}) - -test_that("legend directions are set correctly", { - - p <- ggplot(mtcars, aes(disp, mpg, shape = factor(cyl), colour = drat)) + - geom_point() + - theme_test() - - expect_doppelganger( - "vertical legend direction", - p + theme(legend.direction = "vertical") - ) - - expect_doppelganger( - "horizontal legend direction", - p + theme(legend.direction = "horizontal") - ) -}) - -test_that("guide_axis_logticks calculates appropriate ticks", { - - test_scale <- function(transform = transform_identity(), limits = c(NA, NA)) { - scale <- scale_x_continuous(transform = transform) - scale$train(scale$transform(limits)) - view_scale_primary(scale) - } - - train_guide <- function(guide, scale) { - params <- guide$params - params$position <- "bottom" - guide$train(params, scale, "x") - } - - guide <- guide_axis_logticks(negative.small = 10) - outcome <- c((1:10)*10, (2:10)*100) - - # Test the classic log10 transformation - scale <- test_scale(transform_log10(), c(10, 1000)) - key <- train_guide(guide, scale)$logkey - - expect_equal(sort(key$x), log10(outcome)) - expect_equal(key$.type, rep(c(1,2,3), c(3, 2, 14))) - - # Test compound transformation - scale <- test_scale(transform_compose(transform_log10(), transform_reverse()), c(10, 1000)) - key <- train_guide(guide, scale)$logkey - - expect_equal(sort(key$x), -log10(rev(outcome))) - - # Test transformation with negatives - scale <- test_scale(transform_pseudo_log(), c(-1000, 1000)) - key <- train_guide(guide, scale)$logkey - - unlog <- sort(transform_pseudo_log()$inverse(key$x)) - expect_equal(unlog, c(-rev(outcome), 0, outcome)) - expect_equal(key$.type, rep(c(1,2,3), c(7, 4, 28))) - - # Test expanded argument - scale <- test_scale(transform_log10(), c(20, 900)) - scale$continuous_range <- c(1, 3) - - guide <- guide_axis_logticks(expanded = TRUE) - key <- train_guide(guide, scale)$logkey - - expect_equal(sort(key$x), log10(outcome)) - - guide <- guide_axis_logticks(expanded = FALSE) - key <- train_guide(guide, scale)$logkey - - expect_equal(sort(key$x), log10(outcome[-c(1, length(outcome))])) - - # Test with prescaled input - guide <- guide_axis_logticks(prescale.base = 2) - scale <- test_scale(limits = log2(c(10, 1000))) - - key <- train_guide(guide, scale)$logkey - expect_equal(sort(key$x), log2(outcome)) - - # Should warn when scale also has transformation - scale <- test_scale(transform_log10(), limits = c(10, 1000)) - expect_snapshot_warning(train_guide(guide, scale)$logkey) -}) - -test_that("guide_legend uses key.spacing correctly", { - p <- ggplot(mtcars, aes(disp, mpg, colour = factor(carb))) + - geom_point() + - guides(colour = guide_legend(ncol = 2)) + - theme_test() + - theme( - legend.key.spacing.x = unit(2, "lines"), - legend.key.spacing.y = unit(1, "lines") - ) - - expect_doppelganger("legend with widely spaced keys", p) -}) - test_that("empty guides are dropped", { df <- data.frame(x = 1:2) @@ -561,292 +190,8 @@ test_that("bins can be parsed by guides for all scale types", { ) }) -test_that("legends can be forced to display unrelated geoms", { - - df <- data.frame(x = 1:2) - - p <- ggplot(df, aes(x, x)) + - geom_tile(fill = "red", show.legend = TRUE) + - scale_colour_discrete( - limits = c("A", "B") - ) - - b <- ggplot_build(p) - legend <- b$plot$guides$params[[1]] - - expect_equal( - legend$decor[[1]]$data$fill, - c("red", "red") - ) -}) - # Visual tests ------------------------------------------------------------ -test_that("axis guides are drawn correctly", { - theme_test_axis <- theme_test() + theme(axis.line = element_line(linewidth = 0.5)) - test_draw_axis <- function(n_breaks = 3, - break_positions = seq_len(n_breaks) / (n_breaks + 1), - labels = as.character, - positions = c("top", "right", "bottom", "left"), - theme = theme_test_axis, - ...) { - - break_labels <- labels(seq_along(break_positions)) - - # create the axes - axes <- lapply(positions, function(position) { - draw_axis(break_positions, break_labels, axis_position = position, theme = theme, ...) - }) - axes_grob <- gTree(children = do.call(gList, axes)) - - # arrange them so there's some padding on each side - gt <- gtable( - widths = unit(c(0.05, 0.9, 0.05), "npc"), - heights = unit(c(0.05, 0.9, 0.05), "npc") - ) - gt <- gtable_add_grob(gt, list(axes_grob), 2, 2, clip = "off") - plot(gt) - } - - # basic - expect_doppelganger("axis guides basic", function() test_draw_axis()) - expect_doppelganger("axis guides, zero breaks", function() test_draw_axis(n_breaks = 0)) - - # overlapping text - expect_doppelganger( - "axis guides, check overlap", - function() test_draw_axis(20, labels = function(b) comma(b * 1e9), check.overlap = TRUE) - ) - - # rotated text - expect_doppelganger( - "axis guides, zero rotation", - function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 0) - ) - - expect_doppelganger( - "axis guides, positive rotation", - function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 45) - ) - - expect_doppelganger( - "axis guides, negative rotation", - function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = -45) - ) - - expect_doppelganger( - "axis guides, vertical rotation", - function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = 90) - ) - - expect_doppelganger( - "axis guides, vertical negative rotation", - function() test_draw_axis(10, labels = function(b) comma(b * 1e3), angle = -90) - ) - - # dodged text - expect_doppelganger( - "axis guides, text dodged into rows/cols", - function() test_draw_axis(10, labels = function(b) comma(b * 1e9), n.dodge = 2) - ) -}) - -test_that("axis guides are drawn correctly in plots", { - expect_doppelganger("align facet labels, facets horizontal", - ggplot(mpg, aes(hwy, reorder(model, hwy))) + - geom_point() + - facet_grid(manufacturer ~ ., scales = "free", space = "free") + - theme_test() + - theme(strip.text.y = element_text(angle = 0)) - ) - expect_doppelganger("align facet labels, facets vertical", - ggplot(mpg, aes(reorder(model, hwy), hwy)) + - geom_point() + - facet_grid(. ~ manufacturer, scales = "free", space = "free") + - theme_test() + - theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) - ) - expect_doppelganger("thick axis lines", - ggplot(mtcars, aes(wt, mpg)) + - geom_point() + - theme_test() + - theme(axis.line = element_line(linewidth = 5, lineend = "square")) - ) -}) - -test_that("axis guides can be customized", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - scale_y_continuous( - sec.axis = dup_axis(guide = guide_axis(n.dodge = 2)), - guide = guide_axis(n.dodge = 2) - ) + - scale_x_discrete(guide = guide_axis(n.dodge = 2)) - - expect_doppelganger("guide_axis() customization", plot) -}) - -test_that("guides can be specified in guides()", { - plot <- ggplot(mpg, aes(class, hwy)) + - geom_point() + - guides( - x = guide_axis(n.dodge = 2), - y = guide_axis(n.dodge = 2), - x.sec = guide_axis(n.dodge = 2), - y.sec = guide_axis(n.dodge = 2) - ) - - expect_doppelganger("guides specified in guides()", plot) -}) - -test_that("guides have the final say in x and y", { - df <- data_frame(x = 1, y = 1) - plot <- ggplot(df, aes(x, y)) + - geom_point() + - guides( - x = guide_none(title = "x (primary)"), - y = guide_none(title = "y (primary)"), - x.sec = guide_none(title = "x (secondary)"), - y.sec = guide_none(title = "y (secondary)") - ) - - expect_doppelganger("position guide titles", plot) -}) - -test_that("Axis titles won't be blown away by coord_*()", { - df <- data_frame(x = 1, y = 1) - plot <- ggplot(df, aes(x, y)) + - geom_point() + - guides( - x = guide_axis(title = "x (primary)"), - y = guide_axis(title = "y (primary)"), - x.sec = guide_axis(title = "x (secondary)"), - y.sec = guide_axis(title = "y (secondary)") - ) - - expect_doppelganger("guide titles with coord_trans()", plot + coord_trans()) - # TODO - # expect_doppelganger("guide titles with coord_polar()", plot + coord_polar()) - # TODO - # expect_doppelganger("guide titles with coord_sf()", plot + coord_sf()) -}) - -test_that("guide_axis() draws minor ticks correctly", { - p <- ggplot(mtcars, aes(wt, disp)) + - geom_point() + - theme(axis.ticks.length = unit(1, "cm"), - axis.ticks.x.bottom = element_line(linetype = 2), - axis.ticks.length.x.top = unit(-0.5, "cm"), - axis.minor.ticks.x.bottom = element_line(colour = "red"), - axis.minor.ticks.length.y.left = unit(-0.5, "cm"), - axis.minor.ticks.length.x.top = unit(-0.5, "cm"), - axis.minor.ticks.length.x.bottom = unit(0.75, "cm"), - axis.minor.ticks.length.y.right = unit(5, "cm")) + - scale_x_continuous(labels = label_math()) + - guides( - # Test for styling and style inheritance - x = guide_axis(minor.ticks = TRUE), - # # Test for opposed lengths - y = guide_axis(minor.ticks = TRUE), - # # Test for flipped lenghts - x.sec = guide_axis(minor.ticks = TRUE), - # # Test that minor.length doesn't influence spacing when no minor ticks are drawn - y.sec = guide_axis(minor.ticks = FALSE) - ) - expect_doppelganger("guides with minor ticks", p) -}) - -test_that("absent titles don't take up space", { - - p <- ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + - geom_point() + - theme( - legend.title = element_blank(), - legend.margin = margin(), - legend.position = "top", - legend.justification = "left", - legend.key = element_rect(colour = "black"), - axis.line = element_line(colour = "black") - ) - - expect_doppelganger("left aligned legend key", p) -}) - -test_that("axis guides can be capped", { - p <- ggplot(mtcars, aes(hp, disp)) + - geom_point() + - theme(axis.line = element_line()) + - guides( - x = guide_axis(cap = "both"), - y = guide_axis(cap = "upper"), - y.sec = guide_axis(cap = "lower"), - x.sec = guide_axis(cap = "none") - ) - expect_doppelganger("axis guides with capped ends", p) -}) - -test_that("guide_axis_stack stacks axes", { - - left <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "left") - right <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "right") - bottom <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "bottom") - top <- guide_axis_stack("axis", guide_axis(cap = "both"), title = "top") - - p <- ggplot(mtcars, aes(hp, disp)) + - geom_point() + - theme(axis.line = element_line()) + - guides(x = bottom, x.sec = top, y = left, y.sec = right) - expect_doppelganger("stacked axes", p) - - bottom <- guide_axis_stack("axis_theta", guide_axis_theta(cap = "both")) - top <- guide_axis_stack("axis_theta", guide_axis_theta(cap = "both")) - - p <- ggplot(mtcars, aes(hp, disp)) + - geom_point() + - theme(axis.line = element_line()) + - coord_radial(start = 0.25 * pi, end = 1.75 * pi, inner.radius = 0.5) + - guides(theta = top, theta.sec = bottom, r = left, r.sec = right) - expect_doppelganger("stacked radial axes", p) - -}) - -test_that("logticks look as they should", { - - p <- ggplot(data.frame(x = c(-100, 100), y = c(10, 1000)), aes(x, y)) + - geom_point() + - scale_y_continuous( - transform = transform_compose(transform_log10(), transform_reverse()), - expand = expansion(add = 0.5) - ) + - scale_x_continuous( - breaks = c(-100, -10, -1, 0, 1, 10, 100) - ) + - coord_trans(x = transform_pseudo_log()) + - theme_test() + - theme(axis.line = element_line(colour = "black"), - panel.border = element_blank(), - axis.ticks.length.x.top = unit(-2.75, "pt")) + - guides( - x = guide_axis_logticks( - title = "Pseudo-logticks with 1 as smallest tick", - negative.small = 1 - ), - y = guide_axis_logticks( - title = "Inverted logticks with swapped tick lengths", - long = 0.75, short = 2.25 - ), - x.sec = guide_axis_logticks( - negative.small = 0.1, - title = "Negative length pseudo-logticks with 0.1 as smallest tick" - ), - y.sec = guide_axis_logticks( - expanded = FALSE, cap = "both", - title = "Capped and not-expanded inverted logticks" - ) - ) - expect_doppelganger("logtick axes with customisation", p) -}) - test_that("guides are positioned correctly", { df <- data_frame(x = 1, y = 1, z = factor("a")) @@ -1033,53 +378,6 @@ test_that("guides title and text are positioned correctly", { expect_doppelganger("legends with all title justifications", p) }) -test_that("size and linewidth affect key size", { - df <- data_frame(x = c(0, 1, 2)) - p <- ggplot(df, aes(x, x)) + - geom_point(aes(size = x)) + - geom_line(aes(linewidth = 2 - x)) + - scale_size_continuous(range = c(1, 12)) + - scale_linewidth_continuous(range = c(1, 20)) - - expect_doppelganger("enlarged guides", p) -}) - -test_that("colorbar can be styled", { - df <- data_frame(x = c(0, 1, 2)) - p <- ggplot(df, aes(x, x, color = x)) + geom_point() - - expect_doppelganger("white-to-red colorbar, white ticks, no frame", - p + scale_color_gradient(low = 'white', high = 'red') - ) - - expect_doppelganger("customized colorbar", - p + scale_color_gradient( - low = 'white', high = 'red', - guide = guide_colorbar( - theme = theme( - legend.frame = element_rect(colour = "green", linewidth = 1.5 / .pt), - legend.ticks = element_line("black", linewidth = 2.5 / .pt), - legend.ticks.length = unit(0.4, "npc") - ), alpha = 0.75 - ) - ) + labs(subtitle = "white-to-red semitransparent colorbar, long thick black ticks, green frame") - ) -}) - -test_that("guides can handle multiple aesthetics for one scale", { - df <- data_frame(x = c(1, 2, 3), - y = c(6, 5, 7)) - - p <- ggplot(df, aes(x, y, color = x, fill = y)) + - geom_point(shape = 21, size = 3, stroke = 2) + - scale_colour_viridis_c( - name = "value", - option = "B", aesthetics = c("colour", "fill") - ) - - expect_doppelganger("one combined colorbar for colour and fill aesthetics", p) -}) - test_that("bin guide can be styled correctly", { df <- data_frame(x = c(1, 2, 3), y = c(6, 5, 7)) @@ -1184,79 +482,25 @@ test_that("binning scales understand the different combinations of limits, break expect_snapshot_warning(ggplotGrob(p + scale_color_binned(labels = 1:4, show.limits = TRUE))) }) -test_that("guide_axis_theta sets relative angle", { - - p <- ggplot(mtcars, aes(disp, mpg)) + - geom_point() + - scale_x_continuous(breaks = breaks_width(25)) + - coord_radial(inner.radius = 0.5) + - guides( - theta = guide_axis_theta(angle = 0, cap = "none"), - theta.sec = guide_axis_theta(angle = 90, cap = "both") - ) + - theme(axis.line = element_line(colour = "black")) - - expect_doppelganger("guide_axis_theta with angle adapting to theta", p) -}) - -test_that("guide_axis_theta can be used in cartesian coordinates", { - - p <- ggplot(mtcars, aes(disp, mpg)) + - geom_point() + - guides(x = "axis_theta", y = "axis_theta", - x.sec = "axis_theta", y.sec = "axis_theta") + - theme( - axis.line.x.bottom = element_line(colour = "tomato"), - axis.line.x.top = element_line(colour = "limegreen"), - axis.line.y.left = element_line(colour = "dodgerblue"), - axis.line.y.right = element_line(colour = "orchid") - ) - - expect_doppelganger("guide_axis_theta in cartesian coordinates", p) -}) - test_that("a warning is generated when guides( = FALSE) is specified", { df <- data_frame(x = c(1, 2, 4), y = c(6, 5, 7)) # warn on guide( = FALSE) - expect_warning(g <- guides(colour = FALSE), "The `` argument of `guides()` cannot be `FALSE`. Use \"none\" instead as of ggplot2 3.3.4.", fixed = TRUE) + lifecycle::expect_deprecated(g <- guides(colour = FALSE)) expect_equal(g$guides[["colour"]], "none") # warn on scale_*(guide = FALSE) p <- ggplot(df, aes(x, y, colour = x)) + scale_colour_continuous(guide = FALSE) - expect_snapshot_warning(ggplot_build(p)) + lifecycle::expect_deprecated(ggplot_build(p)) }) test_that("guides() warns if unnamed guides are provided", { - expect_warning( - guides("axis"), - "All guides are unnamed." - ) - expect_warning( - guides(x = "axis", "axis"), - "The 2nd guide is unnamed" - ) + expect_snapshot_warning(guides("axis")) + expect_snapshot_warning(guides(x = "axis", "axis")) expect_null(guides()) }) -test_that("legend.byrow works in `guide_legend()`", { - - df <- data.frame(x = 1:6, f = LETTERS[1:6]) - - p <- ggplot(df, aes(x, x, colour = f)) + - geom_point() + - scale_colour_discrete( - guide = guide_legend( - ncol = 3, - theme = theme(legend.byrow = TRUE) - ) - ) - - expect_doppelganger("legend.byrow = TRUE", p) - -}) - test_that("old S3 guides can be implemented", { my_env <- env() diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index 6a26578c0b..b8b002a3db 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -116,13 +116,13 @@ test_that("plot.tag.position rejects invalid input", { expect_snapshot_error( ggplotGrob(p + theme(plot.tag.position = "foobar")) ) - expect_error( + expect_snapshot( ggplotGrob(p + theme(plot.tag.position = c(0, 0.5, 1))), - "must have length 2" + error = TRUE ) - expect_error( + expect_snapshot( ggplotGrob(p + theme(plot.tag.position = c(0, 0), plot.tag.location = "margin")), - "cannot be used with `\"margin\"" + error = TRUE ) }) diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 51f0cd9eee..964211a4ee 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -18,18 +18,15 @@ test_that("aesthetics go in aes_params", { }) test_that("unknown params create warning", { - expect_warning(geom_point(blah = "red"), "unknown parameters") + expect_snapshot_warning(geom_point(blah = "red")) }) test_that("unknown aesthetics create warning", { - expect_warning(geom_point(aes(blah = "red")), "unknown aesthetics") + expect_snapshot_warning(geom_point(aes(blah = "red"))) }) test_that("empty aesthetics create warning", { - expect_warning( - geom_point(fill = NULL, shape = character()), - "Ignoring empty aesthetics" - ) + expect_snapshot_warning(geom_point(fill = NULL, shape = character())) }) test_that("invalid aesthetics throws errors", { @@ -43,7 +40,7 @@ test_that("invalid aesthetics throws errors", { }) test_that("unknown NULL aesthetic doesn't create warning (#1909)", { - expect_warning(geom_point(aes(blah = NULL)), NA) + expect_silent(geom_point(aes(blah = NULL))) }) test_that("column vectors are allowed (#2609)", { @@ -55,13 +52,13 @@ test_that("column vectors are allowed (#2609)", { test_that("missing aesthetics trigger informative error", { df <- data_frame(x = 1:10) - expect_error( + expect_snapshot( ggplot_build(ggplot(df) + geom_line()), - "requires the following missing aesthetics:" + error = TRUE ) - expect_error( + expect_snapshot( ggplot_build(ggplot(df) + geom_col()), - "requires the following missing aesthetics:" + error = TRUE ) }) @@ -154,10 +151,7 @@ test_that("layer names can be resolved", { expect_equal(names(p$layers), c("foo", "bar")) l <- geom_point(name = "foobar") - expect_error( - p + l + l, - "names are duplicated" - ) + expect_snapshot(p + l + l, error = TRUE) }) diff --git a/tests/testthat/test-performance.R b/tests/testthat/test-performance.R index 1c65622b4a..bd737f7c26 100644 --- a/tests/testthat/test-performance.R +++ b/tests/testthat/test-performance.R @@ -12,7 +12,7 @@ testappend <- list( ) test_that("modifyList is masked", { - expect_error(modifyList(testlist, testappend)) + expect_snapshot(modifyList(testlist, testappend), error = TRUE) }) test_that("modify_list retains unreferenced elements", { diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index 9107de1d92..14b79d3cad 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -51,5 +51,5 @@ test_that("position_dodge warns about missing required aesthetics", { mapping = aes(x = NULL) ) - expect_error(ggplot_build(p), "requires the following missing aesthetics") + expect_snapshot(ggplot_build(p), error = TRUE) }) diff --git a/tests/testthat/test-qplot.R b/tests/testthat/test-qplot.R index 58e8fa1e14..74ab153c39 100644 --- a/tests/testthat/test-qplot.R +++ b/tests/testthat/test-qplot.R @@ -46,7 +46,7 @@ test_that("qplot() evaluates layers in package environment", { } lifecycle::expect_deprecated( - expect_error(p <- qplot(1, 1, geom = "line"), NA) + expect_no_error(p <- qplot(1, 1, geom = "line")) ) }) diff --git a/tests/testthat/test-scale-date.R b/tests/testthat/test-scale-date.R index 1183fcd756..33356545af 100644 --- a/tests/testthat/test-scale-date.R +++ b/tests/testthat/test-scale-date.R @@ -72,14 +72,6 @@ test_that("datetime colour scales work", { test_that("date(time) scales throw warnings when input is numeric", { p <- ggplot(data.frame(x = 1, y = 1), aes(x, y)) + geom_point() - expect_warning( - ggplot_build(p + scale_x_date()), - "The value was converted to a object." - ) - - expect_warning( - ggplot_build(p + scale_x_datetime()), - "The value was converted to a object." - ) - + expect_snapshot_warning(ggplot_build(p + scale_x_date())) + expect_snapshot_warning(ggplot_build(p + scale_x_datetime())) }) diff --git a/tests/testthat/test-scale-discrete.R b/tests/testthat/test-scale-discrete.R index 9e8eeaf717..50f7b585fe 100644 --- a/tests/testthat/test-scale-discrete.R +++ b/tests/testthat/test-scale-discrete.R @@ -134,12 +134,12 @@ test_that("discrete scale defaults can be set globally", { test_that("Scale is checked in default colour scale", { # Check scale type - expect_error(scale_colour_discrete(type = scale_colour_gradient)) - expect_error(scale_fill_discrete(type = scale_fill_gradient)) + expect_snapshot(scale_colour_discrete(type = scale_colour_gradient), error = TRUE) + expect_snapshot(scale_fill_discrete(type = scale_fill_gradient), error = TRUE) # Check aesthetic - expect_error(scale_colour_discrete(type = scale_fill_hue)) - expect_error(scale_fill_discrete(type = scale_colour_hue)) + expect_snapshot(scale_colour_discrete(type = scale_fill_hue), error = TRUE) + expect_snapshot(scale_fill_discrete(type = scale_colour_hue), error = TRUE) }) test_that("Aesthetics with no continuous interpretation fails when called", { @@ -153,7 +153,7 @@ test_that("mapped_discrete vectors behaves as predicted", { expect_null(mapped_discrete(NULL)) expect_s3_class(mapped_discrete(c(0, 3.5)), "mapped_discrete") expect_s3_class(mapped_discrete(seq_len(4)), "mapped_discrete") - expect_error(mapped_discrete(letters)) + expect_snapshot(mapped_discrete(letters), error = TRUE) x <- mapped_discrete(1:10) expect_s3_class(x[2:4], "mapped_discrete") @@ -192,14 +192,14 @@ test_that("invalid palettes trigger errors", { p <- ggplot(df, aes(x, y)) + geom_point() - expect_error( + expect_snapshot( ggplot_build(p + scale_x_discrete(palette = function(x) LETTERS[1:3])), - "must return a .+ vector\\." + error = TRUE ) - expect_error( + expect_snapshot( ggplot_build(p + scale_x_discrete(palette = function(x) 1:2)), - "must return at least 3 values" + error = TRUE ) }) diff --git a/tests/testthat/test-scale-expansion.R b/tests/testthat/test-scale-expansion.R index 26d25abfdc..378742de8c 100644 --- a/tests/testthat/test-scale-expansion.R +++ b/tests/testthat/test-scale-expansion.R @@ -1,6 +1,6 @@ test_that("expand_scale() produces a deprecation warning", { - expect_warning(expand_scale(), "deprecated") + lifecycle::expect_deprecated(expand_scale()) }) test_that("expansion() checks input", { diff --git a/tests/testthat/test-scale-gradient.R b/tests/testthat/test-scale-gradient.R index 3b3a1944dd..771490f945 100644 --- a/tests/testthat/test-scale-gradient.R +++ b/tests/testthat/test-scale-gradient.R @@ -20,8 +20,7 @@ test_that("midpoints are transformed", { scale$train(scale$transform(c(1, 1000))) ans <- scale$rescale(c(0, 3), c(0.25, 1)) - expect_warning( - scale_colour_gradient2(midpoint = 0, transform = "log10"), - "introduced infinite values" + expect_snapshot_warning( + scale_colour_gradient2(midpoint = 0, transform = "log10") ) }) diff --git a/tests/testthat/test-scale-manual.R b/tests/testthat/test-scale-manual.R index 2ad47425f7..324485952b 100644 --- a/tests/testthat/test-scale-manual.R +++ b/tests/testthat/test-scale-manual.R @@ -54,8 +54,7 @@ test_that("insufficient values raise an error", { df <- data_frame(x = 1, y = 1:3, z = factor(c(1:2, NA), exclude = NULL)) p <- ggplot(df, aes(x, y, colour = z)) + geom_point() - expect_error(ggplot_build(p + scale_colour_manual(values = "black")), - "Insufficient values") + expect_snapshot(ggplot_build(p + scale_colour_manual(values = "black")), error = TRUE) # Should be sufficient ggplot_build(p + scale_colour_manual(values = c("black", "black"))) @@ -122,7 +121,7 @@ test_that("fewer values (#3451)", { # unnamed character vector s2 <- scale_colour_manual(values = c("4", "8"), na.value = NA) s2$train(c("4", "6", "8")) - expect_error(s2$map(c("4", "6", "8")), "Insufficient values") + expect_snapshot(s2$map(c("4", "6", "8")), error = TRUE) }) test_that("limits and breaks (#4619)", { diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index c3a314cacc..4599b0bc03 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -7,10 +7,8 @@ test_that("labels match breaks, even when outside limits", { }) test_that("labels match breaks", { - expect_error(scale_x_discrete(breaks = 1:3, labels = 1:2), - "must have the same length") - expect_error(scale_x_continuous(breaks = 1:3, labels = 1:2), - "must have the same length") + expect_snapshot(scale_x_discrete(breaks = 1:3, labels = 1:2), error = TRUE) + expect_snapshot(scale_x_continuous(breaks = 1:3, labels = 1:2), error = TRUE) }) test_that("labels don't have to match null breaks", { @@ -137,7 +135,7 @@ test_that("discrete scales with no data have no breaks or labels", { }) test_that("passing continuous limits to a discrete scale generates a warning", { - expect_warning(scale_x_discrete(limits = 1:3), "Continuous limits supplied to discrete scale") + expect_snapshot_warning(scale_x_discrete(limits = 1:3)) }) test_that("suppressing breaks, minor_breask, and labels works", { @@ -152,20 +150,38 @@ test_that("suppressing breaks, minor_breask, and labels works", { lims <- as.Date(c("2000/1/1", "2000/2/1")) expect_null(scale_x_date(breaks = NULL, limits = lims)$get_breaks()) # NA is defunct, should throw error - expect_error(scale_x_date(breaks = NA, limits = lims)$get_breaks()) + expect_snapshot( + scale_x_date(breaks = NA, limits = lims)$get_breaks(), + error = TRUE + ) expect_null(scale_x_date(labels = NULL, limits = lims)$get_labels()) - expect_error(scale_x_date(labels = NA, limits = lims)$get_labels()) + expect_snapshot( + scale_x_date(labels = NA, limits = lims)$get_labels(), + error = TRUE + ) expect_null(scale_x_date(minor_breaks = NULL, limits = lims)$get_breaks_minor()) - expect_error(scale_x_date(minor_breaks = NA, limits = lims)$get_breaks_minor()) + expect_snapshot( + scale_x_date(minor_breaks = NA, limits = lims)$get_breaks_minor(), + error = TRUE + ) # date, datetime lims <- as.POSIXct(c("2000/1/1 0:0:0", "2010/1/1 0:0:0")) expect_null(scale_x_datetime(breaks = NULL, limits = lims)$get_breaks()) - expect_error(scale_x_datetime(breaks = NA, limits = lims)$get_breaks()) + expect_snapshot( + scale_x_datetime(breaks = NA, limits = lims)$get_breaks(), + error = TRUE + ) expect_null(scale_x_datetime(labels = NULL, limits = lims)$get_labels()) - expect_error(scale_x_datetime(labels = NA, limits = lims)$get_labels()) + expect_snapshot( + scale_x_datetime(labels = NA, limits = lims)$get_labels(), + error = TRUE + ) expect_null(scale_x_datetime(minor_breaks = NULL, limits = lims)$get_breaks_minor()) - expect_error(scale_x_datetime(minor_breaks = NA, limits = lims)$get_breaks_minor()) + expect_snapshot( + scale_x_datetime(minor_breaks = NA, limits = lims)$get_breaks_minor(), + error = TRUE + ) }) test_that("scale_breaks with explicit NA options (deprecated)", { @@ -174,34 +190,34 @@ test_that("scale_breaks with explicit NA options (deprecated)", { # X sxc <- scale_x_continuous(breaks = NA) sxc$train(1:3) - expect_error(sxc$get_breaks()) - expect_error(sxc$get_breaks_minor()) + expect_snapshot(sxc$get_breaks(), error = TRUE) + expect_snapshot(sxc$get_breaks_minor(), error = TRUE) # Y syc <- scale_y_continuous(breaks = NA) syc$train(1:3) - expect_error(syc$get_breaks()) - expect_error(syc$get_breaks_minor()) + expect_snapshot(syc$get_breaks(), error = TRUE) + expect_snapshot(syc$get_breaks_minor(), error = TRUE) # Alpha sac <- scale_alpha_continuous(breaks = NA) sac$train(1:3) - expect_error(sac$get_breaks()) + expect_snapshot(sac$get_breaks(), error = TRUE) # Size ssc <- scale_size_continuous(breaks = NA) ssc$train(1:3) - expect_error(ssc$get_breaks()) + expect_snapshot(ssc$get_breaks(), error = TRUE) # Fill sfc <- scale_fill_continuous(breaks = NA) sfc$train(1:3) - expect_error(sfc$get_breaks()) + expect_snapshot(sfc$get_breaks(), error = TRUE) # Colour scc <- scale_colour_continuous(breaks = NA) scc$train(1:3) - expect_error(scc$get_breaks()) + expect_snapshot(scc$get_breaks(), error = TRUE) }) test_that("breaks can be specified by names of labels", { diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 0ba2989e39..c44910011e 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -115,10 +115,12 @@ test_that("oob affects position values", { mid_censor <- cdata(base + y_scale(c(3, 7), censor)) handle <- GeomBar$handle_na - expect_warning(low_censor[[1]] <- handle(low_censor[[1]], list(na.rm = FALSE)), - "Removed 1 row containing missing values or values outside the scale range") - expect_warning(mid_censor[[1]] <- handle(mid_censor[[1]], list(na.rm = FALSE)), - "Removed 3 rows containing missing values or values outside the scale range") + expect_snapshot_warning( + low_censor[[1]] <- handle(low_censor[[1]], list(na.rm = FALSE)), + ) + expect_snapshot_warning( + mid_censor[[1]] <- handle(mid_censor[[1]], list(na.rm = FALSE)), + ) low_squish <- cdata(base + y_scale(c(0, 5), squish)) mid_squish <- cdata(base + y_scale(c(3, 7), squish)) @@ -201,7 +203,7 @@ test_that("scales warn when transforms introduces non-finite values", { geom_point(size = 5) + scale_y_log10() - expect_warning(ggplot_build(p), "log-10 transformation introduced infinite values.") + expect_snapshot_warning(ggplot_build(p)) }) test_that("size and alpha scales throw appropriate warnings for factors", { @@ -214,21 +216,18 @@ test_that("size and alpha scales throw appropriate warnings for factors", { p <- ggplot(df, aes(x, y)) # There should be warnings when unordered factors are mapped to size/alpha - expect_warning( - ggplot_build(p + geom_point(aes(size = d))), - "Using size for a discrete variable is not advised." + expect_snapshot_warning( + ggplot_build(p + geom_point(aes(size = d))) ) - expect_warning( - ggplot_build(p + geom_point(aes(alpha = d))), - "Using alpha for a discrete variable is not advised." + expect_snapshot_warning( + ggplot_build(p + geom_point(aes(alpha = d))) ) - expect_warning( - ggplot_build(p + geom_line(aes(linewidth = d, group = 1))), - "Using linewidth for a discrete variable is not advised." + expect_snapshot_warning( + ggplot_build(p + geom_line(aes(linewidth = d, group = 1))) ) # There should be no warnings for ordered factors - expect_warning(ggplot_build(p + geom_point(aes(size = o))), NA) - expect_warning(ggplot_build(p + geom_point(aes(alpha = o))), NA) + expect_no_warning(ggplot_build(p + geom_point(aes(size = o)))) + expect_no_warning(ggplot_build(p + geom_point(aes(alpha = o)))) }) test_that("shape scale throws appropriate warnings for factors", { @@ -241,12 +240,11 @@ test_that("shape scale throws appropriate warnings for factors", { p <- ggplot(df, aes(x, y)) # There should be no warnings when unordered factors are mapped to shape - expect_warning(ggplot_build(p + geom_point(aes(shape = d))), NA) + expect_no_warning(ggplot_build(p + geom_point(aes(shape = d)))) # There should be warnings for ordered factors - expect_warning( - ggplot_build(p + geom_point(aes(shape = o))), - "Using shapes for an ordinal variable is not advised" + expect_snapshot_warning( + ggplot_build(p + geom_point(aes(shape = o))) ) }) diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index 9b55054604..5baedf9223 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -194,7 +194,7 @@ test_that("setting boundary and center", { df <- data_frame(x = c(0, 30)) # Error if both boundary and center are specified - expect_error(comp_bin(df, boundary = 5, center = 0), "one of `boundary` and `center`") + expect_snapshot(comp_bin(df, boundary = 5, center = 0), error = TRUE) res <- comp_bin(df, binwidth = 10, boundary = 0, pad = FALSE) expect_identical(res$count, c(1, 0, 1)) @@ -216,7 +216,7 @@ test_that("weights are added", { }) test_that("bin errors at high bin counts", { - expect_error(bin_breaks_width(c(1, 2e6), 1), "The number of histogram bins") + expect_snapshot(bin_breaks_width(c(1, 2e6), 1), error = TRUE) }) # stat_count -------------------------------------------------------------- diff --git a/tests/testthat/test-stat-contour.R b/tests/testthat/test-stat-contour.R index bab39b7b6d..b603d5072f 100644 --- a/tests/testthat/test-stat-contour.R +++ b/tests/testthat/test-stat-contour.R @@ -3,7 +3,7 @@ test_that("a warning is issued when there is more than one z per x+y", { p <- ggplot(tbl, aes(x, y, z = z)) + geom_contour() # Ignore other warnings than the one stat_contour() issued suppressWarnings( - expect_warning(ggplot_build(p), "Zero contours were generated") + expect_snapshot_warning(ggplot_build(p)) ) }) @@ -14,7 +14,7 @@ test_that("contouring sparse data results in a warning", { # TODO: These multiple warnings should be summarized nicely. Until this gets # fixed, this test ignores all the following errors than the first one. suppressWarnings( - expect_warning(ggplot_build(p), "Zero contours were generated") + expect_snapshot_warning(ggplot_build(p)) ) }) @@ -93,9 +93,8 @@ test_that("stat_contour() removes duplicated coordinates", { layer <- stat_contour() expect_silent(layer$stat$setup_data(df)) - expect_warning( - new <- layer$stat$setup_data(transform(df, group = 1)), - "has duplicated" + expect_snapshot_warning( + new <- layer$stat$setup_data(transform(df, group = 1)) ) expect_equal(new, df[1:4,], ignore_attr = TRUE) }) diff --git a/tests/testthat/test-stat-density.R b/tests/testthat/test-stat-density.R index 0894fc2944..62104feb7a 100644 --- a/tests/testthat/test-stat-density.R +++ b/tests/testthat/test-stat-density.R @@ -80,12 +80,11 @@ test_that("stat_density handles data outside of `bounds`", { cutoff <- mtcars$mpg[1] # Both `x` and `weight` should be filtered out for out of `bounds` points - expect_warning( + expect_snapshot_warning( data_actual <- get_layer_data( ggplot(mtcars, aes(mpg, weight = cyl)) + stat_density(bounds = c(cutoff, Inf)) - ), - "outside of `bounds`" + ) ) mtcars_filtered <- mtcars[mtcars$mpg >= cutoff, ] @@ -120,7 +119,7 @@ test_that("stat_density works in both directions", { }) test_that("compute_density returns useful df and throws warning when <2 values", { - expect_warning(dens <- compute_density(1, NULL, from = 0, to = 0)) + expect_snapshot_warning(dens <- compute_density(1, NULL, from = 0, to = 0)) expect_equal(nrow(dens), 1) expect_named(dens, c("x", "density", "scaled", "ndensity", "count", "wdensity", "n")) diff --git a/tests/testthat/test-stat-ecdf.R b/tests/testthat/test-stat-ecdf.R index ce839bb3c4..1ea0a69a56 100644 --- a/tests/testthat/test-stat-ecdf.R +++ b/tests/testthat/test-stat-ecdf.R @@ -45,22 +45,13 @@ test_that("weighted ecdf computes sensible results", { test_that("weighted ecdf warns about weird weights", { # Should warn when provided with illegal weights - expect_warning( - wecdf(1:10, c(NA, rep(1, 9))), - "does not support non-finite" - ) + expect_snapshot_warning(wecdf(1:10, c(NA, rep(1, 9)))) # Should warn when provided with near-0 weights - expect_warning( - wecdf(1:10, .Machine$double.eps), - "might be unstable" - ) + expect_snapshot_warning(wecdf(1:10, .Machine$double.eps)) # Should error when weights sum to 0 - expect_error( - wecdf(1:10, rep(c(-1, 1), 5)), - "Cannot compute eCDF" - ) + expect_snapshot(wecdf(1:10, rep(c(-1, 1), 5)), error = TRUE) }) # See #5113 and #5112 diff --git a/tests/testthat/test-stat-function.R b/tests/testthat/test-stat-function.R index 483578d97f..f9073086df 100644 --- a/tests/testthat/test-stat-function.R +++ b/tests/testthat/test-stat-function.R @@ -134,7 +134,7 @@ test_that("Warn when drawing multiple copies of the same function", { df <- data_frame(x = 1:3, y = letters[1:3]) p <- ggplot(df, aes(x, color = y)) + stat_function(fun = identity) f <- function() {pdf(NULL); print(p); dev.off()} - expect_warning(f(), "Multiple drawing groups") + expect_snapshot_warning(f()) }) test_that("Line style can be changed via provided data", { diff --git a/tests/testthat/test-stat-ydensity.R b/tests/testthat/test-stat-ydensity.R index 3b70fc7673..d43fbcc0e3 100644 --- a/tests/testthat/test-stat-ydensity.R +++ b/tests/testthat/test-stat-ydensity.R @@ -13,15 +13,13 @@ test_that("`drop = FALSE` preserves groups with 1 observations", { p <- ggplot(df, mapping = aes(x, y, fill = g)) - expect_warning( - ld <- get_layer_data(p + geom_violin(drop = TRUE)), - "Groups with fewer than two datapoints have been dropped" + expect_snapshot_warning( + ld <- get_layer_data(p + geom_violin(drop = TRUE)) ) expect_length(unique(ld$x), 3) - expect_warning( - ld <- get_layer_data(p + geom_violin(drop = FALSE)), - "Cannot compute density for groups with fewer than two datapoints" + expect_snapshot_warning( + ld <- get_layer_data(p + geom_violin(drop = FALSE)) ) expect_length(unique(ld$x), 4) }) diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index 25c30e2fb1..8545b485fd 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -7,13 +7,13 @@ test_that("plot succeeds even if some computation fails", { p2 <- p1 + stat_summary(fun = function(x) stop("Failed computation")) - expect_warning(b2 <- ggplot_build(p2), "Computation failed") + expect_snapshot_warning(b2 <- ggplot_build(p2)) expect_length(b2$data, 2) }) test_that("error message is thrown when aesthetics are missing", { p <- ggplot(mtcars) + stat_sum() - expect_error(ggplot_build(p), "x and y\\.$") + expect_snapshot(ggplot_build(p), error = TRUE) }) test_that("erroneously dropped aesthetics are found and issue a warning", { @@ -29,7 +29,7 @@ test_that("erroneously dropped aesthetics are found and issue a warning", { g = rep(1:2, each = 5) ) p1 <- ggplot(df1, aes(x, fill = g)) + geom_density() - expect_warning(ggplot_build(p1), "aesthetics were dropped") + expect_snapshot_warning(ggplot_build(p1)) # case 2-1) dropped partially @@ -59,10 +59,7 @@ test_that("erroneously dropped aesthetics are found and issue a warning", { p3 <- ggplot(df3, aes(id, colour = colour, fill = fill)) + geom_bar() + scale_fill_continuous(na.value = "#123") - expect_warning( - b3 <- ggplot_build(p3), - "The following aesthetics were dropped during statistical transformation: .*colour.*" - ) + expect_snapshot_warning(b3 <- ggplot_build(p3)) # colour is dropped because group a's colour is not constant (GeomBar$default_aes$colour is NA) expect_true(all(is.na(b3$data[[1]]$colour))) diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 36ad577c65..cf98a1bb3f 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -49,7 +49,7 @@ test_that("modifying theme element properties with + operator works", { t <- theme_grey() + theme() expect_identical(t, theme_grey()) - expect_error(theme_grey() + "asdf") + expect_snapshot(theme_grey() + "asdf", error = TRUE) }) test_that("adding theme object to ggplot object with + operator works", { @@ -115,7 +115,7 @@ test_that("replacing theme elements with %+replace% operator works", { t <- theme_grey() %+replace% theme() expect_identical(t, theme_grey()) - expect_error(theme_grey() + "asdf") + expect_snapshot(theme_grey() + "asdf", error = TRUE) }) test_that("calculating theme element inheritance works", { @@ -368,10 +368,7 @@ test_that("elements can be merged", { merge_element(element_line(colour = "blue"), line_base), element_line(colour = "blue", linewidth = 10) ) - expect_error( - merge_element(text_base, rect_base), - "Only elements of the same class can be merged" - ) + expect_snapshot(merge_element(text_base, rect_base), error = TRUE) }) test_that("theme elements that don't inherit from element can be combined", { diff --git a/tests/testthat/test-utilities-checks.R b/tests/testthat/test-utilities-checks.R index 0619ccc707..6d27c4e85b 100644 --- a/tests/testthat/test-utilities-checks.R +++ b/tests/testthat/test-utilities-checks.R @@ -8,14 +8,14 @@ test_that("check_device checks R versions correctly", { # R 4.0.0 doesn't support any new features with_mocked_bindings( getRversion = function() package_version("4.0.0"), - expect_warning(check_device("gradients"), "R 4.0.0 does not support"), + expect_snapshot_warning(check_device("gradients")), .package = "base" ) # R 4.1.0 doesn't support vectorised patterns with_mocked_bindings( getRversion = function() package_version("4.1.0"), - expect_warning(check_device("gradients"), "R 4.1.0 does not support"), + expect_snapshot_warning(check_device("gradients")), .package = "base" ) @@ -29,7 +29,7 @@ test_that("check_device checks R versions correctly", { # Glyphs are only supported in R 4.3.0 onwards with_mocked_bindings( getRversion = function() package_version("4.2.0"), - expect_warning(check_device("glyphs"), "R 4.2.0 does not support"), + expect_snapshot_warning(check_device("glyphs")), .package = "base" ) @@ -56,13 +56,13 @@ test_that("check_device finds device capabilities", { with_mocked_bindings( dev.capabilities = function() list(clippingPaths = FALSE), - expect_warning(check_device("clippingPaths"), "does not support"), + expect_snapshot_warning(check_device("clippingPaths")), .package = "grDevices" ) with_mocked_bindings( dev.cur = function() c(foobar = 1), - expect_warning(check_device(".test_feature"), "Unable to check"), + expect_snapshot_warning(check_device(".test_feature")), .package = "grDevices" ) @@ -77,7 +77,7 @@ test_that("check_device finds ragg capabilities", { ragg::agg_tiff(tmp) expect_true(check_device("gradients")) - expect_warning(check_device("compositing"), "does not support") + expect_snapshot_warning(check_device("compositing")) dev.off() }) @@ -92,7 +92,7 @@ test_that("check_device finds svglite capabilities", { svglite::svglite(tmp) expect_true(check_device("gradients")) - expect_warning(check_device("compositing"), "does not support") + expect_snapshot_warning(check_device("compositing")) dev.off() }) diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index a602eb22c7..107e22e063 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -106,9 +106,7 @@ test_that("remove_missing checks input", { test_that("characters survive remove_missing", { data <- data_frame0(x = c("A", NA)) - expect_warning( - new <- remove_missing(data, finite = TRUE) - ) + expect_snapshot_warning(new <- remove_missing(data, finite = TRUE)) expect_equal(new, data_frame0(x = "A")) }) @@ -140,20 +138,17 @@ test_that("vec_rbind0 can combined ordered factors", { # However, it was technically challenging to reduce the numbers of warnings # See #5139 for more details - expect_warning( - expect_warning( - expect_warning( + lifecycle::expect_deprecated( + lifecycle::expect_deprecated( + lifecycle::expect_deprecated( { test <- vec_rbind0( data_frame0(a = factor(c("A", "B"), ordered = TRUE)), data_frame0(a = factor(c("B", "C"), ordered = TRUE)) ) - }, - " and ", class = "lifecycle_warning_deprecated" - ), - " and ", class = "lifecycle_warning_deprecated" - ), - " and ", class = "lifecycle_warning_deprecated" + } + ) + ) ) # Should be not , hence the 'exact' diff --git a/vignettes/articles/faq-annotation.Rmd b/vignettes/articles/faq-annotation.Rmd index b92e93e9e1..a5a5c61f3c 100644 --- a/vignettes/articles/faq-annotation.Rmd +++ b/vignettes/articles/faq-annotation.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Annotation" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) library(dplyr) knitr::opts_chunk$set( diff --git a/vignettes/articles/faq-axes.Rmd b/vignettes/articles/faq-axes.Rmd index a6996dbe36..f37195a84f 100644 --- a/vignettes/articles/faq-axes.Rmd +++ b/vignettes/articles/faq-axes.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Axes" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) knitr::opts_chunk$set( fig.dpi = 300, @@ -36,7 +37,8 @@ Set the angle of the text in the `axis.text.x` or `axis.text.y` components of th In the following plot the labels on the x-axis are overlapping. -```{r msleep-order-sleep-total} +```{r} +#| label: msleep-order-sleep-total #| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." @@ -46,7 +48,8 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Rotate axis labels: We can do this by components of the `theme()`, specifically the `axis.text.x` component. Applying some vertical and horizontal justification to the labels centers them at the axis ticks. The `angle` can be set as desired within the 0 to 360 degree range, here we set it to 90 degrees. -```{r msleep-order-sleep-total-rotate} +```{r} +#| label: msleep-order-sleep-total-rotate #| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The x-axis labels are oriented #| vertically and are readable." @@ -57,7 +60,8 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Flip the axes: Use the y-axis for long labels. -```{r msleep-order-sleep-total-flip} +```{r} +#| label: msleep-order-sleep-total-flip #| fig.alt: "A boxplot showing the total amount of sleep on the x-axis for 19 #| taxonomical orders of mammals on the y-axis. The y-axis labels are oriented #| horizontally and are readable." @@ -67,7 +71,8 @@ ggplot(msleep, aes(y = order, x = sleep_total)) + - Dodge axis labels: Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc., and customise the `guide` argument with the `guide_axis()` function. In this case we want to customise the x-axis, and the variable on the x-axis is discrete, so we'll use `scale_x_continuous()`. In the `guide` argument we use the `guide_axis()` and specify how many rows to dodge the labels into with `n.dodge`. This is likely a trial-and-error exercise, depending on the lengths of your labels and the width of your plot. In this case we've settled on 3 rows to render the labels. -```{r msleep-order-sleep-total-dodge} +```{r} +#| label: msleep-order-sleep-total-dodge #| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis are dodged to three levels so that they remain readable." @@ -78,7 +83,8 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Omit overlapping labels: Alternatively, you can set `guide_axis(check.overlap = TRUE)` to omit axis labels that overlap. ggplot2 will prioritize the first, last, and middle labels. Note that this option might be more preferable for axes representing variables that have an inherent ordering that is obvious to the audience of the plot, so that it's trivial to guess what the missing labels are. (This is not the case for the following plot.) -```{r msleep-order-sleep-total-check-overlap} +```{r} +#| label: msleep-order-sleep-total-check-overlap #| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. Several of the x-axis labels #| have been omitted, but the one that remain are readable and don't overlap." @@ -99,7 +105,8 @@ Add a `theme()` layer and set relevant arguments, e.g. `axis.title.x`, `axis.tex Suppose we want to remove the axis labels entirely. -```{r ref.label="msleep-order-sleep-total"} +```{r} +#| ref-label: msleep-order-sleep-total #| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." diff --git a/vignettes/articles/faq-bars.Rmd b/vignettes/articles/faq-bars.Rmd index 3cbacf4d79..daae53ef58 100644 --- a/vignettes/articles/faq-bars.Rmd +++ b/vignettes/articles/faq-bars.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Barplots" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) library(dplyr) library(tidyr) diff --git a/vignettes/articles/faq-customising.Rmd b/vignettes/articles/faq-customising.Rmd index 0112d64627..9b008af042 100644 --- a/vignettes/articles/faq-customising.Rmd +++ b/vignettes/articles/faq-customising.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Customising" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) library(tibble) knitr::opts_chunk$set( @@ -370,7 +371,8 @@ ggplot(mpg, aes(x = hwy, y = cty, color = class)) + If you would like all plots within a session/document to use a particular base size, you can set it with `set_theme()`. Run the following at the beginning of your session or include on top of your R Markdown document. -```{r eval = FALSE} +```{r} +#| eval: false set_theme(theme_gray(base_size = 18)) ``` diff --git a/vignettes/articles/faq-faceting.Rmd b/vignettes/articles/faq-faceting.Rmd index bb7112edbb..d5a6926d83 100644 --- a/vignettes/articles/faq-faceting.Rmd +++ b/vignettes/articles/faq-faceting.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Faceting" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) knitr::opts_chunk$set( fig.dpi = 300, @@ -77,7 +78,8 @@ In `facet_grid()` these values are determined by the number of levels of the var Similarly, you can also use `facet_grid()` to facet by a single categorical variable as well. In the formula notation, you use a `.` to indicate that no faceting should be done along that axis, i.e. `cyl ~ .` facets across the y-axis (within a column) while `. ~ cyl` facets across the x-axis (within a row). -```{r out.width = "50%"} +```{r} +#| out-width: 50% #| fig.alt: #| - "A histogram showing the city miles per gallon distribution. The plot has #| four panels in a 4-row, 1-column layout, showing four numbers of cylinders." @@ -303,7 +305,8 @@ df You can plot `price` versus `time` and facet by `country`, but the resulting plot can be a bit difficult to read due to the shared y-axis label. -```{r warning = FALSE} +```{r} +#| warning: false #| fig.alt: "A timeseries plot showing price over time for two countries, Japan #| and the US, in two panels in a 2-row, 1-column layout. The countries are #| indicated at the top of each panel. The two y-axes have different ranges." diff --git a/vignettes/articles/faq-reordering.Rmd b/vignettes/articles/faq-reordering.Rmd index d820c7a50e..3bbc180d6f 100644 --- a/vignettes/articles/faq-reordering.Rmd +++ b/vignettes/articles/faq-reordering.Rmd @@ -13,7 +13,8 @@ title: "FAQ: Reordering" } ``` -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) library(dplyr) library(tibble) diff --git a/vignettes/extending-ggplot2.Rmd b/vignettes/extending-ggplot2.Rmd index adac6896ea..c10fbcf4c2 100644 --- a/vignettes/extending-ggplot2.Rmd +++ b/vignettes/extending-ggplot2.Rmd @@ -9,7 +9,8 @@ vignette: > %\VignetteEncoding{UTF-8} --- -```{r, include = FALSE} +```{r} +#| include: false knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 7, fig.align = "center") library(ggplot2) ``` @@ -28,7 +29,8 @@ It's strange to say, but this is a case where inventing a new OO system was actu Here's a quick demo of ggproto in action: -```{r ggproto-intro} +```{r} +#| label: ggproto-intro A <- ggproto("A", NULL, x = 1, inc = function(self) { @@ -53,7 +55,8 @@ To create a new geom or stat, you will just create a new ggproto that inherits f We'll start by creating a very simple stat: one that gives the convex hull (the _c_ hull) of a set of points. First we create a new ggproto object that inherits from `Stat`: -```{r chull} +```{r} +#| label: chull StatChull <- ggproto("StatChull", Stat, compute_group = function(data, scales) { data[chull(data$x, data$y), , drop = FALSE] @@ -374,7 +377,8 @@ It's harder to create a new geom than a new stat because you also need to know s It's easiest to start with a simple example. The code below is a simplified version of `geom_point()`: -```{r GeomSimplePoint} +```{r} +#| label: GeomSimplePoint #| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The points are larger than the default." GeomSimplePoint <- ggproto("GeomSimplePoint", Geom, @@ -625,7 +629,8 @@ title | `element_text()` | all text in title elements (plot, axes & lege These set default properties that are inherited by more specific settings. These are most useful for setting an overall "background" colour and overall font settings (e.g. family and size). -```{r axis-line-ex} +```{r} +#| label: axis-line-ex #| fig.alt: #| - "Scatterplot of three observations arranged diagonally. The axis titles 'x' #| and 'y' are coloured in black" @@ -1150,7 +1155,8 @@ guide_key <- function( Our new guide can now be used inside the `guides()` function or as the `guide` argument in a position scale. -```{r key_example} +```{r} +#| label: key_example #| fig.alt: > #| Scatterplot of engine displacement versus highway miles per #| gallon. The x-axis axis ticks are at 2.5, 3.5, 4.5, 5.5 and 6.5. @@ -1174,7 +1180,8 @@ We'll edit the method so that the labels are drawn with a `colour` set in the ke In addition to the `key` and `params` variable we've seen before, we now also have an `elements` variable, which is a list of precomputed theme elements. We can use the `elements$text` element to draw a graphical object (grob) in the style of axis text. Perhaps the most finicky thing about drawing guides is that a lot of settings depend on the guide's `position` parameter. -```{r key_ggproto_edit} +```{r} +#| label: key_ggproto_edit # Same as before GuideKey <- ggproto( "Guide", GuideAxis, @@ -1205,7 +1212,8 @@ GuideKey <- ggproto( Because we are incorporating the `...` argument to `guide_key()` in the key, adding a `colour` column to the key is straightforward. We can check that are guide looks correct in the different positions around the panel. -```{r key_example_2} +```{r} +#| label: key_example_2 #| fig.alt: > #| Scatterplot of engine displacement versus highway miles per #| gallon. There are two x-axes at the bottom and top of the plot. The bottom diff --git a/vignettes/ggplot2-in-packages.Rmd b/vignettes/ggplot2-in-packages.Rmd index 691dac0298..06c6a30eec 100644 --- a/vignettes/ggplot2-in-packages.Rmd +++ b/vignettes/ggplot2-in-packages.Rmd @@ -9,7 +9,8 @@ vignette: > %\VignetteEncoding{UTF-8} --- -```{r, include = FALSE} +```{r} +#| include: false knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.show = "hide") library(ggplot2) ``` @@ -28,7 +29,8 @@ mpg_drv_summary <- function() { } ``` -```{r, include=FALSE} +```{r} +#| include: false # make sure this function runs! mpg_drv_summary() ``` @@ -44,7 +46,8 @@ mpg_drv_summary <- function() { } ``` -```{r, include=FALSE} +```{r} +#| include: false # make sure this function runs! mpg_drv_summary() ``` @@ -100,7 +103,8 @@ col_summary(mpg, "drv", "year") If the column name or expression is supplied by the user, you can also pass it to `aes()` or `vars()` using `{{ col }}`. This tidy eval operator captures the expression supplied by the user and forwards it to another tidy eval-enabled function such as `aes()` or `vars()`. -```{r, eval = (packageVersion("rlang") >= "0.3.4.9003")} +```{r} +#| eval: !expr (packageVersion("rlang") >= "0.3.4.9003") col_summary <- function(df, col, by) { ggplot(df) + geom_bar(aes(y = {{ col }})) + @@ -225,14 +229,16 @@ theme_custom <- function(...) { } ``` -```{r, include=FALSE} +```{r} +#| include: false # make sure this function runs! mpg_drv_summary() + theme_custom() ``` Generally, if you add a method for a ggplot2 generic like `autoplot()`, ggplot2 should be in `Imports`. If for some reason you would like to keep ggplot2 in `Suggests`, it is possible to register your generics only if ggplot2 is installed using `vctrs::s3_register()`. If you do this, you should copy and paste the source of `vctrs::s3_register()` into your own package to avoid adding a [vctrs](https://vctrs.r-lib.org/) dependency. -```{r, eval=FALSE} +```{r} +#| eval: false .onLoad <- function(...) { if (requireNamespace("ggplot2", quietly = TRUE)) { vctrs::s3_register("ggplot2::autoplot", "discrete_distr") diff --git a/vignettes/ggplot2-specs.Rmd b/vignettes/ggplot2-specs.Rmd index 7829f05f6a..79c6f29d01 100644 --- a/vignettes/ggplot2-specs.Rmd +++ b/vignettes/ggplot2-specs.Rmd @@ -9,7 +9,8 @@ vignette: > %\VignetteEncoding{UTF-8} --- -```{r, include = FALSE} +```{r} +#| include: false library(ggplot2) knitr::opts_chunk$set(fig.dpi = 96, collapse = TRUE, comment = "#>") ``` @@ -106,7 +107,9 @@ with this mistake. * The appearance of the line end is controlled by the `lineend` paramter, and can be one of "round", "butt" (the default), or "square". - ```{r, out.width = "30%", fig.show = "hold"} + ```{r} + #| out-width: 30% + #| fig-show: hold #| fig.alt: #| - "A plot showing a line with an angle. A thinner red line is placed over #| a thicker black line. The black line ends where the red line ends." @@ -134,7 +137,9 @@ with this mistake. * The appearance of line joins is controlled by `linejoin` and can be one of "round" (the default), "mitre", or "bevel". - ```{r, out.width = "30%", fig.show = "hold"} + ```{r} + #| out-width: 30% + #| fig-show: hold #| fig.alt: #| - "A plot showing a thin red line on top of a thick black line shaped like #| the letter 'V'. The corner in the black V-shape is rounded." @@ -192,7 +197,10 @@ Shapes take five types of values: * The __name__ of the shape: - ```{r out.width = "90%", fig.asp = 0.4, fig.width = 8} + ```{r} + #| out-width: 90% + #| fig-asp: 0.4 + #| fig-width: 8 #| fig.alt: "An irregular 6-by-7 grid of point symbols annotated by the #| names that can be used to represent the symbols. Broadly, from top to #| bottom, the symbols are circles, squares, diamonds, triangles and diff --git a/vignettes/ggplot2.Rmd b/vignettes/ggplot2.Rmd index 36193b65a4..988bbd8310 100644 --- a/vignettes/ggplot2.Rmd +++ b/vignettes/ggplot2.Rmd @@ -9,7 +9,8 @@ vignette: > %\VignetteEncoding{UTF-8} --- -```{r, include = FALSE} +```{r} +#| include: false knitr::opts_chunk$set( collapse = TRUE, comment = "#>" @@ -22,7 +23,9 @@ This allows you to 'speak' a graph from composable elements, instead of being li More complete information about how to use ggplot2 can be found in the [book](https://ggplot2-book.org/), but here you'll find a brief overview of the plot components and some terse examples to build a plot like this: -```{r cake, echo = FALSE} +```{r} +#| label: cake +#| echo: false #| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and @@ -40,7 +43,9 @@ ggplot(mpg, aes(cty, hwy)) + For structure, we go over the 7 composable parts that come together as a set of instructions on how to draw a chart. -```{r overview_graphic, echo=FALSE} +```{r} +#| label: overview_graphic +#| echo: false #| fig.alt: "A schematic displaying seven overlaying rhombuses indicating the #| different composable parts. From bottom to top, the labels read 'Data', #| 'Mapping', 'Layers', 'Scales', 'Facets', 'Coordinates' and 'Theme'." @@ -81,7 +86,9 @@ The system works best if the data is provided in a [tidy](https://tidyr.tidyvers As the first step in many plots, you would pass the data to the `ggplot()` function, which stores the data to be used later by other parts of the plotting system. For example, if we intend to make a graphic about the `mpg` dataset, we would start as follows: -```{r example_data, fig.show='hide'} +```{r} +#| label: example_data +#| fig-show: hide ggplot(data = mpg) ``` @@ -92,7 +99,9 @@ The [mapping](https://ggplot2-book.org/getting-started.html#aesthetics) of a plo A mapping can be made by using the `aes()` function to make pairs of graphical attributes and parts of the data. If we want the `cty` and `hwy` columns to map to the x- and y-coordinates in the plot, we can do that as follows: -```{r example_mapping, fig.show='hide'} +```{r} +#| label: example_mapping +#| fig-show: hide ggplot(mpg, mapping = aes(x = cty, y = hwy)) ``` @@ -107,7 +116,9 @@ Every layer consists of three important parts: A layer can be constructed using the `geom_*()` and `stat_*()` functions. These functions often determine one of the three parts of a layer, while the other two can still be specified. Here is how we can use two layers to display the `cty` and `hwy` columns of the `mpg` dataset as points and stack a trend line on top. -```{r example_layer, fig.show='hold'} +```{r} +#| label: example_layer +#| fig-show: hold #| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The plot has a blue trendline with a positive slope." ggplot(mpg, aes(cty, hwy)) + @@ -124,7 +135,8 @@ Scales are responsible for updating the limits of a plot, setting the breaks, fo To use scales, one can use one of the scale functions that are patterned as `scale_{aesthetic}_{type}()` functions, where `{aesthetic}` is one of the pairings made in the mapping part of a plot. To map the `class` column in the `mpg` dataset to the viridis colour palette, we can write the following: -```{r example_scales} +```{r} +#| label: example_scales #| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars." ggplot(mpg, aes(cty, hwy, colour = class)) + @@ -140,7 +152,8 @@ It is a powerful tool to quickly split up the data into smaller panels, based on The facets have their own mapping that can be given as a formula. To plot subsets of the `mpg` dataset based on levels of the `drv` and `year` variables, we can use `facet_grid()` as follows: -```{r example_facets} +```{r} +#| label: example_facets #| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars. #| The plot has six panels in a 2-row, 3-column layout, showing the #| combinations of three types of drive train and year of manifacture." @@ -156,7 +169,8 @@ While typically Cartesian coordinates are used, the coordinate system powers the We can also use coordinates to display a plot with a fixed aspect ratio so that one unit has the same length in both the x and y directions. The `coord_fixed()` function sets this ratio automatically. -```{r example_coords} +```{r} +#| label: example_coords #| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The aspect ratio of the plot is such that units on the x-axis #| have the same length as units on the y-axis." @@ -171,7 +185,8 @@ The [theme](https://ggplot2-book.org/themes) system controls almost any visuals To tweak the look of the plot, one can use many of the built-in `theme_*()` functions and/or detail specific aspects with the `theme()` function. The `element_*()` functions control the graphical attributes of theme components. -```{r example_theme} +```{r} +#| label: example_theme #| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars. The #| legend of the colour is displayed on top of the plot. The plot has thick @@ -190,7 +205,8 @@ ggplot(mpg, aes(cty, hwy, colour = class)) + As mentioned at the start, you can layer all of the pieces to build a customized plot of your data, like the one shown at the beginning of this vignette: -```{r outro} +```{r} +#| label: outro #| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and diff --git a/vignettes/profiling.Rmd b/vignettes/profiling.Rmd index a0a77340df..d08f8e5a26 100644 --- a/vignettes/profiling.Rmd +++ b/vignettes/profiling.Rmd @@ -10,7 +10,9 @@ vignette: > %\VignetteEncoding{UTF-8} --- -```{r setup, include = FALSE} +```{r} +#| label: setup +#| include: false knitr::opts_chunk$set( collapse = TRUE, comment = "#>" @@ -33,7 +35,9 @@ profile <- profvis(for (i in seq_len(100)) ggplotGrob(p)) profile ``` -```{r, eval=FALSE, include=FALSE} +```{r} +#| eval: false +#| include: false saveRDS(profile, file.path('profilings', paste0(packageVersion('ggplot2'), '.rds'))) ``` From 2959336f7eb8298f9c696975115a54aec50838a9 Mon Sep 17 00:00:00 2001 From: Jonathan Carroll Date: Wed, 30 Oct 2024 18:39:25 +1030 Subject: [PATCH 145/264] Typo in geom-map.R (#6163) * Typo in geom-map.R * document --- R/geom-map.R | 2 +- man/geom_map.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/geom-map.R b/R/geom-map.R index 7f4b860378..0632ba36ee 100644 --- a/R/geom-map.R +++ b/R/geom-map.R @@ -22,7 +22,7 @@ NULL #' # how `geom_map()` works. It requires two data frames: #' # One contains the coordinates of each polygon (`positions`), and is #' # provided via the `map` argument. The other contains the -#' # other the values associated with each polygon (`values`). An id +#' # values associated with each polygon (`values`). An id #' # variable links the two together. #' #' ids <- factor(c("1.1", "2.1", "1.2", "2.2", "1.3", "2.3")) diff --git a/man/geom_map.Rd b/man/geom_map.Rd index 58e83adad4..55c06b5b26 100644 --- a/man/geom_map.Rd +++ b/man/geom_map.Rd @@ -126,7 +126,7 @@ Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. # how `geom_map()` works. It requires two data frames: # One contains the coordinates of each polygon (`positions`), and is # provided via the `map` argument. The other contains the -# other the values associated with each polygon (`values`). An id +# values associated with each polygon (`values`). An id # variable links the two together. ids <- factor(c("1.1", "2.1", "1.2", "2.2", "1.3", "2.3")) From 3faa53a27465c8770954bf9191f4edc20de9ea96 Mon Sep 17 00:00:00 2001 From: Elio Campitelli Date: Wed, 30 Oct 2024 19:11:06 +1100 Subject: [PATCH 146/264] Checks if svglite is installed when saving to svg. (#6168) Closes #6166 --- NEWS.md | 1 + R/save.R | 5 ++++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 540e662f0c..34750ee04c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -232,6 +232,7 @@ documentation updates. * `annotate()` now warns about `stat` or `position` arguments (@teunbrand, #5151) * `guide_coloursteps(even.steps = FALSE)` now works with discrete data that has been formatted by `cut()` (@teunbrand, #3877). +* `ggsave()` now offers to install svglite if needed (@eliocamp, #6166). # ggplot2 3.5.0 diff --git a/R/save.R b/R/save.R index ffe6945410..b06c567b2e 100644 --- a/R/save.R +++ b/R/save.R @@ -277,7 +277,10 @@ plot_dev <- function(device, filename = NULL, dpi = 300, call = caller_env()) { ps = eps, tex = function(filename, ...) grDevices::pictex(file = filename, ...), pdf = function(filename, ..., version = "1.4") grDevices::pdf(file = filename, ..., version = version), - svg = function(filename, ...) svglite::svglite(file = filename, ...), + svg = function(filename, ...) { + check_installed("svglite", reason = "to save as SVG.") + svglite::svglite(file = filename, ...) + }, # win.metafile() doesn't have `bg` arg so we need to absorb it before passing `...` emf = function(..., bg = NULL) grDevices::win.metafile(...), wmf = function(..., bg = NULL) grDevices::win.metafile(...), From bf75f3029e53a9a377ff777090f781ea35527698 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 30 Oct 2024 10:22:20 +0100 Subject: [PATCH 147/264] Restore `geom_sf()`'s `linetype` aesthetic (#6132) * pass linetype * include linetype in one of the visual tests --- R/geom-sf.R | 3 ++- .../_snaps/geom-sf/north-carolina-county-boundaries.svg | 2 +- tests/testthat/test-geom-sf.R | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/R/geom-sf.R b/R/geom-sf.R index 2e9aee78b8..dfc3926153 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -238,7 +238,8 @@ GeomSf <- ggproto("GeomSf", Geom, linewidth[is_point] <- stroke[is_point] gp <- gpar( - col = colour, fill = fill, fontsize = font_size, lwd = linewidth, + col = colour, fill = fill, fontsize = font_size, + lwd = linewidth, lty = data$linetype, lineend = lineend, linejoin = linejoin, linemitre = linemitre ) diff --git a/tests/testthat/_snaps/geom-sf/north-carolina-county-boundaries.svg b/tests/testthat/_snaps/geom-sf/north-carolina-county-boundaries.svg index 40e2e8c503..ebb2ccaf03 100644 --- a/tests/testthat/_snaps/geom-sf/north-carolina-county-boundaries.svg +++ b/tests/testthat/_snaps/geom-sf/north-carolina-county-boundaries.svg @@ -36,7 +36,7 @@ - + diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index e0db498a2b..ed6914ba61 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -177,7 +177,7 @@ test_that("geom_sf draws correctly", { expect_no_error(ggplot_build(plot)) expect_doppelganger("North Carolina county boundaries", - ggplot() + geom_sf(data = nc) + coord_sf(datum = 4326) + ggplot() + geom_sf(data = nc, linetype = 2) + coord_sf(datum = 4326) ) pts <- sf::st_sf(a = 1:2, geometry = sf::st_sfc(sf::st_point(0:1), sf::st_point(1:2))) From 8a4c25a8cd201d0bb427367cb9a17b6151250f80 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 30 Oct 2024 11:04:46 +0100 Subject: [PATCH 148/264] Check continuous scale limits (#6114) * re-import standalone rlang files * add length checker * add `allow_na` option to `check_object()` * simplify coord limit check * use `check_length()` more often * add `check_continuous_limits()` * add test * fix snapshots * relax coord requirements * TIL: is.vector() is FALSE, whereas is_vector() is TRUE * restore previous error * update snapshots --- R/bin.R | 8 +-- R/coord-.R | 12 +---- R/import-standalone-obj-type.R | 29 ++++++++--- R/import-standalone-types-check.R | 20 +++++++- R/limits.R | 16 ++---- R/plot-build.R | 11 ++-- R/scale-.R | 14 +++++- R/utilities-checks.R | 58 ++++++++++++++++++++++ tests/testthat/_snaps/coord-.md | 4 +- tests/testthat/_snaps/coord-cartesian.md | 4 +- tests/testthat/_snaps/coord-flip.md | 4 +- tests/testthat/_snaps/coord-map.md | 4 +- tests/testthat/_snaps/coord-transform.md | 4 +- tests/testthat/_snaps/coord_sf.md | 4 +- tests/testthat/_snaps/labels.md | 2 +- tests/testthat/_snaps/limits.md | 2 +- tests/testthat/_snaps/qplot.md | 2 +- tests/testthat/_snaps/scale-date.md | 2 +- tests/testthat/_snaps/scales.md | 16 ++++++ tests/testthat/_snaps/stat-bin.md | 4 +- tests/testthat/test-scales-breaks-labels.R | 2 +- tests/testthat/test-scales.R | 5 ++ 22 files changed, 163 insertions(+), 64 deletions(-) diff --git a/R/bin.R b/R/bin.R index a7784d02e5..055721f0e4 100644 --- a/R/bin.R +++ b/R/bin.R @@ -54,9 +54,7 @@ bin_breaks <- function(breaks, closed = c("right", "left")) { bin_breaks_width <- function(x_range, width = NULL, center = NULL, boundary = NULL, closed = c("right", "left")) { - if (length(x_range) != 2) { - cli::cli_abort("{.arg x_range} must have two elements.") - } + check_length(x_range, 2L) # binwidth seems to be the argument name supplied to width. (stat-bin and stat-bindot) check_number_decimal(width, min = 0, allow_infinite = FALSE, arg = "binwidth") @@ -106,9 +104,7 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL, bin_breaks_bins <- function(x_range, bins = 30, center = NULL, boundary = NULL, closed = c("right", "left")) { - if (length(x_range) != 2) { - cli::cli_abort("{.arg x_range} must have two elements.") - } + check_length(x_range, 2L) check_number_whole(bins, min = 1) if (zero_range(x_range)) { diff --git a/R/coord-.R b/R/coord-.R index 6764cf62a3..5e711cf95c 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -281,14 +281,6 @@ check_coord_limits <- function( if (is.null(limits)) { return(invisible(NULL)) } - if (!obj_is_vector(limits) || length(limits) != 2) { - what <- "{.obj_type_friendly {limits}}" - if (is.vector(limits)) { - what <- paste0(what, " of length {length(limits)}") - } - cli::cli_abort( - paste0("{.arg {arg}} must be a vector of length 2, not ", what, "."), - call = call - ) - } + check_object(limits, is_vector, "a vector", arg = arg, call = call) + check_length(limits, 2L, arg = arg, call = call) } diff --git a/R/import-standalone-obj-type.R b/R/import-standalone-obj-type.R index 72cfe37dc2..47268d620d 100644 --- a/R/import-standalone-obj-type.R +++ b/R/import-standalone-obj-type.R @@ -1,17 +1,27 @@ # Standalone file: do not edit by hand -# Source: +# Source: https://github.com/r-lib/rlang/blob/HEAD/R/standalone-obj-type.R +# Generated by: usethis::use_standalone("r-lib/rlang", "obj-type") # ---------------------------------------------------------------------- # # --- # repo: r-lib/rlang # file: standalone-obj-type.R -# last-updated: 2022-10-04 +# last-updated: 2024-02-14 # license: https://unlicense.org # imports: rlang (>= 1.1.0) # --- # # ## Changelog # +# 2024-02-14: +# - `obj_type_friendly()` now works for S7 objects. +# +# 2023-05-01: +# - `obj_type_friendly()` now only displays the first class of S3 objects. +# +# 2023-03-30: +# - `stop_input_type()` now handles `I()` input literally in `arg`. +# # 2022-10-04: # - `obj_type_friendly(value = TRUE)` now shows numeric scalars # literally. @@ -65,7 +75,7 @@ obj_type_friendly <- function(x, value = TRUE) { if (inherits(x, "quosure")) { type <- "quosure" } else { - type <- paste(class(x), collapse = "/") + type <- class(x)[[1L]] } return(sprintf("a <%s> object", type)) } @@ -261,19 +271,19 @@ vec_type_friendly <- function(x, length = FALSE) { #' Return OO type #' @param x Any R object. #' @return One of `"bare"` (for non-OO objects), `"S3"`, `"S4"`, -#' `"R6"`, or `"R7"`. +#' `"R6"`, or `"S7"`. #' @noRd obj_type_oo <- function(x) { if (!is.object(x)) { return("bare") } - class <- inherits(x, c("R6", "R7_object"), which = TRUE) + class <- inherits(x, c("R6", "S7_object"), which = TRUE) if (class[[1]]) { "R6" } else if (class[[2]]) { - "R7" + "S7" } else if (isS4(x)) { "S4" } else { @@ -315,10 +325,15 @@ stop_input_type <- function(x, if (length(what)) { what <- oxford_comma(what) } + if (inherits(arg, "AsIs")) { + format_arg <- identity + } else { + format_arg <- cli$format_arg + } message <- sprintf( "%s must be %s, not %s.", - cli$format_arg(arg), + format_arg(arg), what, obj_type_friendly(x, value = show_value) ) diff --git a/R/import-standalone-types-check.R b/R/import-standalone-types-check.R index 6782d69b10..ef8c5a1d5e 100644 --- a/R/import-standalone-types-check.R +++ b/R/import-standalone-types-check.R @@ -1,5 +1,6 @@ # Standalone file: do not edit by hand -# Source: +# Source: https://github.com/r-lib/rlang/blob/HEAD/R/standalone-types-check.R +# Generated by: usethis::use_standalone("r-lib/rlang", "types-check") # ---------------------------------------------------------------------- # # --- @@ -13,6 +14,9 @@ # # ## Changelog # +# 2024-08-15: +# - `check_character()` gains an `allow_na` argument (@martaalcalde, #1724) +# # 2023-03-13: # - Improved error messages of number checkers (@teunbrand) # - Added `allow_infinite` argument to `check_number_whole()` (@mgirlich). @@ -461,15 +465,28 @@ check_formula <- function(x, # Vectors ----------------------------------------------------------------- +# TODO: Figure out what to do with logical `NA` and `allow_na = TRUE` + check_character <- function(x, ..., + allow_na = TRUE, allow_null = FALSE, arg = caller_arg(x), call = caller_env()) { + if (!missing(x)) { if (is_character(x)) { + if (!allow_na && any(is.na(x))) { + abort( + sprintf("`%s` can't contain NA values.", arg), + arg = arg, + call = call + ) + } + return(invisible(NULL)) } + if (allow_null && is_null(x)) { return(invisible(NULL)) } @@ -479,7 +496,6 @@ check_character <- function(x, x, "a character vector", ..., - allow_na = FALSE, allow_null = allow_null, arg = arg, call = call diff --git a/R/limits.R b/R/limits.R index 2e31220ec8..bca92392a9 100644 --- a/R/limits.R +++ b/R/limits.R @@ -113,9 +113,7 @@ ylim <- function(...) { limits <- function(lims, var, call = caller_env()) UseMethod("limits") #' @export limits.numeric <- function(lims, var, call = caller_env()) { - if (length(lims) != 2) { - cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) - } + check_length(lims, 2L, arg = var, call = call) if (!anyNA(lims) && lims[1] > lims[2]) { trans <- "reverse" } else { @@ -143,23 +141,17 @@ limits.factor <- function(lims, var, call = caller_env()) { } #' @export limits.Date <- function(lims, var, call = caller_env()) { - if (length(lims) != 2) { - cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) - } + check_length(lims, 2L, arg = var, call = call) make_scale("date", var, limits = lims, call = call) } #' @export limits.POSIXct <- function(lims, var, call = caller_env()) { - if (length(lims) != 2) { - cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) - } + check_length(lims, 2L, arg = var, call = call) make_scale("datetime", var, limits = lims, call = call) } #' @export limits.POSIXlt <- function(lims, var, call = caller_env()) { - if (length(lims) != 2) { - cli::cli_abort("{.arg {var}} must be a two-element vector.", call = call) - } + check_length(lims, 2L, arg = var, call = call) make_scale("datetime", var, limits = as.POSIXct(lims), call = call) } diff --git a/R/plot-build.R b/R/plot-build.R index a624469b75..873f79a32c 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -358,13 +358,10 @@ table_add_tag <- function(table, label, theme) { ), call = expr(theme())) } - if (length(position) != 2) { - cli::cli_abort(paste0( - "A {.cls numeric} {.arg plot.tag.position} ", - "theme setting must have length 2." - ), - call = expr(theme())) - } + check_length( + position, 2L, call = expr(theme()), + arg = I("A {.cls numeric} {.arg plot.tag.position}") + ) top <- left <- right <- bottom <- FALSE } else { # Break position into top/left/right/bottom diff --git a/R/scale-.R b/R/scale-.R index bb56743bdb..d7c0f42252 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -128,12 +128,14 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam } transform <- as.transform(transform) + limits <- allow_lambda(limits) + if (!is.null(limits) && !is.function(limits)) { limits <- transform$transform(limits) } + check_continuous_limits(limits, call = call) # Convert formula to function if appropriate - limits <- allow_lambda(limits) breaks <- allow_lambda(breaks) labels <- allow_lambda(labels) rescaler <- allow_lambda(rescaler) @@ -1400,6 +1402,16 @@ check_transformation <- function(x, transformed, name, arg = NULL, call = NULL) cli::cli_warn(msg, call = call) } +check_continuous_limits <- function(limits, ..., + arg = caller_arg(limits), + call = caller_env()) { + if (is.null(limits) || is.function(limits)) { + return(invisible()) + } + check_numeric(limits, arg = arg, call = call, allow_na = TRUE) + check_length(limits, 2L, arg = arg, call = call) +} + trans_support_nbreaks <- function(trans) { "n" %in% names(formals(trans$breaks)) } diff --git a/R/utilities-checks.R b/R/utilities-checks.R index a1ed1b5091..d444e8c3d0 100644 --- a/R/utilities-checks.R +++ b/R/utilities-checks.R @@ -7,6 +7,7 @@ check_object <- function(x, check_fun, what, ..., + allow_na = FALSE, allow_null = FALSE, arg = caller_arg(x), call = caller_env()) { @@ -18,6 +19,9 @@ check_object <- function(x, if (allow_null && is_null(x)) { return(invisible(NULL)) } + if (allow_na && all(is.na(x))) { + return(invisible(NULL)) + } } stop_input_type( @@ -69,6 +73,60 @@ check_inherits <- function(x, ) } +check_length <- function(x, length = integer(), ..., min = 0, max = Inf, + arg = caller_arg(x), call = caller_env()) { + if (missing(x)) { + stop_input_type(x, "a vector", arg = arg, call = call) + } + + n <- length(x) + if (n %in% length) { + return(invisible(NULL)) + } + fmt <- if (inherits(arg, "AsIs")) identity else function(x) sprintf("`%s`", x) + if (length(length) > 0) { + type <- paste0("a vector of length ", oxford_comma(length)) + if (length(length) == 1) { + type <- switch( + sprintf("%d", length), + "0" = "an empty vector", + "1" = "a scalar of length 1", + type + ) + } + msg <- sprintf( + "%s must be %s, not length %d.", + fmt(arg), type, n + ) + cli::cli_abort(msg, call = call, arg = arg) + } + + range <- pmax(range(min, max, na.rm = TRUE), 0) + if (n >= min & n <= max) { + return(invisible(NULL)) + } + if (identical(range[1], range[2])) { + check_length(x, range[1], arg = arg, call = call) + return(invisible(NULL)) + } + + type <- if (range[2] == 1) "scalar" else "vector" + + what <- paste0("a length between ", range[1], " and ", range[2]) + if (identical(range[2], Inf)) { + what <- paste0("at least length ", range[1]) + } + if (identical(range[1], 0)) { + what <- paste0("at most length ", range[2]) + } + + msg <- sprintf( + "`%s` must be a %s with %s, not length %d.", + fmt(arg), type, what, n + ) + cli::cli_abort(msg, call = call, arg = arg) +} + #' Check graphics device capabilities #' #' This function makes an attempt to estimate whether the graphics device is diff --git a/tests/testthat/_snaps/coord-.md b/tests/testthat/_snaps/coord-.md index acf9ad78c6..563c7f475d 100644 --- a/tests/testthat/_snaps/coord-.md +++ b/tests/testthat/_snaps/coord-.md @@ -24,7 +24,7 @@ check_coord_limits(xlim(1, 2)) Condition Error: - ! `xlim(1, 2)` must be a vector of length 2, not a object. + ! `xlim(1, 2)` must be a vector, not a object. --- @@ -32,5 +32,5 @@ check_coord_limits(1:3) Condition Error: - ! `1:3` must be a vector of length 2, not an integer vector of length 3. + ! `1:3` must be a vector of length 2, not length 3. diff --git a/tests/testthat/_snaps/coord-cartesian.md b/tests/testthat/_snaps/coord-cartesian.md index e7ed10569a..5bf397e20c 100644 --- a/tests/testthat/_snaps/coord-cartesian.md +++ b/tests/testthat/_snaps/coord-cartesian.md @@ -1,8 +1,8 @@ # cartesian coords throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector, not a object. --- - `ylim` must be a vector of length 2, not an integer vector of length 3. + `ylim` must be a vector of length 2, not length 3. diff --git a/tests/testthat/_snaps/coord-flip.md b/tests/testthat/_snaps/coord-flip.md index 99806717ba..101fb0908d 100644 --- a/tests/testthat/_snaps/coord-flip.md +++ b/tests/testthat/_snaps/coord-flip.md @@ -1,8 +1,8 @@ # flip coords throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector, not a object. --- - `ylim` must be a vector of length 2, not an integer vector of length 3. + `ylim` must be a vector of length 2, not length 3. diff --git a/tests/testthat/_snaps/coord-map.md b/tests/testthat/_snaps/coord-map.md index 011a6dd41f..e74d005cad 100644 --- a/tests/testthat/_snaps/coord-map.md +++ b/tests/testthat/_snaps/coord-map.md @@ -1,10 +1,10 @@ # coord map throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector, not a object. --- - `ylim` must be a vector of length 2, not an integer vector of length 3. + `ylim` must be a vector of length 2, not length 3. # coord_map throws informative warning about guides diff --git a/tests/testthat/_snaps/coord-transform.md b/tests/testthat/_snaps/coord-transform.md index 2aaa3c156f..cec8af5ae2 100644 --- a/tests/testthat/_snaps/coord-transform.md +++ b/tests/testthat/_snaps/coord-transform.md @@ -8,9 +8,9 @@ # coord_trans() throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector, not a object. --- - `ylim` must be a vector of length 2, not an integer vector of length 3. + `ylim` must be a vector of length 2, not length 3. diff --git a/tests/testthat/_snaps/coord_sf.md b/tests/testthat/_snaps/coord_sf.md index bb43424d33..7eb42bf074 100644 --- a/tests/testthat/_snaps/coord_sf.md +++ b/tests/testthat/_snaps/coord_sf.md @@ -21,9 +21,9 @@ # coord_sf() throws error when limits are badly specified - `xlim` must be a vector of length 2, not a object. + `xlim` must be a vector, not a object. --- - `ylim` must be a vector of length 2, not an integer vector of length 3. + `ylim` must be a vector of length 2, not length 3. diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index 80b541e2e4..2a4bd75ff4 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -31,7 +31,7 @@ ggplotGrob(p + theme(plot.tag.position = c(0, 0.5, 1))) Condition Error in `theme()`: - ! A `plot.tag.position` theme setting must have length 2. + ! A `plot.tag.position` must be a vector of length 2, not length 3. --- diff --git a/tests/testthat/_snaps/limits.md b/tests/testthat/_snaps/limits.md index b7f4ffd960..f52f2e94e5 100644 --- a/tests/testthat/_snaps/limits.md +++ b/tests/testthat/_snaps/limits.md @@ -4,5 +4,5 @@ --- - `linewidth` must be a two-element vector. + `linewidth` must be a vector of length 2, not length 1. diff --git a/tests/testthat/_snaps/qplot.md b/tests/testthat/_snaps/qplot.md index 6513d2deb0..c95b8b3d2d 100644 --- a/tests/testthat/_snaps/qplot.md +++ b/tests/testthat/_snaps/qplot.md @@ -1,4 +1,4 @@ # qplot() only work with character geom - `geom` must be a character vector, not a object. + `geom` must be a character vector, not a object. diff --git a/tests/testthat/_snaps/scale-date.md b/tests/testthat/_snaps/scale-date.md index 9717f0f785..a2c1e51e73 100644 --- a/tests/testthat/_snaps/scale-date.md +++ b/tests/testthat/_snaps/scale-date.md @@ -6,5 +6,5 @@ --- A value was passed to a Datetime scale. - i The value was converted to a object. + i The value was converted to a object. diff --git a/tests/testthat/_snaps/scales.md b/tests/testthat/_snaps/scales.md index 40298a1836..549769419c 100644 --- a/tests/testthat/_snaps/scales.md +++ b/tests/testthat/_snaps/scales.md @@ -99,3 +99,19 @@ The `scale_name` argument of `binned_scale()` is deprecated as of ggplot2 3.5.0. +# continuous scales warn about faulty `limits` + + Code + scale_x_continuous(limits = c("A", "B")) + Condition + Error in `scale_x_continuous()`: + ! `limits` must be a vector, not a character vector. + +--- + + Code + scale_x_continuous(limits = 1:3) + Condition + Error in `scale_x_continuous()`: + ! `limits` must be a vector of length 2, not length 3. + diff --git a/tests/testthat/_snaps/stat-bin.md b/tests/testthat/_snaps/stat-bin.md index f92e737d94..2b5ee05525 100644 --- a/tests/testthat/_snaps/stat-bin.md +++ b/tests/testthat/_snaps/stat-bin.md @@ -29,7 +29,7 @@ --- - `x_range` must have two elements. + `x_range` must be a vector of length 2, not length 1. --- @@ -45,7 +45,7 @@ --- - `x_range` must have two elements. + `x_range` must be a vector of length 2, not length 1. --- diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index 4599b0bc03..899c048e71 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -77,7 +77,7 @@ test_that("out-of-range breaks are dropped", { test_that("no minor breaks when only one break", { sc1 <- scale_x_discrete(limits = "a") - sc2 <- scale_x_continuous(limits = 1) + sc2 <- scale_x_continuous(limits = c(1, 1)) expect_length(sc1$get_breaks_minor(), 0) expect_length(sc2$get_breaks_minor(), 0) diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index c44910011e..d9286b513f 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -729,6 +729,11 @@ test_that("Discrete scales with only NAs return `na.value`", { expect_equal(sc$map(x), c(NA_real_, NA_real_)) }) +test_that("continuous scales warn about faulty `limits`", { + expect_snapshot(scale_x_continuous(limits = c("A", "B")), error = TRUE) + expect_snapshot(scale_x_continuous(limits = 1:3), error = TRUE) +}) + test_that("discrete scales work with NAs in arbitrary positions", { # Prevents intermediate caching of palettes map <- function(x, limits) { From 579e2d53dec0af0384ecba81afe82db88a70dd9a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 30 Oct 2024 11:05:15 +0100 Subject: [PATCH 149/264] Using `after_scale()` in `Geom$default_aes` field (#6137) * append to modifiers * add test * include test for `get_geom_defaults()` * add news bullet --- NEWS.md | 2 ++ R/geom-.R | 7 +++++++ tests/testthat/test-aes-calculated.R | 23 +++++++++++++++++++++++ 3 files changed, 32 insertions(+) diff --git a/NEWS.md b/NEWS.md index 34750ee04c..c1d127b555 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now + evaluated in the context of data (@teunbrand, #6135) * Fixed bug where binned scales wouldn't simultaneously accept transformations and function-limits (@teunbrand, #6144). * Fixed bug where the `ggplot2::`-prefix did not work with `stage()` diff --git a/R/geom-.R b/R/geom-.R index bb409ba0cf..dae3027e1b 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -136,6 +136,13 @@ Geom <- ggproto("Geom", themed_defaults <- eval_from_theme(default_aes, theme) default_aes[names(themed_defaults)] <- themed_defaults + # Mark staged/scaled defaults as modifier (#6135) + delayed <- is_scaled_aes(default_aes) | is_staged_aes(default_aes) + if (any(delayed)) { + modifiers <- defaults(modifiers, default_aes[delayed]) + default_aes <- default_aes[!delayed] + } + missing_eval <- lapply(default_aes, eval_tidy) # Needed for geoms with defaults set to NULL (e.g. GeomSf) missing_eval <- compact(missing_eval) diff --git a/tests/testthat/test-aes-calculated.R b/tests/testthat/test-aes-calculated.R index ac77df4c48..2d389106cf 100644 --- a/tests/testthat/test-aes-calculated.R +++ b/tests/testthat/test-aes-calculated.R @@ -146,3 +146,26 @@ test_that("stage allows aesthetics that are only mapped to start", { ) }) + +test_that("A geom can have scaled defaults (#6135)", { + + test_geom <- ggproto( + NULL, GeomPoint, + default_aes = modify_list( + GeomPoint$default_aes, + aes(colour = after_scale(alpha(fill, 0.5)), fill = "black") + ) + ) + + df <- data.frame(x = 1:3, fill = c("#FF0000", "#00FF00", "#0000FF")) + + ld <- layer_data( + ggplot(df, aes(x, x, fill = I(fill))) + + stat_identity(geom = test_geom) + ) + + expect_equal(ld$colour, c("#FF000080", "#00FF0080", '#0000FF80')) + + defaults <- get_geom_defaults(test_geom) + expect_equal(defaults$colour, c("#00000080")) +}) From b29b83151a8415093cadc8aead5024452ed7eae6 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 30 Oct 2024 12:30:54 +0100 Subject: [PATCH 150/264] Treatment options for zeroes in histograms (#6139) * add `keep.zeroes` option * add test * document * add news bullet --- NEWS.md | 1 + R/stat-bin.R | 29 ++++++++++++++++++++++++++++- man/geom_histogram.Rd | 6 ++++++ tests/testthat/test-stat-bin.R | 14 ++++++++++++++ 4 files changed, 49 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index c1d127b555..83e411a4dd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -188,6 +188,7 @@ * The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, `labs()` and several guides (@teunbrand, #3196). * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). +* Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) # ggplot2 3.5.1 diff --git a/R/stat-bin.R b/R/stat-bin.R index c085f818a2..9c571ae519 100644 --- a/R/stat-bin.R +++ b/R/stat-bin.R @@ -26,6 +26,10 @@ #' or left edges of bins are included in the bin. #' @param pad If `TRUE`, adds empty bins at either end of x. This ensures #' frequency polygons touch 0. Defaults to `FALSE`. +#' @param keep.zeroes Treatment of zero count bins. If `"all"` (default), such +#' bins are kept as-is. If `"none"`, all zero count bins are filtered out. +#' If `"inner"` only zero count bins at the flanks are filtered out, but not +#' in the middle. #' @eval rd_computed_vars( #' count = "number of points in bin.", #' density = "density of points in bin, scaled to integrate to 1.", @@ -55,6 +59,7 @@ stat_bin <- function(mapping = NULL, data = NULL, closed = c("right", "left"), pad = FALSE, na.rm = FALSE, + keep.zeroes = "all", orientation = NA, show.legend = NA, inherit.aes = TRUE) { @@ -77,6 +82,7 @@ stat_bin <- function(mapping = NULL, data = NULL, pad = pad, na.rm = na.rm, orientation = orientation, + keep.zeroes = keep.zeroes, ... ) ) @@ -89,6 +95,10 @@ stat_bin <- function(mapping = NULL, data = NULL, StatBin <- ggproto("StatBin", Stat, setup_params = function(self, data, params) { params$flipped_aes <- has_flipped_aes(data, params, main_is_orthogonal = FALSE) + params$keep.zeroes <- arg_match0( + params$keep.zeroes %||% "all", + c("all", "none", "inner"), arg_nm = "keep.zeroes" + ) has_x <- !(is.null(data$x) && is.null(params$x)) has_y <- !(is.null(data$y) && is.null(params$y)) @@ -139,7 +149,7 @@ StatBin <- ggproto("StatBin", Stat, compute_group = function(data, scales, binwidth = NULL, bins = NULL, center = NULL, boundary = NULL, closed = c("right", "left"), pad = FALSE, - breaks = NULL, flipped_aes = FALSE, + breaks = NULL, flipped_aes = FALSE, keep.zeroes = "all", # The following arguments are not used, but must # be listed so parameters are computed correctly origin = NULL, right = NULL, drop = NULL) { @@ -163,6 +173,14 @@ StatBin <- ggproto("StatBin", Stat, boundary = boundary, closed = closed) } bins <- bin_vector(data[[x]], bins, weight = data$weight, pad = pad) + + keep <- switch( + keep.zeroes, + none = bins$count != 0, + inner = inner_runs(bins$count != 0), + TRUE + ) + bins <- vec_slice(bins, keep) bins$flipped_aes <- flipped_aes flip_data(bins, flipped_aes) }, @@ -174,3 +192,12 @@ StatBin <- ggproto("StatBin", Stat, dropped_aes = "weight" # after statistical transformation, weights are no longer available ) +inner_runs <- function(x) { + rle <- vec_unrep(x) + nruns <- nrow(rle) + inner <- rep(TRUE, nruns) + i <- unique(c(1, nruns)) + inner[i] <- inner[i] & rle$key[i] + rep(inner, rle$times) +} + diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index a241aa2ba4..32f9c39610 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -46,6 +46,7 @@ stat_bin( closed = c("right", "left"), pad = FALSE, na.rm = FALSE, + keep.zeroes = "all", orientation = NA, show.legend = NA, inherit.aes = TRUE @@ -172,6 +173,11 @@ or left edges of bins are included in the bin.} \item{pad}{If \code{TRUE}, adds empty bins at either end of x. This ensures frequency polygons touch 0. Defaults to \code{FALSE}.} + +\item{keep.zeroes}{Treatment of zero count bins. If \code{"all"} (default), such +bins are kept as-is. If \code{"none"}, all zero count bins are filtered out. +If \code{"inner"} only zero count bins at the flanks are filtered out, but not +in the middle.} } \description{ Visualise the distribution of a single continuous variable by dividing diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index 5baedf9223..a114748daf 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -118,6 +118,20 @@ test_that("stat_bin() provides width (#3522)", { expect_equal(out$xmax - out$xmin, rep(binwidth, 10)) }) +test_that("stat_bin(keep.zeroes) options work as intended", { + p <- ggplot(data.frame(x = c(1, 2, 2, 3, 5, 6, 6, 7)), aes(x)) + + scale_x_continuous(limits = c(-1, 9)) + + ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "all")) + expect_equal(ld$x, -1:9) + + ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "inner")) + expect_equal(ld$x, c(1:7)) + + ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "none")) + expect_equal(ld$x, c(1:3, 5:7)) +}) + # Underlying binning algorithm -------------------------------------------- test_that("bins() computes fuzz with non-finite breaks", { From cc329df041573c4ca0ce31b491de0144506c12f6 Mon Sep 17 00:00:00 2001 From: Michael Chirico Date: Fri, 1 Nov 2024 05:32:46 -0700 Subject: [PATCH 151/264] Fix ragg version check (#6175) --- tests/testthat/test-utilities-checks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-utilities-checks.R b/tests/testthat/test-utilities-checks.R index 6d27c4e85b..af8c5ce468 100644 --- a/tests/testthat/test-utilities-checks.R +++ b/tests/testthat/test-utilities-checks.R @@ -70,7 +70,7 @@ test_that("check_device finds device capabilities", { test_that("check_device finds ragg capabilities", { skip_if( - getRversion() < "4.2.0" || !is_installed("ragg", version = "1.2.0"), + getRversion() < "4.2.0" || !is_installed("ragg", version = "1.2.6"), "Cannot test {ragg} capabilities." ) tmp <- withr::local_tempfile(fileext = ".tiff") From e594b49fdd5e4d95bf1031edaf6c7ccfc0cdedb0 Mon Sep 17 00:00:00 2001 From: Michael Chirico Date: Mon, 4 Nov 2024 01:15:29 -0800 Subject: [PATCH 152/264] Adjust version for svglite skip (#6176) * Adjust version for svglite skip * Also in test-patterns.R --- tests/testthat/test-patterns.R | 2 +- tests/testthat/test-utilities-checks.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-patterns.R b/tests/testthat/test-patterns.R index 8e2b64d82e..2f68904dbe 100644 --- a/tests/testthat/test-patterns.R +++ b/tests/testthat/test-patterns.R @@ -61,7 +61,7 @@ test_that("fill_alpha works as expected", { test_that("geoms can use pattern fills", { skip_if_not_installed("grid", "4.2.0") - skip_if_not_installed("svglite", "2.1.0") + skip_if_not_installed("svglite", "2.1.2") # Workaround for vdiffr's lack of pattern support # See also https://github.com/r-lib/vdiffr/issues/132 diff --git a/tests/testthat/test-utilities-checks.R b/tests/testthat/test-utilities-checks.R index af8c5ce468..c1d7578fa7 100644 --- a/tests/testthat/test-utilities-checks.R +++ b/tests/testthat/test-utilities-checks.R @@ -84,7 +84,7 @@ test_that("check_device finds ragg capabilities", { test_that("check_device finds svglite capabilities", { skip_if( - getRversion() < "4.2.0" || !is_installed("svglite", version = "2.1.0"), + getRversion() < "4.2.0" || !is_installed("svglite", version = "2.1.2"), "Cannot test {svglite} capabilities." ) tmp <- withr::local_tempfile(fileext = ".svg") From f220ded8eb9775d0efe44b8d2e01605b912ee6e8 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 10:45:16 +0100 Subject: [PATCH 153/264] Extra boxplot features (#5423) * expand default aes * crossbar can use boxplot's median line settings * insert new aesthetics * adapt key drawing * update snapshots * fix legend linewidth * document * capture outlier settings in list * Use fixed parameters instead of aesthetics * Adjust key drawing * Add test * Document * document box arguments * add `middle_gp` and `box_gp` to `geom_crossbar()` * adapt legend keys * redocument * fix news bullet * skip failing test --- NEWS.md | 2 + R/geom-boxplot.R | 138 ++++++++++----- R/geom-crossbar.R | 42 ++++- R/legend-draw.R | 67 +++++-- man/geom_boxplot.Rd | 36 +++- man/geom_linerange.Rd | 14 ++ .../horizontal-boxplot-and-crossbar.svg | 4 + .../_snaps/geom-boxplot/customised-style.svg | 167 ++++++++++++++++++ .../_snaps/geom-boxplot/outlier-colours.svg | 6 + .../testthat/_snaps/geom-boxplot/staples.svg | 6 + tests/testthat/test-geom-boxplot.R | 12 ++ tests/testthat/test-patterns.R | 3 + 12 files changed, 437 insertions(+), 60 deletions(-) create mode 100644 tests/testthat/_snaps/geom-boxplot/customised-style.svg diff --git a/NEWS.md b/NEWS.md index 83e411a4dd..df9de4b689 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_boxplot()` gains additional arguments to style the colour, linetype and + linewidths of the box, whiskers, median line and staples (@teunbrand, #5126) * (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now evaluated in the context of data (@teunbrand, #6135) * Fixed bug where binned scales wouldn't simultaneously accept transformations diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index 1ac23ba80f..efb6dd14bd 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -43,11 +43,20 @@ #' needs to show the full data range, please use `outlier.shape = NA` instead. #' @param outlier.colour,outlier.color,outlier.fill,outlier.shape,outlier.size,outlier.stroke,outlier.alpha #' Default aesthetics for outliers. Set to `NULL` to inherit from the -#' aesthetics used for the box. -#' -#' In the unlikely event you specify both US and UK spellings of colour, the -#' US spelling will take precedence. -#' +#' data's aesthetics. +#' @param whisker.colour,whisker.color,whisker.linetype,whisker.linewidth +#' Default aesthetics for the whiskers. Set to `NULL` to inherit from the +#' data's aesthetics. +#' @param median.colour,median.color,median.linetype,median.linewidth +#' Default aesthetics for the median line. Set to `NULL` to inherit from the +#' data's aesthetics. +#' @param staple.colour,staple.color,staple.linetype,staple.linewidth +#' Default aesthetics for the staples. Set to `NULL` to inherit from the +#' data's aesthetics. Note that staples don't appear unless the `staplewidth` +#' argument is set to a non-zero size. +#' @param box.colour,box.color,box.linetype,box.linewidth +#' Default aesthetics for the boxes. Set to `NULL` to inherit from the +#' data's aesthetics. #' @param notch If `FALSE` (default) make a standard box plot. If #' `TRUE`, make a notched box plot. Notches are used to compare groups; #' if the notches of two boxes do not overlap, this suggests that the medians @@ -60,6 +69,9 @@ #' `TRUE`, boxes are drawn with widths proportional to the #' square-roots of the number of observations in the groups (possibly #' weighted, using the `weight` aesthetic). +#' @note In the unlikely event you specify both US and UK spellings of colour, +#' the US spelling will take precedence. +#' #' @export #' @references McGill, R., Tukey, J. W. and Larsen, W. A. (1978) Variations of #' box plots. The American Statistician 32, 12-16. @@ -121,6 +133,22 @@ geom_boxplot <- function(mapping = NULL, data = NULL, outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, + whisker.colour = NULL, + whisker.color = NULL, + whisker.linetype = NULL, + whisker.linewidth = NULL, + staple.colour = NULL, + staple.color = NULL, + staple.linetype = NULL, + staple.linewidth = NULL, + median.colour = NULL, + median.color = NULL, + median.linetype = NULL, + median.linewidth = NULL, + box.colour = NULL, + box.color = NULL, + box.linetype = NULL, + box.linewidth = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, @@ -140,6 +168,39 @@ geom_boxplot <- function(mapping = NULL, data = NULL, } } + outlier_gp <- list( + colour = outlier.color %||% outlier.colour, + fill = outlier.fill, + shape = outlier.shape, + size = outlier.size, + stroke = outlier.stroke, + alpha = outlier.alpha + ) + + whisker_gp <- list( + colour = whisker.color %||% whisker.colour, + linetype = whisker.linetype, + linewidth = whisker.linewidth + ) + + staple_gp <- list( + colour = staple.color %||% staple.colour, + linetype = staple.linetype, + linewidth = staple.linewidth + ) + + median_gp <- list( + colour = median.color %||% median.colour, + linetype = median.linetype, + linewidth = median.linewidth + ) + + box_gp <- list( + colour = box.color %||% box.colour, + linetype = box.linetype, + linewidth = box.linewidth + ) + check_number_decimal(staplewidth) check_bool(outliers) @@ -153,12 +214,11 @@ geom_boxplot <- function(mapping = NULL, data = NULL, inherit.aes = inherit.aes, params = list2( outliers = outliers, - outlier.colour = outlier.color %||% outlier.colour, - outlier.fill = outlier.fill, - outlier.shape = outlier.shape, - outlier.size = outlier.size, - outlier.stroke = outlier.stroke, - outlier.alpha = outlier.alpha, + outlier_gp = outlier_gp, + whisker_gp = whisker_gp, + staple_gp = staple_gp, + median_gp = median_gp, + box_gp = box_gp, notch = notch, notchwidth = notchwidth, staplewidth = staplewidth, @@ -222,10 +282,9 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, }, draw_group = function(self, data, panel_params, coord, lineend = "butt", - linejoin = "mitre", fatten = 2, outlier.colour = NULL, - outlier.fill = NULL, outlier.shape = NULL, - outlier.size = NULL, outlier.stroke = 0.5, - outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, + linejoin = "mitre", fatten = 2, outlier_gp = NULL, + whisker_gp = NULL, staple_gp = NULL, median_gp = NULL, + box_gp = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, flipped_aes = FALSE) { data <- check_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) @@ -237,36 +296,30 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, )) } - common <- list( - colour = data$colour, - linewidth = data$linewidth, - linetype = data$linetype, - fill = fill_alpha(data$fill, data$alpha), - group = data$group - ) + common <- list(fill = fill_alpha(data$fill, data$alpha), group = data$group) whiskers <- data_frame0( x = c(data$x, data$x), xend = c(data$x, data$x), y = c(data$upper, data$lower), yend = c(data$ymax, data$ymin), + colour = rep(whisker_gp$colour %||% data$colour, 2), + linetype = rep(whisker_gp$linetype %||% data$linetype, 2), + linewidth = rep(whisker_gp$linewidth %||% data$linewidth, 2), alpha = c(NA_real_, NA_real_), !!!common, .size = 2 ) whiskers <- flip_data(whiskers, flipped_aes) - box <- data_frame0( - xmin = data$xmin, - xmax = data$xmax, - ymin = data$lower, - y = data$middle, - ymax = data$upper, - ynotchlower = ifelse(notch, data$notchlower, NA), - ynotchupper = ifelse(notch, data$notchupper, NA), - notchwidth = notchwidth, - alpha = data$alpha, - !!!common + box <- transform( + data, + y = middle, + ymax = upper, + ymin = lower, + ynotchlower = ifelse(notch, notchlower, NA), + ynotchupper = ifelse(notch, notchupper, NA), + notchwidth = notchwidth ) box <- flip_data(box, flipped_aes) @@ -274,13 +327,13 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, outliers <- data_frame0( y = data$outliers[[1]], x = data$x[1], - colour = outlier.colour %||% data$colour[1], - fill = outlier.fill %||% data$fill[1], - shape = outlier.shape %||% data$shape[1], - size = outlier.size %||% data$size[1], - stroke = outlier.stroke %||% data$stroke[1], + colour = outlier_gp$colour %||% data$colour[1], + fill = outlier_gp$fill %||% data$fill[1], + shape = outlier_gp$shape %||% data$shape[1] %||% 19, + size = outlier_gp$size %||% data$size[1] %||% 1.5, + stroke = outlier_gp$stroke %||% data$stroke[1] %||% 0.5, fill = NA, - alpha = outlier.alpha %||% data$alpha[1], + alpha = outlier_gp$alpha %||% data$alpha[1], .size = length(data$outliers[[1]]) ) outliers <- flip_data(outliers, flipped_aes) @@ -296,6 +349,9 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, xend = rep((data$xmax - data$x) * staplewidth + data$x, 2), y = c(data$ymax, data$ymin), yend = c(data$ymax, data$ymin), + linetype = rep(staple_gp$linetype %||% data$linetype, 2), + linewidth = rep(staple_gp$linewidth %||% data$linewidth, 2), + colour = rep(staple_gp$colour %||% data$colour, 2), alpha = c(NA_real_, NA_real_), !!!common, .size = 2 @@ -320,7 +376,9 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, coord, lineend = lineend, linejoin = linejoin, - flipped_aes = flipped_aes + flipped_aes = flipped_aes, + middle_gp = median_gp, + box_gp = box_gp ) )) }, diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index 1f7c66f832..be7ce1f658 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -1,13 +1,40 @@ #' @export #' @rdname geom_linerange +#' @param middle.colour,middle.color,middle.linetype,middle.linewidth +#' Default aesthetics for the middle line. Set to `NULL` to inherit from the +#' data's aesthetics. +#' @param box.colour,box.color,box.linetype,box.linewidth +#' Default aesthetics for the boxes. Set to `NULL` to inherit from the +#' data's aesthetics. geom_crossbar <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity", ..., + middle.colour = NULL, + middle.color = NULL, + middle.linetype = NULL, + middle.linewidth = NULL, + box.colour = NULL, + box.color = NULL, + box.linetype = NULL, + box.linewidth = NULL, fatten = 2.5, na.rm = FALSE, orientation = NA, show.legend = NA, inherit.aes = TRUE) { + + middle_gp <- list( + colour = middle.color %||% middle.colour, + linetype = middle.linetype, + linewidth = middle.linewidth + ) + + box_gp <- list( + colour = box.color %||% box.colour, + linetype = box.linetype, + linewidth = box.linewidth + ) + layer( data = data, mapping = mapping, @@ -17,6 +44,8 @@ geom_crossbar <- function(mapping = NULL, data = NULL, show.legend = show.legend, inherit.aes = inherit.aes, params = list2( + middle_gp = middle_gp, + box_gp = box_gp, fatten = fatten, na.rm = na.rm, orientation = orientation, @@ -54,11 +83,13 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, draw_panel = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre", fatten = 2.5, width = NULL, - flipped_aes = FALSE) { + flipped_aes = FALSE, middle_gp = NULL, box_gp = NULL) { + data <- check_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) middle <- transform(data, x = xmin, xend = xmax, yend = y, linewidth = linewidth * fatten, alpha = NA) + middle <- data_frame0(!!!defaults(compact(middle_gp), middle)) has_notch <- !is.null(data$ynotchlower) && !is.null(data$ynotchupper) && !is.na(data$ynotchlower) && !is.na(data$ynotchupper) @@ -87,9 +118,9 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, data$ymax ), alpha = rep(data$alpha, 11), - colour = rep(data$colour, 11), + colour = rep(data$colour, 11), linewidth = rep(data$linewidth, 11), - linetype = rep(data$linetype, 11), + linetype = rep(data$linetype, 11), fill = rep(data$fill, 11), group = rep(seq_len(nrow(data)), 11) ) @@ -99,13 +130,14 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, x = c(data$xmin, data$xmin, data$xmax, data$xmax, data$xmin), y = c(data$ymax, data$ymin, data$ymin, data$ymax, data$ymax), alpha = rep(data$alpha, 5), - colour = rep(data$colour, 5), + colour = rep(data$colour, 5), linewidth = rep(data$linewidth, 5), - linetype = rep(data$linetype, 5), + linetype = rep(data$linetype, 5), fill = rep(data$fill, 5), group = rep(seq_len(nrow(data)), 5) # each bar forms it's own group ) } + box <- data_frame0(!!!defaults(compact(box_gp), box)) box <- flip_data(box, flipped_aes) middle <- flip_data(middle, flipped_aes) diff --git a/R/legend-draw.R b/R/legend-draw.R index ccfb035872..0f734f8fea 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -110,20 +110,49 @@ draw_key_boxplot <- function(data, params, size) { linejoin = params$linejoin %||% "mitre" ) + whisker <- gg_par( + col = params$whisker_gp$colour, + lty = params$whisker_gp$linetype, + lwd = params$whisker_gp$linewidth + ) + + median <- gg_par( + col = params$median_gp$colour, + lty = params$median_gp$linetype, + lwd = params$median_gp$linewidth + ) + + box <- gg_par( + col = params$box_gp$colour, + lty = params$box_gp$linetype, + lwd = params$box_gp$linewidth + ) + + staple_size <- 0.5 + c(0.375, -0.375) * params$staplewidth + staple <- gg_par( + col = params$staple_gp$colour, + lty = params$staple_gp$linetype, + lwd = params$staple_gp$linewidth + ) + if (isTRUE(params$flipped_aes)) { grobTree( - linesGrob(c(0.1, 0.25), 0.5), - linesGrob(c(0.75, 0.9), 0.5), - rectGrob(width = 0.5, height = 0.75), - linesGrob(0.5, c(0.125, 0.875)), + linesGrob(c(0.1, 0.25), 0.5, gp = whisker), + linesGrob(c(0.75, 0.9), 0.5, gp = whisker), + rectGrob(width = 0.5, height = 0.75, gp = box), + linesGrob(0.5, c(0.125, 0.875), gp = median), + linesGrob(0.1, staple_size, gp = staple), + linesGrob(0.9, staple_size, gp = staple), gp = gp ) } else { grobTree( - linesGrob(0.5, c(0.1, 0.25)), - linesGrob(0.5, c(0.75, 0.9)), - rectGrob(height = 0.5, width = 0.75), - linesGrob(c(0.125, 0.875), 0.5), + linesGrob(0.5, c(0.1, 0.25), gp = whisker), + linesGrob(0.5, c(0.75, 0.9), gp = whisker), + rectGrob(height = 0.5, width = 0.75, gp = box), + linesGrob(c(0.125, 0.875), 0.5, gp = median), + linesGrob(staple_size, 0.1, gp = staple), + linesGrob(staple_size, 0.9, gp = staple), gp = gp ) } @@ -140,16 +169,30 @@ draw_key_crossbar <- function(data, params, size) { lineend = params$lineend %||% "butt", linejoin = params$linejoin %||% "mitre" ) + + middle <- gg_par( + col = params$middle_gp$colour, + lty = params$middle_gp$linetype, + lwd = params$middle_gp$linewidth + ) + + box <- gg_par( + col = params$box_gp$colour, + lty = params$box_gp$linetype, + lwd = params$box_gp$linewidth + ) + + if (isTRUE(params$flipped_aes)) { grobTree( - rectGrob(height = 0.75, width = 0.5), - linesGrob(0.5, c(0.125, 0.875)), + rectGrob(height = 0.75, width = 0.5, gp = box), + linesGrob(0.5, c(0.125, 0.875), gp = middle), gp = gp ) } else { grobTree( - rectGrob(height = 0.5, width = 0.75), - linesGrob(c(0.125, 0.875), 0.5), + rectGrob(height = 0.5, width = 0.75, gp = box), + linesGrob(c(0.125, 0.875), 0.5, gp = middle), gp = gp ) } diff --git a/man/geom_boxplot.Rd b/man/geom_boxplot.Rd index 3fc39d212b..d5026c013f 100644 --- a/man/geom_boxplot.Rd +++ b/man/geom_boxplot.Rd @@ -19,6 +19,22 @@ geom_boxplot( outlier.size = NULL, outlier.stroke = 0.5, outlier.alpha = NULL, + whisker.colour = NULL, + whisker.color = NULL, + whisker.linetype = NULL, + whisker.linewidth = NULL, + staple.colour = NULL, + staple.color = NULL, + staple.linetype = NULL, + staple.linewidth = NULL, + median.colour = NULL, + median.color = NULL, + median.linetype = NULL, + median.linewidth = NULL, + box.colour = NULL, + box.color = NULL, + box.linetype = NULL, + box.linewidth = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, @@ -112,10 +128,20 @@ only, not the full data range. If outliers need to be hidden and the axes needs to show the full data range, please use \code{outlier.shape = NA} instead.} \item{outlier.colour, outlier.color, outlier.fill, outlier.shape, outlier.size, outlier.stroke, outlier.alpha}{Default aesthetics for outliers. Set to \code{NULL} to inherit from the -aesthetics used for the box. +data's aesthetics.} -In the unlikely event you specify both US and UK spellings of colour, the -US spelling will take precedence.} +\item{whisker.colour, whisker.color, whisker.linetype, whisker.linewidth}{Default aesthetics for the whiskers. Set to \code{NULL} to inherit from the +data's aesthetics.} + +\item{staple.colour, staple.color, staple.linetype, staple.linewidth}{Default aesthetics for the staples. Set to \code{NULL} to inherit from the +data's aesthetics. Note that staples don't appear unless the \code{staplewidth} +argument is set to a non-zero size.} + +\item{median.colour, median.color, median.linetype, median.linewidth}{Default aesthetics for the median line. Set to \code{NULL} to inherit from the +data's aesthetics.} + +\item{box.colour, box.color, box.linetype, box.linewidth}{Default aesthetics for the boxes. Set to \code{NULL} to inherit from the +data's aesthetics.} \item{notch}{If \code{FALSE} (default) make a standard box plot. If \code{TRUE}, make a notched box plot. Notches are used to compare groups; @@ -166,6 +192,10 @@ The boxplot compactly displays the distribution of a continuous variable. It visualises five summary statistics (the median, two hinges and two whiskers), and all "outlying" points individually. } +\note{ +In the unlikely event you specify both US and UK spellings of colour, +the US spelling will take precedence. +} \section{Orientation}{ This geom treats each axis differently and, thus, can thus have two orientations. Often the orientation is easy to deduce from a combination of the given mappings and the types of positional scales in use. Thus, ggplot2 will by default try to guess which orientation the layer should have. Under rare circumstances, the orientation is ambiguous and guessing may fail. In that case the orientation can be specified directly using the \code{orientation} parameter, which can be either \code{"x"} or \code{"y"}. The value gives the axis that the geom should run along, \code{"x"} being the default orientation you would expect for the geom. diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index 87bc5c8e75..e706dea94b 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -14,6 +14,14 @@ geom_crossbar( stat = "identity", position = "identity", ..., + middle.colour = NULL, + middle.color = NULL, + middle.linetype = NULL, + middle.linewidth = NULL, + box.colour = NULL, + box.color = NULL, + box.linetype = NULL, + box.linewidth = NULL, fatten = 2.5, na.rm = FALSE, orientation = NA, @@ -133,6 +141,12 @@ lists which parameters it can accept. \link[=draw_key]{key glyphs}, to change the display of the layer in the legend. }} +\item{middle.colour, middle.color, middle.linetype, middle.linewidth}{Default aesthetics for the middle line. Set to \code{NULL} to inherit from the +data's aesthetics.} + +\item{box.colour, box.color, box.linetype, box.linewidth}{Default aesthetics for the boxes. Set to \code{NULL} to inherit from the +data's aesthetics.} + \item{fatten}{A multiplicative factor used to increase the size of the middle bar in \code{geom_crossbar()} and the middle point in \code{geom_pointrange()}.} diff --git a/tests/testthat/_snaps/draw-key/horizontal-boxplot-and-crossbar.svg b/tests/testthat/_snaps/draw-key/horizontal-boxplot-and-crossbar.svg index d787461ca4..addbc59e92 100644 --- a/tests/testthat/_snaps/draw-key/horizontal-boxplot-and-crossbar.svg +++ b/tests/testthat/_snaps/draw-key/horizontal-boxplot-and-crossbar.svg @@ -71,11 +71,15 @@ + + + + a b diff --git a/tests/testthat/_snaps/geom-boxplot/customised-style.svg b/tests/testthat/_snaps/geom-boxplot/customised-style.svg new file mode 100644 index 0000000000..612ec93728 --- /dev/null +++ b/tests/testthat/_snaps/geom-boxplot/customised-style.svg @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 +6 +7 + + + + + + + + + + + + + +2seater +compact +midsize +minivan +pickup +subcompact +suv +class +displ + +class + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2seater +compact +midsize +minivan +pickup +subcompact +suv +customised style + + diff --git a/tests/testthat/_snaps/geom-boxplot/outlier-colours.svg b/tests/testthat/_snaps/geom-boxplot/outlier-colours.svg index c3fcba0018..309ffcc43d 100644 --- a/tests/testthat/_snaps/geom-boxplot/outlier-colours.svg +++ b/tests/testthat/_snaps/geom-boxplot/outlier-colours.svg @@ -72,16 +72,22 @@ + + + + + + 4 6 8 diff --git a/tests/testthat/_snaps/geom-boxplot/staples.svg b/tests/testthat/_snaps/geom-boxplot/staples.svg index b0bf785867..b2f4054294 100644 --- a/tests/testthat/_snaps/geom-boxplot/staples.svg +++ b/tests/testthat/_snaps/geom-boxplot/staples.svg @@ -78,16 +78,22 @@ + + + + + + 4 6 8 diff --git a/tests/testthat/test-geom-boxplot.R b/tests/testthat/test-geom-boxplot.R index dabcb6ddeb..81d37cc5a9 100644 --- a/tests/testthat/test-geom-boxplot.R +++ b/tests/testthat/test-geom-boxplot.R @@ -96,4 +96,16 @@ test_that("boxplot draws correctly", { expect_doppelganger("staples", ggplot(mtcars, aes(x = factor(cyl), y = drat, colour = factor(cyl))) + geom_boxplot(staplewidth = 0.5) ) + expect_doppelganger( + "customised style", + ggplot(mpg, aes(class, displ, colour = class)) + + geom_boxplot( + outlier.shape = 6, + whisker.linetype = 2, + median.colour = "red", + box.colour = "black", + staple.linewidth = 1, + staplewidth = 0.25 + ) + ) }) diff --git a/tests/testthat/test-patterns.R b/tests/testthat/test-patterns.R index 2f68904dbe..4939c393b0 100644 --- a/tests/testthat/test-patterns.R +++ b/tests/testthat/test-patterns.R @@ -62,6 +62,9 @@ test_that("geoms can use pattern fills", { skip_if_not_installed("grid", "4.2.0") skip_if_not_installed("svglite", "2.1.2") + # TODO: ideally we should test this on all platforms, but currently they + # don't all produce the same result + skip_if_not(.Platform$OS.type == "windows") # Workaround for vdiffr's lack of pattern support # See also https://github.com/r-lib/vdiffr/issues/132 From e67bf20210254e591d17f747433e3dde63550a4c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:18:49 +0100 Subject: [PATCH 154/264] Contours for non-axis aligned grids (#5911) * attempt contour calculation in unrotated space * add test * add news bullet * fix mistake in calculation * protect against huge amounts of data --- NEWS.md | 2 ++ R/stat-contour.R | 58 ++++++++++++++++++++++++++++++ tests/testthat/test-stat-contour.R | 23 ++++++++++++ 3 files changed, 83 insertions(+) diff --git a/NEWS.md b/NEWS.md index df9de4b689..9d08380189 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_contour()` should be able to recognise a rotated grid of points + (@teunbrand, #4320) * `geom_boxplot()` gains additional arguments to style the colour, linetype and linewidths of the box, whiskers, median line and staples (@teunbrand, #5126) * (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now diff --git a/R/stat-contour.R b/R/stat-contour.R index e0590f2ec9..0602ed3899 100644 --- a/R/stat-contour.R +++ b/R/stat-contour.R @@ -104,6 +104,9 @@ StatContour <- ggproto("StatContour", Stat, compute_group = function(data, scales, z.range, bins = NULL, binwidth = NULL, breaks = NULL, na.rm = FALSE) { + # Undo data rotation + rotation <- estimate_contour_angle(data$x, data$y) + data[c("x", "y")] <- rotate_xy(data$x, data$y, -rotation) breaks <- contour_breaks(z.range, bins, binwidth, breaks) @@ -113,6 +116,8 @@ StatContour <- ggproto("StatContour", Stat, path_df$level <- as.numeric(path_df$level) path_df$nlevel <- rescale_max(path_df$level) + # Re-apply data rotation + path_df[c("x", "y")] <- rotate_xy(path_df$x, path_df$y, rotation) path_df } ) @@ -138,6 +143,11 @@ StatContourFilled <- ggproto("StatContourFilled", Stat, }, compute_group = function(data, scales, z.range, bins = NULL, binwidth = NULL, breaks = NULL, na.rm = FALSE) { + + # Undo data rotation + rotation <- estimate_contour_angle(data$x, data$y) + data[c("x", "y")] <- rotate_xy(data$x, data$y, -rotation) + breaks <- contour_breaks(z.range, bins, binwidth, breaks) isobands <- withr::with_options(list(OutDec = "."), xyz_to_isobands(data, breaks)) @@ -149,6 +159,8 @@ StatContourFilled <- ggproto("StatContourFilled", Stat, path_df$level_high <- breaks[as.numeric(path_df$level) + 1] path_df$level_mid <- 0.5*(path_df$level_low + path_df$level_high) path_df$nlevel <- rescale_max(path_df$level_high) + # Re-apply data rotation + path_df[c("x", "y")] <- rotate_xy(path_df$x, path_df$y, rotation) path_df } @@ -356,3 +368,49 @@ contour_deduplicate <- function(data, check = c("x", "y", "group", "PANEL")) { } data } + +estimate_contour_angle <- function(x, y) { + + # Compute most frequent angle among first 20 points + all_angles <- atan2(diff(head(y, 20L)), diff(head(x, 20L))) + freq <- tabulate(match(all_angles, unique(all_angles))) + i <- which.max(freq) + + # If this angle represents less than half of the angles, we probably + # have unordered data, in which case the approach above is invalid + if ((freq[i] / sum(freq)) < 0.5) { + # In such case, try approach with convex hull + hull <- grDevices::chull(x, y) + hull <- c(hull, hull[1]) + # Find largest edge along hull + dx <- diff(x[hull]) + dy <- diff(y[hull]) + i <- which.max(sqrt(dx^2 + dy^2)) + # Take angle of largest edge + angle <- atan2(dy[i], dx[i]) + } else { + angle <- all_angles[i] + } + + # No need to rotate contour data when angle is straight + straight <- abs(angle - c(-1, -0.5, 0, 0.5, 1) * pi) < sqrt(.Machine$double.eps) + if (any(straight)) { + return(0) + } + angle +} + +rotate_xy <- function(x, y, angle) { + # Skip rotation if angle was straight + if (angle == 0) { + return(list(x = x, y = y)) + } + cos <- cos(angle) + sin <- sin(angle) + # Using zapsmall to make `unique0` later recognise values that may have + # rounding errors. + list( + x = zapsmall(cos * x - sin * y, digits = 13), + y = zapsmall(sin * x + cos * y, digits = 13) + ) +} diff --git a/tests/testthat/test-stat-contour.R b/tests/testthat/test-stat-contour.R index b603d5072f..df9a27132c 100644 --- a/tests/testthat/test-stat-contour.R +++ b/tests/testthat/test-stat-contour.R @@ -99,3 +99,26 @@ test_that("stat_contour() removes duplicated coordinates", { expect_equal(new, df[1:4,], ignore_attr = TRUE) }) +test_that("stat_contour() can infer rotations", { + df <- data_frame0( + x = c(0, 1, 2, 1), + y = c(1, 2, 1, 0), + z = c(1, 1, 2, 2) + ) + + ld <- layer_data( + ggplot(df, aes(x, y, z = z)) + geom_contour(breaks = 1.5) + ) + expect_equal(ld$x, c(1.5, 0.5)) + expect_equal(ld$y, c(1.5, 0.5)) + + # Also for unordered data + df <- df[c(1, 4, 2, 3), ] + + ld <- layer_data( + ggplot(df, aes(x, y, z = z)) + geom_contour(breaks = 1.5) + ) + + expect_equal(ld$x, c(0.5, 1.5)) + expect_equal(ld$y, c(0.5, 1.5)) +}) From 926f2906b6987682bb64be4a76b10949e5023596 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:22:36 +0100 Subject: [PATCH 155/264] Deprecate `geom_errorbarh()` (#5961) * copy `geom-errorbarh.R` contents into `geom-errorbar.R` file * rewire `geom_errorbarh()` via `geom_errorbar(orientation = "y")` * is copy of * document `geom_errorbarh()` as deprecated along with rest of interval geoms * throw deprecation warnings * excuse `geom_errorbarh()` from test * document * fix mistakes in passing args * Let `GeomErrorbarh` throw deprecation message with same `id` * test for deprecation messages --- DESCRIPTION | 1 - R/geom-errorbar.R | 44 +++++++++ R/geom-errorbarh.R | 91 ----------------- R/geom-linerange.R | 3 +- man/geom_errorbarh.Rd | 147 ---------------------------- man/geom_linerange.Rd | 20 +++- man/ggplot2-ggproto.Rd | 35 ++++--- tests/testthat/test-function-args.R | 2 +- tests/testthat/test-geom-errorbar.R | 16 +++ 9 files changed, 97 insertions(+), 262 deletions(-) delete mode 100644 R/geom-errorbarh.R delete mode 100644 man/geom_errorbarh.Rd create mode 100644 tests/testthat/test-geom-errorbar.R diff --git a/DESCRIPTION b/DESCRIPTION index 77755980b7..d093ea0e31 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -151,7 +151,6 @@ Collate: 'geom-density2d.R' 'geom-dotplot.R' 'geom-errorbar.R' - 'geom-errorbarh.R' 'geom-freqpoly.R' 'geom-function.R' 'geom-hex.R' diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R index 3e40b20318..7551f0be59 100644 --- a/R/geom-errorbar.R +++ b/R/geom-errorbar.R @@ -23,6 +23,35 @@ geom_errorbar <- function(mapping = NULL, data = NULL, ) } +#' @export +#' @rdname geom_linerange +#' @note +#' `geom_errorbarh()` is `r lifecycle::badge("deprecated")`. Use +#' `geom_errorbar(orientation = "y")` instead. +geom_errorbarh <- function(mapping = NULL, data = NULL, + stat = "identity", position = "identity", + ..., + orientation = "y", + na.rm = FALSE, + show.legend = NA, + inherit.aes = TRUE) { + deprecate_soft0( + "3.5.2", "geom_errobarh()", "geom_errorbar(orientation = \"y\")", + id = "no-more-errorbarh" + ) + geom_errorbar( + mapping = mapping, + data = data, + stat = stat, + position = position, + ..., + orientation = orientation, + na.rm = na.rm, + show.legend = show.legend, + inherit.aes = inherit.aes + ) +} + #' @rdname ggplot2-ggproto #' @format NULL #' @usage NULL @@ -80,3 +109,18 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom, rename_size = TRUE ) + +#' @rdname ggplot2-ggproto +#' @format NULL +#' @usage NULL +#' @export +GeomErrorbarh <- ggproto( + "GeomErrorbarh", GeomErrorbar, + setup_params = function(data, params) { + deprecate_soft0( + "3.5.2", "geom_errobarh()", "geom_errorbar(orientation = \"y\")", + id = "no-more-errorbarh" + ) + GeomLinerange$setup_params(data, params) + } +) diff --git a/R/geom-errorbarh.R b/R/geom-errorbarh.R deleted file mode 100644 index c38b9b7cd6..0000000000 --- a/R/geom-errorbarh.R +++ /dev/null @@ -1,91 +0,0 @@ -#' Horizontal error bars -#' -#' A rotated version of [geom_errorbar()]. -#' -#' @eval rd_aesthetics("geom", "errorbarh") -#' @inheritParams layer -#' @inheritParams geom_point -#' @export -#' @examples -#' df <- data.frame( -#' trt = factor(c(1, 1, 2, 2)), -#' resp = c(1, 5, 3, 4), -#' group = factor(c(1, 2, 1, 2)), -#' se = c(0.1, 0.3, 0.3, 0.2) -#' ) -#' -#' # Define the top and bottom of the errorbars -#' -#' p <- ggplot(df, aes(resp, trt, colour = group)) -#' p + -#' geom_point() + -#' geom_errorbarh(aes(xmax = resp + se, xmin = resp - se)) -#' -#' p + -#' geom_point() + -#' geom_errorbarh(aes(xmax = resp + se, xmin = resp - se, height = .2)) -geom_errorbarh <- function(mapping = NULL, data = NULL, - stat = "identity", position = "identity", - ..., - na.rm = FALSE, - show.legend = NA, - inherit.aes = TRUE) { - layer( - data = data, - mapping = mapping, - stat = stat, - geom = GeomErrorbarh, - position = position, - show.legend = show.legend, - inherit.aes = inherit.aes, - params = list2( - na.rm = na.rm, - ... - ) - ) -} - - -#' @rdname ggplot2-ggproto -#' @format NULL -#' @usage NULL -#' @export -GeomErrorbarh <- ggproto("GeomErrorbarh", Geom, - - default_aes = aes( - colour = from_theme(ink), - linewidth = from_theme(linewidth), - linetype = from_theme(linetype), - height = 0.5, - alpha = NA - ), - - draw_key = draw_key_path, - - required_aes = c("xmin", "xmax", "y"), - - setup_data = function(data, params) { - data$height <- data$height %||% - params$height %||% (resolution(data$y, FALSE, TRUE) * 0.9) - - transform(data, - ymin = y - height / 2, ymax = y + height / 2, height = NULL - ) - }, - - draw_panel = function(self, data, panel_params, coord, height = NULL, lineend = "butt") { - data <- check_linewidth(data, snake_class(self)) - GeomPath$draw_panel(data_frame0( - x = vec_interleave(data$xmax, data$xmax, NA, data$xmax, data$xmin, NA, data$xmin, data$xmin), - y = vec_interleave(data$ymin, data$ymax, NA, data$y, data$y, NA, data$ymin, data$ymax), - colour = rep(data$colour, each = 8), - alpha = rep(data$alpha, each = 8), - linewidth = rep(data$linewidth, each = 8), - linetype = rep(data$linetype, each = 8), - group = rep(1:(nrow(data)), each = 8), - .size = nrow(data) * 8 - ), panel_params, coord, lineend = lineend) - }, - - rename_size = TRUE -) diff --git a/R/geom-linerange.R b/R/geom-linerange.R index 83360800e2..085d8f98a9 100644 --- a/R/geom-linerange.R +++ b/R/geom-linerange.R @@ -11,8 +11,7 @@ #' `geom_pointrange()`. #' @seealso #' [stat_summary()] for examples of these guys in use, -#' [geom_smooth()] for continuous analogue, -#' [geom_errorbarh()] for a horizontal error bar. +#' [geom_smooth()] for continuous analogue #' @export #' @inheritParams layer #' @inheritParams geom_bar diff --git a/man/geom_errorbarh.Rd b/man/geom_errorbarh.Rd deleted file mode 100644 index 4e6fb3aae9..0000000000 --- a/man/geom_errorbarh.Rd +++ /dev/null @@ -1,147 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/geom-errorbarh.R -\name{geom_errorbarh} -\alias{geom_errorbarh} -\title{Horizontal error bars} -\usage{ -geom_errorbarh( - mapping = NULL, - data = NULL, - stat = "identity", - position = "identity", - ..., - na.rm = FALSE, - show.legend = NA, - inherit.aes = TRUE -) -} -\arguments{ -\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}}. If specified and -\code{inherit.aes = TRUE} (the default), it is combined with the default mapping -at the top level of the plot. You must supply \code{mapping} if there is no plot -mapping.} - -\item{data}{The data to be displayed in this layer. There are three -options: - -If \code{NULL}, the default, the data is inherited from the plot -data as specified in the call to \code{\link[=ggplot]{ggplot()}}. - -A \code{data.frame}, or other object, will override the plot -data. All objects will be fortified to produce a data frame. See -\code{\link[=fortify]{fortify()}} for which variables will be created. - -A \code{function} will be called with a single argument, -the plot data. The return value must be a \code{data.frame}, and -will be used as the layer data. A \code{function} can be created -from a \code{formula} (e.g. \code{~ head(.x, 10)}).} - -\item{stat}{The statistical transformation to use on the data for this layer. -When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used to override the default coupling between geoms and -stats. The \code{stat} argument accepts the following: -\itemize{ -\item A \code{Stat} ggproto subclass, for example \code{StatCount}. -\item A string naming the stat. To give the stat as a string, strip the -function name of the \code{stat_} prefix. For example, to use \code{stat_count()}, -give the stat as \code{"count"}. -\item For more information and other ways to specify the stat, see the -\link[=layer_stats]{layer stat} documentation. -}} - -\item{position}{A position adjustment to use on the data for this layer. This -can be used in various ways, including to prevent overplotting and -improving the display. The \code{position} argument accepts the following: -\itemize{ -\item The result of calling a position function, such as \code{position_jitter()}. -This method allows for passing extra arguments to the position. -\item A string naming the position adjustment. To give the position as a -string, strip the function name of the \code{position_} prefix. For example, -to use \code{position_jitter()}, give the position as \code{"jitter"}. -\item For more information and other ways to specify the position, see the -\link[=layer_positions]{layer position} documentation. -}} - -\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}'s \code{params} argument. These -arguments broadly fall into one of 4 categories below. Notably, further -arguments to the \code{position} argument, or aesthetics that are required -can \emph{not} be passed through \code{...}. Unknown arguments that are not part -of the 4 categories below are ignored. -\itemize{ -\item Static aesthetics that are not mapped to a scale, but are at a fixed -value and apply to the layer as a whole. For example, \code{colour = "red"} -or \code{linewidth = 3}. The geom's documentation has an \strong{Aesthetics} -section that lists the available options. The 'required' aesthetics -cannot be passed on to the \code{params}. Please note that while passing -unmapped aesthetics as vectors is technically possible, the order and -required length is not guaranteed to be parallel to the input data. -\item When constructing a layer using -a \verb{stat_*()} function, the \code{...} argument can be used to pass on -parameters to the \code{geom} part of the layer. An example of this is -\code{stat_density(geom = "area", outline.type = "both")}. The geom's -documentation lists which parameters it can accept. -\item Inversely, when constructing a layer using a -\verb{geom_*()} function, the \code{...} argument can be used to pass on parameters -to the \code{stat} part of the layer. An example of this is -\code{geom_area(stat = "density", adjust = 0.5)}. The stat's documentation -lists which parameters it can accept. -\item The \code{key_glyph} argument of \code{\link[=layer]{layer()}} may also be passed on through -\code{...}. This can be one of the functions described as -\link[=draw_key]{key glyphs}, to change the display of the layer in the legend. -}} - -\item{na.rm}{If \code{FALSE}, the default, missing values are removed with -a warning. If \code{TRUE}, missing values are silently removed.} - -\item{show.legend}{logical. Should this layer be included in the legends? -\code{NA}, the default, includes if any aesthetics are mapped. -\code{FALSE} never includes, and \code{TRUE} always includes. -It can also be a named logical vector to finely select the aesthetics to -display. To include legend keys for all levels, even -when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, -but unobserved levels are omitted.} - -\item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, -rather than combining with them. This is most useful for helper functions -that define both data and aesthetics and shouldn't inherit behaviour from -the default plot specification, e.g. \code{\link[=borders]{borders()}}.} -} -\description{ -A rotated version of \code{\link[=geom_errorbar]{geom_errorbar()}}. -} -\section{Aesthetics}{ - -\code{geom_errorbarh()} understands the following aesthetics (required aesthetics are in bold): -\itemize{ -\item \strong{\code{\link[=aes_position]{xmin}}} -\item \strong{\code{\link[=aes_position]{xmax}}} -\item \strong{\code{\link[=aes_position]{y}}} -\item \code{\link[=aes_colour_fill_alpha]{alpha}} -\item \code{\link[=aes_colour_fill_alpha]{colour}} -\item \code{\link[=aes_group_order]{group}} -\item \code{height} -\item \code{\link[=aes_linetype_size_shape]{linetype}} -\item \code{\link[=aes_linetype_size_shape]{linewidth}} -} -Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. -} - -\examples{ -df <- data.frame( - trt = factor(c(1, 1, 2, 2)), - resp = c(1, 5, 3, 4), - group = factor(c(1, 2, 1, 2)), - se = c(0.1, 0.3, 0.3, 0.2) -) - -# Define the top and bottom of the errorbars - -p <- ggplot(df, aes(resp, trt, colour = group)) -p + - geom_point() + - geom_errorbarh(aes(xmax = resp + se, xmin = resp - se)) - -p + - geom_point() + - geom_errorbarh(aes(xmax = resp + se, xmin = resp - se, height = .2)) -} diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index e706dea94b..93f340656e 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -4,6 +4,7 @@ \name{geom_crossbar} \alias{geom_crossbar} \alias{geom_errorbar} +\alias{geom_errorbarh} \alias{geom_linerange} \alias{geom_pointrange} \title{Vertical intervals: lines, crossbars & errorbars} @@ -41,6 +42,18 @@ geom_errorbar( inherit.aes = TRUE ) +geom_errorbarh( + mapping = NULL, + data = NULL, + stat = "identity", + position = "identity", + ..., + orientation = "y", + na.rm = FALSE, + show.legend = NA, + inherit.aes = TRUE +) + geom_linerange( mapping = NULL, data = NULL, @@ -176,6 +189,10 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} Various ways of representing a vertical interval defined by \code{x}, \code{ymin} and \code{ymax}. Each case draws a single graphical object. } +\note{ +\code{geom_errorbarh()} is \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}. Use +\code{geom_errorbar(orientation = "y")} instead. +} \section{Orientation}{ This geom treats each axis differently and, thus, can thus have two orientations. Often the orientation is easy to deduce from a combination of the given mappings and the types of positional scales in use. Thus, ggplot2 will by default try to guess which orientation the layer should have. Under rare circumstances, the orientation is ambiguous and guessing may fail. In that case the orientation can be specified directly using the \code{orientation} parameter, which can be either \code{"x"} or \code{"y"}. The value gives the axis that the geom should run along, \code{"x"} being the default orientation you would expect for the geom. @@ -249,6 +266,5 @@ geom_errorbar( } \seealso{ \code{\link[=stat_summary]{stat_summary()}} for examples of these guys in use, -\code{\link[=geom_smooth]{geom_smooth()}} for continuous analogue, -\code{\link[=geom_errorbarh]{geom_errorbarh()}} for a horizontal error bar. +\code{\link[=geom_smooth]{geom_smooth()}} for continuous analogue } diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd index c3384f1e45..963df0278c 100644 --- a/man/ggplot2-ggproto.Rd +++ b/man/ggplot2-ggproto.Rd @@ -9,24 +9,23 @@ % R/geom-boxplot.R, R/geom-col.R, R/geom-path.R, R/geom-contour.R, % R/geom-crossbar.R, R/geom-segment.R, R/geom-curve.R, R/geom-ribbon.R, % R/geom-density.R, R/geom-density2d.R, R/geom-dotplot.R, R/geom-errorbar.R, -% R/geom-errorbarh.R, R/geom-function.R, R/geom-hex.R, R/geom-hline.R, -% R/geom-label.R, R/geom-linerange.R, R/geom-point.R, R/geom-pointrange.R, -% R/geom-quantile.R, R/geom-rug.R, R/geom-smooth.R, R/geom-spoke.R, -% R/geom-text.R, R/geom-tile.R, R/geom-violin.R, R/geom-vline.R, -% R/guide-.R, R/guide-axis.R, R/guide-axis-logticks.R, R/guide-axis-stack.R, -% R/guide-axis-theta.R, R/guide-legend.R, R/guide-bins.R, R/guide-colorbar.R, -% R/guide-colorsteps.R, R/guide-custom.R, R/guide-none.R, R/guide-old.R, -% R/layout.R, R/position-.R, R/position-dodge.R, R/position-dodge2.R, -% R/position-identity.R, R/position-jitter.R, R/position-jitterdodge.R, -% R/position-nudge.R, R/position-stack.R, R/scale-.R, R/scale-binned.R, -% R/scale-continuous.R, R/scale-date.R, R/scale-discrete-.R, -% R/scale-identity.R, R/stat-align.R, R/stat-bin.R, R/stat-bin2d.R, -% R/stat-bindot.R, R/stat-binhex.R, R/stat-boxplot.R, R/stat-contour.R, -% R/stat-count.R, R/stat-density-2d.R, R/stat-density.R, R/stat-ecdf.R, -% R/stat-ellipse.R, R/stat-function.R, R/stat-identity.R, R/stat-qq-line.R, -% R/stat-qq.R, R/stat-quantilemethods.R, R/stat-smooth.R, R/stat-sum.R, -% R/stat-summary-2d.R, R/stat-summary-bin.R, R/stat-summary-hex.R, -% R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R +% R/geom-function.R, R/geom-hex.R, R/geom-hline.R, R/geom-label.R, +% R/geom-linerange.R, R/geom-point.R, R/geom-pointrange.R, R/geom-quantile.R, +% R/geom-rug.R, R/geom-smooth.R, R/geom-spoke.R, R/geom-text.R, +% R/geom-tile.R, R/geom-violin.R, R/geom-vline.R, R/guide-.R, R/guide-axis.R, +% R/guide-axis-logticks.R, R/guide-axis-stack.R, R/guide-axis-theta.R, +% R/guide-legend.R, R/guide-bins.R, R/guide-colorbar.R, R/guide-colorsteps.R, +% R/guide-custom.R, R/guide-none.R, R/guide-old.R, R/layout.R, R/position-.R, +% R/position-dodge.R, R/position-dodge2.R, R/position-identity.R, +% R/position-jitter.R, R/position-jitterdodge.R, R/position-nudge.R, +% R/position-stack.R, R/scale-.R, R/scale-binned.R, R/scale-continuous.R, +% R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, R/stat-align.R, +% R/stat-bin.R, R/stat-bin2d.R, R/stat-bindot.R, R/stat-binhex.R, +% R/stat-boxplot.R, R/stat-contour.R, R/stat-count.R, R/stat-density-2d.R, +% R/stat-density.R, R/stat-ecdf.R, R/stat-ellipse.R, R/stat-function.R, +% R/stat-identity.R, R/stat-qq-line.R, R/stat-qq.R, R/stat-quantilemethods.R, +% R/stat-smooth.R, R/stat-sum.R, R/stat-summary-2d.R, R/stat-summary-bin.R, +% R/stat-summary-hex.R, R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R \docType{data} \name{ggplot2-ggproto} \alias{ggplot2-ggproto} diff --git a/tests/testthat/test-function-args.R b/tests/testthat/test-function-args.R index 2a78bf9f50..f7be015fa7 100644 --- a/tests/testthat/test-function-args.R +++ b/tests/testthat/test-function-args.R @@ -13,7 +13,7 @@ test_that("geom_xxx and GeomXxx$draw arg defaults match", { geom_fun_names, c("geom_map", "geom_sf", "geom_smooth", "geom_column", "geom_area", "geom_density", "annotation_custom", "annotation_map", "annotation_raster", - "annotation_id") + "annotation_id", "geom_errorbarh") ) # For each geom_xxx function and the corresponding GeomXxx$draw and diff --git a/tests/testthat/test-geom-errorbar.R b/tests/testthat/test-geom-errorbar.R new file mode 100644 index 0000000000..bdfdf3f88d --- /dev/null +++ b/tests/testthat/test-geom-errorbar.R @@ -0,0 +1,16 @@ +test_that("geom_errorbarh throws deprecation messages", { + + lifecycle::expect_deprecated(geom_errorbarh()) + + p <- ggplot( + data.frame(y = "A", min = 0, max = 10), + aes(y = y, xmin = min, xmax = max) + ) + + layer( + geom = "errorbarh", + stat = "identity", + position = "identity" + ) + + lifecycle::expect_deprecated(ggplot_build(p)) +}) From 7b62271adc26af34788800d04b612c56ba42cad7 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 12:02:34 +0100 Subject: [PATCH 156/264] Move {MASS} to Suggests (#5993) * add `check_installed("MASS")` where appropriate * pre-populate parameters * move MASS * conditionally skip that that require MASS * fence in example * Revert "fence in example" This reverts commit 93295f5a3d8c0e45f55023e8179e50298b708072. * fence-in correct piece this time * sneak in forgotten news bullet --- DESCRIPTION | 2 +- NEWS.md | 2 ++ R/stat-density-2d.R | 1 + R/stat-ellipse.R | 8 ++++++++ R/stat-qq.R | 8 ++++++-- man/geom_qq.Rd | 8 ++++++-- tests/testthat/test-stat-density2d.R | 2 ++ tests/testthat/test-stat-ellipsis.R | 2 ++ 8 files changed, 28 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d093ea0e31..585a51285a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -38,7 +38,6 @@ Imports: gtable (>= 0.1.1), isoband, lifecycle (> 1.0.1), - MASS, rlang (>= 1.1.0), scales (>= 1.3.0), stats, @@ -53,6 +52,7 @@ Suggests: knitr, mapproj, maps, + MASS, mgcv, multcomp, munsell, diff --git a/NEWS.md b/NEWS.md index 9d08380189..0eab137d09 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_errorbarh()` is deprecated in favour of + `geom_errorbar(orientation = "y")` (@teunbrand, #5961). * `geom_contour()` should be able to recognise a rotated grid of points (@teunbrand, #4320) * `geom_boxplot()` gains additional arguments to style the colour, linetype and diff --git a/R/stat-density-2d.R b/R/stat-density-2d.R index 3fd6cf60ee..d8bbfed57b 100644 --- a/R/stat-density-2d.R +++ b/R/stat-density-2d.R @@ -138,6 +138,7 @@ StatDensity2d <- ggproto("StatDensity2d", Stat, contour_type = "lines", compute_layer = function(self, data, params, layout) { + check_installed("MASS", reason = "for calculating 2D density.") # first run the regular layer calculation to infer densities data <- ggproto_parent(Stat, self)$compute_layer(data, params, layout) diff --git a/R/stat-ellipse.R b/R/stat-ellipse.R index 7404e9eed6..5d1f41dd55 100644 --- a/R/stat-ellipse.R +++ b/R/stat-ellipse.R @@ -77,6 +77,14 @@ stat_ellipse <- function(mapping = NULL, data = NULL, StatEllipse <- ggproto("StatEllipse", Stat, required_aes = c("x", "y"), + setup_params = function(data, params) { + params$type <- params$type %||% "t" + if (identical(params$type, "t")) { + check_installed("MASS", "for calculating ellipses with `type = \"t\"`.") + } + params + }, + compute_group = function(data, scales, type = "t", level = 0.95, segments = 51, na.rm = FALSE) { calculate_ellipse(data = data, vars = c("x", "y"), type = type, diff --git a/R/stat-qq.R b/R/stat-qq.R index dc3762dacd..4ffab00320 100644 --- a/R/stat-qq.R +++ b/R/stat-qq.R @@ -32,8 +32,12 @@ #' p <- ggplot(df, aes(sample = y)) #' p + stat_qq() + stat_qq_line() #' -#' # Use fitdistr from MASS to estimate distribution params -#' params <- as.list(MASS::fitdistr(df$y, "t")$estimate) +#' # Use fitdistr from MASS to estimate distribution params: +#' # if (requireNamespace("MASS", quietly = TRUE)) { +#' # params <- as.list(MASS::fitdistr(df$y, "t")$estimate) +#' # } +#' # Here, we use pre-computed params +#' params <- list(m = -0.02505057194115, s = 1.122568610124, df = 6.63842653897) #' ggplot(df, aes(sample = y)) + #' stat_qq(distribution = qt, dparams = params["df"]) + #' stat_qq_line(distribution = qt, dparams = params["df"]) diff --git a/man/geom_qq.Rd b/man/geom_qq.Rd index d450b3d948..d6bedf3427 100644 --- a/man/geom_qq.Rd +++ b/man/geom_qq.Rd @@ -214,8 +214,12 @@ df <- data.frame(y = rt(200, df = 5)) p <- ggplot(df, aes(sample = y)) p + stat_qq() + stat_qq_line() -# Use fitdistr from MASS to estimate distribution params -params <- as.list(MASS::fitdistr(df$y, "t")$estimate) +# Use fitdistr from MASS to estimate distribution params: +# if (requireNamespace("MASS", quietly = TRUE)) { +# params <- as.list(MASS::fitdistr(df$y, "t")$estimate) +# } +# Here, we use pre-computed params +params <- list(m = -0.02505057194115, s = 1.122568610124, df = 6.63842653897) ggplot(df, aes(sample = y)) + stat_qq(distribution = qt, dparams = params["df"]) + stat_qq_line(distribution = qt, dparams = params["df"]) diff --git a/tests/testthat/test-stat-density2d.R b/tests/testthat/test-stat-density2d.R index 2ecd50a8cb..b5c41efd7d 100644 --- a/tests/testthat/test-stat-density2d.R +++ b/tests/testthat/test-stat-density2d.R @@ -1,3 +1,5 @@ +skip_if_not_installed("MASS") + test_that("uses scale limits, not data limits", { base <- ggplot(mtcars, aes(wt, mpg)) + stat_density_2d() + diff --git a/tests/testthat/test-stat-ellipsis.R b/tests/testthat/test-stat-ellipsis.R index 0c4406f95c..7615091376 100644 --- a/tests/testthat/test-stat-ellipsis.R +++ b/tests/testthat/test-stat-ellipsis.R @@ -1,3 +1,5 @@ +skip_if_not_installed("MASS") + test_that("stat_ellipsis returns correct data format", { n_seg <- 40 d <- data_frame(x = c(1, 1, 4, 4, 4, 3, 3, 1), y = c(1:4, 1:4), id = rep(1:2, each = 4)) From add05b32b245d2ae8ba2d721690a2f6404601dd8 Mon Sep 17 00:00:00 2001 From: Rodrigo Dal Ben <41629567+RodDalBen@users.noreply.github.com> Date: Mon, 11 Nov 2024 04:35:39 -0700 Subject: [PATCH 157/264] check type for date_breaks and date_minor_breaks (#6044) * check type for date_breaks and date_minor_breaks #5880 * `date_labels` should be string too * add tests * add news bullet --------- Co-authored-by: Teun van den Brand --- NEWS.md | 2 ++ R/scale-date.R | 3 +++ tests/testthat/_snaps/scale-date.md | 26 +++++++++++++++++++++++++- tests/testthat/test-scale-date.R | 17 ++++++++++++++++- 4 files changed, 46 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0eab137d09..3b4926b206 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Date(time) scales now throw appropriate errors when `date_breaks`, + `date_minor_breaks` or `date_labels` are not strings (@RodDalBen, #5880) * `geom_errorbarh()` is deprecated in favour of `geom_errorbar(orientation = "y")` (@teunbrand, #5961). * `geom_contour()` should be able to recognise a rotated grid of points diff --git a/R/scale-date.R b/R/scale-date.R index 36f8b37d83..0decaa4174 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -303,12 +303,15 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), if (is.character(minor_breaks)) minor_breaks <- breaks_width(minor_breaks) if (!is.waive(date_breaks)) { + check_string(date_breaks) breaks <- breaks_width(date_breaks) } if (!is.waive(date_minor_breaks)) { + check_string(date_minor_breaks) minor_breaks <- breaks_width(date_minor_breaks) } if (!is.waive(date_labels)) { + check_string(date_labels) labels <- function(self, x) { tz <- self$timezone %||% "UTC" label_date(date_labels, tz)(x) diff --git a/tests/testthat/_snaps/scale-date.md b/tests/testthat/_snaps/scale-date.md index a2c1e51e73..da37c01413 100644 --- a/tests/testthat/_snaps/scale-date.md +++ b/tests/testthat/_snaps/scale-date.md @@ -1,4 +1,4 @@ -# date(time) scales throw warnings when input is numeric +# date(time) scales throw warnings when input is incorrect A value was passed to a Date scale. i The value was converted to a object. @@ -8,3 +8,27 @@ A value was passed to a Datetime scale. i The value was converted to a object. +--- + + Code + ggplot_build(p + scale_x_date(date_breaks = c(11, 12))) + Condition + Error in `datetime_scale()`: + ! `date_breaks` must be a single string, not a double vector. + +--- + + Code + ggplot_build(p + scale_x_date(date_minor_breaks = c(11, 12))) + Condition + Error in `datetime_scale()`: + ! `date_minor_breaks` must be a single string, not a double vector. + +--- + + Code + ggplot_build(p + scale_x_date(date_labels = c(11, 12))) + Condition + Error in `datetime_scale()`: + ! `date_labels` must be a single string, not a double vector. + diff --git a/tests/testthat/test-scale-date.R b/tests/testthat/test-scale-date.R index 33356545af..a90d203eba 100644 --- a/tests/testthat/test-scale-date.R +++ b/tests/testthat/test-scale-date.R @@ -69,9 +69,24 @@ test_that("datetime colour scales work", { expect_equal(range(get_layer_data(p)$colour), c("#132B43", "#56B1F7")) }) -test_that("date(time) scales throw warnings when input is numeric", { +test_that("date(time) scales throw warnings when input is incorrect", { p <- ggplot(data.frame(x = 1, y = 1), aes(x, y)) + geom_point() expect_snapshot_warning(ggplot_build(p + scale_x_date())) expect_snapshot_warning(ggplot_build(p + scale_x_datetime())) + + expect_snapshot( + ggplot_build(p + scale_x_date(date_breaks = c(11, 12))), + error = TRUE + ) + + expect_snapshot( + ggplot_build(p + scale_x_date(date_minor_breaks = c(11, 12))), + error = TRUE + ) + + expect_snapshot( + ggplot_build(p + scale_x_date(date_labels = c(11, 12))), + error = TRUE + ) }) From eb8bf83cf4427182d621ad104b5d61005ec3af10 Mon Sep 17 00:00:00 2001 From: Carl Suster Date: Mon, 11 Nov 2024 23:48:41 +1100 Subject: [PATCH 158/264] Export `is.waive()` for extensions to use (#6173) * Export is.waive() * Add NEWS bullet about is.waive * Rename is.waive to is.waiver --- NAMESPACE | 1 + NEWS.md | 2 ++ R/axis-secondary.R | 6 +++--- R/coord-sf.R | 10 +++++----- R/facet-null.R | 4 ++-- R/guide-axis-theta.R | 4 ++-- R/guide-custom.R | 2 +- R/labels.R | 2 +- R/layer.R | 4 ++-- R/layout.R | 2 +- R/scale-.R | 14 +++++++------- R/scale-continuous.R | 6 +++--- R/scale-date.R | 18 +++++++++--------- R/scale-discrete-.R | 2 +- R/scale-manual.R | 2 +- R/scale-view.R | 2 +- R/utilities.R | 12 ++++++++---- man/waiver.Rd | 9 ++++++++- 18 files changed, 58 insertions(+), 44 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 852cb97600..63bee440fc 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -475,6 +475,7 @@ export(is.scale) export(is.stat) export(is.theme) export(is.theme_element) +export(is.waiver) export(label_both) export(label_bquote) export(label_context) diff --git a/NEWS.md b/NEWS.md index 3b4926b206..38376bded8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* The helper function `is.waiver()` is now exported to help extensions to work + with `waiver()` objects (@arcresu, #6173). * Date(time) scales now throw appropriate errors when `date_breaks`, `date_minor_breaks` or `date_labels` are not strings (@RodDalBen, #5880) * `geom_errorbarh()` is deprecated in favour of diff --git a/R/axis-secondary.R b/R/axis-secondary.R index 2999bd79b5..401dd5a663 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -129,7 +129,7 @@ is.sec_axis <- function(x) { } set_sec_axis <- function(sec.axis, scale) { - if (!is.waive(sec.axis)) { + if (!is.waiver(sec.axis)) { if (scale$is_discrete()) { if (!identical(.subset2(sec.axis, "trans"), identity)) { cli::cli_abort("Discrete secondary axes must have the {.fn identity} transformation.") @@ -182,9 +182,9 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, if (!is.function(transform)) { cli::cli_abort("Transformation for secondary axes must be a function.") } - if (is.derived(self$name) && !is.waive(scale$name)) self$name <- scale$name + if (is.derived(self$name) && !is.waiver(scale$name)) self$name <- scale$name if (is.derived(self$breaks)) self$breaks <- scale$breaks - if (is.waive(self$breaks)) { + if (is.waiver(self$breaks)) { if (scale$is_discrete()) { self$breaks <- scale$get_breaks() } else { diff --git a/R/coord-sf.R b/R/coord-sf.R index c31af6d393..7d9d2dc2e7 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -108,7 +108,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, x_breaks <- graticule$degree[graticule$type == "E"] if (is.null(scale_x$labels)) { x_labels <- rep(NA, length(x_breaks)) - } else if (is.waive(scale_x$labels)) { + } else if (is.waiver(scale_x$labels)) { x_labels <- graticule$degree_label[graticule$type == "E"] needs_autoparsing[graticule$type == "E"] <- TRUE } else { @@ -133,7 +133,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, y_breaks <- graticule$degree[graticule$type == "N"] if (is.null(scale_y$labels)) { y_labels <- rep(NA, length(y_breaks)) - } else if (is.waive(scale_y$labels)) { + } else if (is.waiver(scale_y$labels)) { y_labels <- graticule$degree_label[graticule$type == "N"] needs_autoparsing[graticule$type == "N"] <- TRUE } else { @@ -534,7 +534,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, label_axes = waiver(), lims_method = "cross", ndiscr = 100, default = FALSE, clip = "on") { - if (is.waive(label_graticule) && is.waive(label_axes)) { + if (is.waiver(label_graticule) && is.waiver(label_axes)) { # if both `label_graticule` and `label_axes` are set to waive then we # use the default of labels on the left and at the bottom label_graticule <- "" @@ -620,13 +620,13 @@ sf_breaks <- function(scale_x, scale_y, bbox, crs) { bbox[is.na(bbox)] <- c(-180, -90, 180, 90)[is.na(bbox)] } - if (!(is.waive(scale_x$breaks) && is.null(scale_x$n.breaks))) { + if (!(is.waiver(scale_x$breaks) && is.null(scale_x$n.breaks))) { x_breaks <- scale_x$get_breaks(limits = bbox[c(1, 3)]) finite <- is.finite(x_breaks) x_breaks <- if (any(finite)) x_breaks[finite] else NULL } - if (!(is.waive(scale_y$breaks) && is.null(scale_y$n.breaks))) { + if (!(is.waiver(scale_y$breaks) && is.null(scale_y$n.breaks))) { y_breaks <- scale_y$get_breaks(limits = bbox[c(2, 4)]) finite <- is.finite(y_breaks) y_breaks <- if (any(finite)) y_breaks[finite] else NULL diff --git a/R/facet-null.R b/R/facet-null.R index c66f39fa03..e263bf0453 100644 --- a/R/facet-null.R +++ b/R/facet-null.R @@ -27,9 +27,9 @@ FacetNull <- ggproto("FacetNull", Facet, layout_null() }, map_data = function(data, layout, params) { - # Need the is.waive check for special case where no data, but aesthetics + # Need the is.waiver check for special case where no data, but aesthetics # are mapped to vectors - if (is.waive(data)) + if (is.waiver(data)) return(data_frame0(PANEL = factor())) if (empty(data)) diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index 2e4f7a6cef..7c7b62a9d0 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -200,7 +200,7 @@ GuideAxisTheta <- ggproto( } # Resolve text angle - if (is.waive(params$angle) || is.null(params$angle)) { + if (is.waiver(params$angle) || is.null(params$angle)) { angle <- elements$text$angle } else { angle <- flip_text_angle(params$angle - rad2deg(key$theta)) @@ -276,7 +276,7 @@ GuideAxisTheta <- ggproto( } # Resolve text angle - if (is.waive(params$angle %||% waiver())) { + if (is.waiver(params$angle %||% waiver())) { angle <- elements$text$angle } else { angle <- flip_text_angle(params$angle - rad2deg(key$theta)) diff --git a/R/guide-custom.R b/R/guide-custom.R index 990712b36b..f602bfc843 100644 --- a/R/guide-custom.R +++ b/R/guide-custom.R @@ -96,7 +96,7 @@ GuideCustom <- ggproto( # Render title params <- replace_null(params, position = position, direction = direction) elems <- GuideLegend$setup_elements(params, self$elements, theme) - if (!is.waive(params$title) && !is.null(params$title)) { + if (!is.waiver(params$title) && !is.null(params$title)) { title <- self$build_title(params$title, elems, params) } else { title <- zeroGrob() diff --git a/R/labels.R b/R/labels.R index 50e3776555..050d42829e 100644 --- a/R/labels.R +++ b/R/labels.R @@ -152,7 +152,7 @@ labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), tag = tag, alt = allow_lambda(alt), alt_insight = alt_insight, .ignore_empty = "all") - is_waive <- vapply(args, is.waive, logical(1)) + is_waive <- vapply(args, is.waiver, logical(1)) args <- args[!is_waive] # remove duplicated arguments args <- args[!duplicated(names(args))] diff --git a/R/layer.R b/R/layer.R index b10c230e1d..639fece4af 100644 --- a/R/layer.R +++ b/R/layer.R @@ -253,7 +253,7 @@ Layer <- ggproto("Layer", NULL, }, layer_data = function(self, plot_data) { - if (is.waive(self$data)) { + if (is.waiver(self$data)) { data <- plot_data } else if (is.function(self$data)) { data <- self$data(plot_data) @@ -263,7 +263,7 @@ Layer <- ggproto("Layer", NULL, } else { data <- self$data } - if (is.null(data) || is.waive(data)) data else unrowname(data) + if (is.null(data) || is.waiver(data)) data else unrowname(data) }, # hook to allow a layer access to the final layer data diff --git a/R/layout.R b/R/layout.R index 1b578111b2..25088798b1 100644 --- a/R/layout.R +++ b/R/layout.R @@ -283,7 +283,7 @@ Layout <- ggproto("Layout", NULL, } else { switch(label, x = ".bottom", y = ".right") } - if (is.null(labels[[label]][[i]]) || is.waive(labels[[label]][[i]])) + if (is.null(labels[[label]][[i]]) || is.waiver(labels[[label]][[i]])) return(zeroGrob()) element_render( diff --git a/R/scale-.R b/R/scale-.R index d7c0f42252..94887df365 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -753,7 +753,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, # don't support conversion to numeric (#5304) if (zero_range(as.numeric(transformation$transform(limits)))) { breaks <- limits[1] - } else if (is.waive(self$breaks)) { + } else if (is.waiver(self$breaks)) { if (!is.null(self$n.breaks) && trans_support_nbreaks(transformation)) { breaks <- transformation$breaks(limits, self$n.breaks) } else { @@ -795,7 +795,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, b <- b[is.finite(b)] transformation <- self$get_transformation() - if (is.waive(self$minor_breaks)) { + if (is.waiver(self$minor_breaks)) { if (is.null(b)) { breaks <- NULL } else { @@ -842,7 +842,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, ) } - if (is.waive(self$labels)) { + if (is.waiver(self$labels)) { labels <- transformation$format(breaks) } else if (is.function(self$labels)) { labels <- self$labels(breaks) @@ -1022,7 +1022,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, ) } - if (is.waive(self$breaks)) { + if (is.waiver(self$breaks)) { breaks <- limits } else if (is.function(self$breaks)) { breaks <- self$breaks(limits) @@ -1084,7 +1084,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, ) } - if (is.waive(self$labels)) { + if (is.waiver(self$labels)) { if (is.numeric(breaks)) { # Only format numbers, because on Windows, format messes up encoding format(breaks, justify = "none") @@ -1244,7 +1244,7 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, "Invalid {.arg breaks} specification. Use {.code NULL}, not {.code NA}.", call = self$call ) - } else if (is.waive(self$breaks)) { + } else if (is.waiver(self$breaks)) { if (self$nice.breaks) { if (!is.null(self$n.breaks) && trans_support_nbreaks(transformation)) { breaks <- transformation$breaks(limits, n = self$n.breaks) @@ -1334,7 +1334,7 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, "Invalid {.arg labels} specification. Use {.code NULL}, not {.code NA}.", call = self$call ) - } else if (is.waive(self$labels)) { + } else if (is.waiver(self$labels)) { labels <- transformation$format(breaks) } else if (is.function(self$labels)) { labels <- self$labels(breaks) diff --git a/R/scale-continuous.R b/R/scale-continuous.R index 9d6eee9ca9..39b5203565 100644 --- a/R/scale-continuous.R +++ b/R/scale-continuous.R @@ -146,21 +146,21 @@ ScaleContinuousPosition <- ggproto("ScaleContinuousPosition", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waive(self$secondary.axis) || self$secondary.axis$empty())) { + if (!(is.waiver(self$secondary.axis) || self$secondary.axis$empty())) { self$secondary.axis$init(self) breaks <- c(breaks, self$secondary.axis$break_info(breaks$range, self)) } breaks }, sec_name = function(self) { - if (is.waive(self$secondary.axis)) { + if (is.waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, title) { - if (!is.waive(self$secondary.axis)) { + if (!is.waiver(self$secondary.axis)) { self$secondary.axis$make_title(title) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(title) diff --git a/R/scale-date.R b/R/scale-date.R index 0decaa4174..436b9b129d 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -302,15 +302,15 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), if (is.character(breaks)) breaks <- breaks_width(breaks) if (is.character(minor_breaks)) minor_breaks <- breaks_width(minor_breaks) - if (!is.waive(date_breaks)) { + if (!is.waiver(date_breaks)) { check_string(date_breaks) breaks <- breaks_width(date_breaks) } - if (!is.waive(date_minor_breaks)) { + if (!is.waiver(date_minor_breaks)) { check_string(date_minor_breaks) minor_breaks <- breaks_width(date_minor_breaks) } - if (!is.waive(date_labels)) { + if (!is.waiver(date_labels)) { check_string(date_labels) labels <- function(self, x) { tz <- self$timezone %||% "UTC" @@ -379,21 +379,21 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waive(self$secondary.axis) || self$secondary.axis$empty())) { + if (!(is.waiver(self$secondary.axis) || self$secondary.axis$empty())) { self$secondary.axis$init(self) breaks <- c(breaks, self$secondary.axis$break_info(breaks$range, self)) } breaks }, sec_name = function(self) { - if (is.waive(self$secondary.axis)) { + if (is.waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, title) { - if (!is.waive(self$secondary.axis)) { + if (!is.waiver(self$secondary.axis)) { self$secondary.axis$make_title(title) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(title) @@ -430,21 +430,21 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waive(self$secondary.axis) || self$secondary.axis$empty())) { + if (!(is.waiver(self$secondary.axis) || self$secondary.axis$empty())) { self$secondary.axis$init(self) breaks <- c(breaks, self$secondary.axis$break_info(breaks$range, self)) } breaks }, sec_name = function(self) { - if (is.waive(self$secondary.axis)) { + if (is.waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, title) { - if (!is.waive(self$secondary.axis)) { + if (!is.waiver(self$secondary.axis)) { self$secondary.axis$make_title(title) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(title) diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index 8fea10caf2..f6fc512f9c 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -170,7 +170,7 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, }, sec_name = function(self) { - if (is.waive(self$secondary.axis)) { + if (is.waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name diff --git a/R/scale-manual.R b/R/scale-manual.R index 7fc9094070..47c647fc02 100644 --- a/R/scale-manual.R +++ b/R/scale-manual.R @@ -171,7 +171,7 @@ manual_scale <- function(aesthetic, values = NULL, breaks = waiver(), } # order values according to breaks - if (is.vector(values) && is.null(names(values)) && !is.waive(breaks) && + if (is.vector(values) && is.null(names(values)) && !is.waiver(breaks) && !is.null(breaks) && !is.function(breaks)) { if (length(breaks) <= length(values)) { names(values) <- breaks diff --git a/R/scale-view.R b/R/scale-view.R index 3cf18147ec..510f99f837 100644 --- a/R/scale-view.R +++ b/R/scale-view.R @@ -45,7 +45,7 @@ view_scale_primary <- function(scale, limits = scale$get_limits(), view_scale_secondary <- function(scale, limits = scale$get_limits(), continuous_range = scale$dimension(limits = limits)) { - if (is.null(scale$secondary.axis) || is.waive(scale$secondary.axis) || scale$secondary.axis$empty()) { + if (is.null(scale$secondary.axis) || is.waiver(scale$secondary.axis) || scale$secondary.axis$empty()) { # if there is no second axis, return the primary scale with no guide # this guide can be overridden using guides() primary_scale <- view_scale_primary(scale, limits, continuous_range) diff --git a/R/utilities.R b/R/utilities.R index 8772ed771b..039376f4df 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -12,7 +12,7 @@ scales::alpha } "%|W|%" <- function(a, b) { - if (!is.waive(a)) a else b + if (!is.waiver(a)) a else b } # Check required aesthetics are present @@ -182,13 +182,17 @@ should_stop <- function(expr) { #' A waiver is a "flag" object, similar to `NULL`, that indicates the #' calling function should just use the default value. It is used in certain #' functions to distinguish between displaying nothing (`NULL`) and -#' displaying a default value calculated elsewhere (`waiver()`) +#' displaying a default value calculated elsewhere (`waiver()`). +#' `is.waiver()` reports whether an object is a waiver. #' #' @export #' @keywords internal waiver <- function() structure(list(), class = "waiver") -is.waive <- function(x) inherits(x, "waiver") +#' @param x An object to test +#' @export +#' @rdname waiver +is.waiver <- function(x) inherits(x, "waiver") pal_binned <- function(palette) { function(x) { @@ -266,7 +270,7 @@ snake_class <- function(x) { } empty <- function(df) { - is.null(df) || nrow(df) == 0 || ncol(df) == 0 || is.waive(df) + is.null(df) || nrow(df) == 0 || ncol(df) == 0 || is.waiver(df) } is.discrete <- function(x) { diff --git a/man/waiver.Rd b/man/waiver.Rd index aeb97bf082..88fa06ba57 100644 --- a/man/waiver.Rd +++ b/man/waiver.Rd @@ -2,14 +2,21 @@ % Please edit documentation in R/utilities.R \name{waiver} \alias{waiver} +\alias{is.waiver} \title{A waiver object.} \usage{ waiver() + +is.waiver(x) +} +\arguments{ +\item{x}{An object to test} } \description{ A waiver is a "flag" object, similar to \code{NULL}, that indicates the calling function should just use the default value. It is used in certain functions to distinguish between displaying nothing (\code{NULL}) and -displaying a default value calculated elsewhere (\code{waiver()}) +displaying a default value calculated elsewhere (\code{waiver()}). +\code{is.waiver()} reports whether an object is a waiver. } \keyword{internal} From 66063903d8e709dc05a1578de25b0845e97366c1 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 14:08:45 +0100 Subject: [PATCH 159/264] Skip viewscales if graticule is empty (#6060) * skip viewscales for empty graticules * add test * add news bullet --- NEWS.md | 1 + R/coord-sf.R | 3 +++ tests/testthat/test-coord_sf.R | 24 ++++++++++++++++++++++++ 3 files changed, 28 insertions(+) diff --git a/NEWS.md b/NEWS.md index 38376bded8..6298f0413e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -199,6 +199,7 @@ `labs()` and several guides (@teunbrand, #3196). * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). * Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) +* `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052) # ggplot2 3.5.1 diff --git a/R/coord-sf.R b/R/coord-sf.R index 7d9d2dc2e7..45cc7a90fb 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -657,6 +657,9 @@ sf_breaks <- function(scale_x, scale_y, bbox, crs) { #' @keywords internal view_scales_from_graticule <- function(graticule, scale, aesthetic, label, label_graticule, bbox) { + if (empty(graticule)) { + return(ggproto(NULL, ViewScale)) + } # Setup position specific parameters # Note that top/bottom doesn't necessarily mean to label the meridians and diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index 12a667be5b..a25d470e3b 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -371,3 +371,27 @@ test_that("coord_sf() throws error when limits are badly specified", { # throws error when limit's length is different than two expect_snapshot_error(ggplot() + coord_sf(ylim=1:3)) }) + +test_that("coord_sf() can render with empty graticules", { + + skip_if_not_installed("sf") + # Skipping this test on CRAN as changes upstream in {sf} might affect + # this test, i.e. when suddenly graticules *do* work + skip_on_cran() + + df <- sf::st_sf( + g = sf::st_sfc(sf::st_point( + # Out of bounds values for lon/lat + c(-600, 1200) + )), + crs = 4326 + ) + + # Double-check graticule is empty, suppressing warnings about oob longlat values + grat <- suppressWarnings(sf::st_graticule(df)) + expect_equal(nrow(grat), 0) + + # Plot should render + p <- suppressWarnings(layer_grob(ggplot(df) + geom_sf())[[1]]) + expect_length(p$x, 1) +}) From 094b957d733e2f0dfd250091982a397a68b32bee Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 11 Nov 2024 14:28:46 +0100 Subject: [PATCH 160/264] Discrete labels from break names (#6148) * return break names * add test * fix #6089 * add news bullet * carry over names * prevent name-dropping * swap `mtfrm()` for `as.character()` --- NEWS.md | 2 ++ R/axis-secondary.R | 4 ++-- R/scale-.R | 6 +++++- tests/testthat/test-scales-breaks-labels.R | 11 +++++++++++ 4 files changed, 20 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 6298f0413e..081504c782 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* When discrete breaks have names, they'll be used as labels by default + (@teunbrand, #6147). * The helper function `is.waiver()` is now exported to help extensions to work with `waiver()` objects (@arcresu, #6173). * Date(time) scales now throw appropriate errors when `date_breaks`, diff --git a/R/axis-secondary.R b/R/axis-secondary.R index 401dd5a663..23d36092b6 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -186,7 +186,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, if (is.derived(self$breaks)) self$breaks <- scale$breaks if (is.waiver(self$breaks)) { if (scale$is_discrete()) { - self$breaks <- scale$get_breaks() + self$breaks <- setNames(nm = scale$get_breaks()) } else { breaks <- scale$get_transformation()$breaks n_breaks <- scale$n.breaks @@ -235,7 +235,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, self$mono_test(scale) breaks <- self$breaks } else { - breaks <- scale$map(self$breaks) + breaks <- setNames(scale$map(self$breaks), names(self$breaks)) } # Get scale's original range before transformation diff --git a/R/scale-.R b/R/scale-.R index 94887df365..b8c03571bd 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -1031,7 +1031,8 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, } # Breaks only occur only on values in domain - in_domain <- intersect(breaks, limits) + breaks <- setNames(as.character(breaks), names(breaks)) + in_domain <- vec_set_intersect(breaks, as.character(limits)) structure(in_domain, pos = match(in_domain, breaks)) }, @@ -1085,6 +1086,9 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, } if (is.waiver(self$labels)) { + if (!is.null(names(breaks))) { + return(names(breaks)) + } if (is.numeric(breaks)) { # Only format numbers, because on Windows, format messes up encoding format(breaks, justify = "none") diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index 899c048e71..42e3d67bb3 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -289,6 +289,17 @@ test_that("equal length breaks and labels can be passed to ViewScales with limit expect_identical(test_view_scale_rev$get_labels(), c(c("0", "20", "40"))) }) +test_that("break names are returned as labels", { + + sc <- scale_x_continuous(breaks = c(A = 10, B = 20, C = 30)) + sc$train(c(10, 30)) + expect_equal(sc$get_labels(), c("A", "B", "C")) + + sc <- scale_x_discrete(breaks = c(foo = "A", bar = "B", qux = "C")) + sc$train(c(LETTERS[1:3])) + expect_equal(sc$get_labels(), c("foo", "bar", "qux")) +}) + # Visual tests ------------------------------------------------------------ test_that("minor breaks draw correctly", { From f46805349d6ca8ca7a99f8966cfa0f29279c2f6c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 13 Nov 2024 09:24:11 +0100 Subject: [PATCH 161/264] `annotation_raster()/_custom()` respond to scale transformations (#6182) * helper for annotation ranges * use helper * update snapshots * use vctrs rules to preserve AsIs * add test * add news bullet * allow mixing AsIs and numeric * clarify AsIs change in news --- NEWS.md | 3 +++ R/annotation-custom.R | 37 +++++++++++++++++++------------ R/annotation-raster.R | 22 ++++++------------ tests/testthat/_snaps/annotate.md | 4 ++-- tests/testthat/test-annotate.R | 29 ++++++++++++++++++++++++ 5 files changed, 64 insertions(+), 31 deletions(-) diff --git a/NEWS.md b/NEWS.md index 081504c782..0c493a8f58 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* Custom and raster annotation now respond to scale transformations, and can + use AsIs variables for relative placement (@teunbrand based on + @yutannihilation's prior work, #3120) * When discrete breaks have names, they'll be used as labels by default (@teunbrand, #6147). * The helper function `is.waiver()` is now exported to help extensions to work diff --git a/R/annotation-custom.R b/R/annotation-custom.R index 4261526b89..76cb26ac2c 100644 --- a/R/annotation-custom.R +++ b/R/annotation-custom.R @@ -70,21 +70,12 @@ GeomCustomAnn <- ggproto("GeomCustomAnn", Geom, draw_panel = function(data, panel_params, coord, grob, xmin, xmax, ymin, ymax) { - if (!inherits(coord, "CoordCartesian")) { - cli::cli_abort("{.fn annotation_custom} only works with {.fn coord_cartesian}.") - } - corners <- data_frame0( - x = c(xmin, xmax), - y = c(ymin, ymax), - .size = 2 + range <- ranges_annotation( + coord, panel_params, xmin, xmax, ymin, ymax, + fun = "annotation_custom" ) - data <- coord$transform(corners, panel_params) - - x_rng <- range(data$x, na.rm = TRUE) - y_rng <- range(data$y, na.rm = TRUE) - - vp <- viewport(x = mean(x_rng), y = mean(y_rng), - width = diff(x_rng), height = diff(y_rng), + vp <- viewport(x = mean(range$x), y = mean(range$y), + width = diff(range$x), height = diff(range$y), just = c("center","center")) editGrob(grob, vp = vp, name = paste(grob$name, annotation_id())) }, @@ -99,3 +90,21 @@ annotation_id <- local({ i } }) + +ranges_annotation <- function(coord, panel_params, xmin, xmax, ymin, ymax, fun) { + if (!inherits(coord, "CoordCartesian")) { + cli::cli_abort("{.fn {fun}} only works with {.fn coord_cartesian}.") + } + data <- data_frame0(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax) + data <- .ignore_data(data)[[1]] + x <- panel_params$x$scale$transform_df(data) + data[names(x)] <- x + y <- panel_params$y$scale$transform_df(data) + data[names(y)] <- y + data <- .expose_data(data)[[1]] + data <- coord$transform(data, panel_params) + list( + x = range(data$xmin, data$xmax, na.rm = TRUE), + y = range(data$ymin, data$ymax, na.rm = TRUE) + ) +} diff --git a/R/annotation-raster.R b/R/annotation-raster.R index 8eb8685883..2635cf05de 100644 --- a/R/annotation-raster.R +++ b/R/annotation-raster.R @@ -73,21 +73,13 @@ GeomRasterAnn <- ggproto("GeomRasterAnn", Geom, draw_panel = function(data, panel_params, coord, raster, xmin, xmax, ymin, ymax, interpolate = FALSE) { - if (!inherits(coord, "CoordCartesian")) { - cli::cli_abort("{.fn annotation_raster} only works with {.fn coord_cartesian}.") - } - corners <- data_frame0( - x = c(xmin, xmax), - y = c(ymin, ymax), - .size = 2 + range <- ranges_annotation( + coord, panel_params, xmin, xmax, ymin, ymax, + fun = "annotation_raster" + ) + rasterGrob(raster, range$x[1], range$y[1], + diff(range$x), diff(range$y), default.units = "native", + just = c("left","bottom"), interpolate = interpolate ) - data <- coord$transform(corners, panel_params) - - x_rng <- range(data$x, na.rm = TRUE) - y_rng <- range(data$y, na.rm = TRUE) - - rasterGrob(raster, x_rng[1], y_rng[1], - diff(x_rng), diff(y_rng), default.units = "native", - just = c("left","bottom"), interpolate = interpolate) } ) diff --git a/tests/testthat/_snaps/annotate.md b/tests/testthat/_snaps/annotate.md index 23c8e0df43..abf4bb83e7 100644 --- a/tests/testthat/_snaps/annotate.md +++ b/tests/testthat/_snaps/annotate.md @@ -2,14 +2,14 @@ Problem while converting geom to grob. i Error occurred in the 1st layer. - Caused by error in `draw_panel()`: + Caused by error in `ranges_annotation()`: ! `annotation_raster()` only works with `coord_cartesian()`. --- Problem while converting geom to grob. i Error occurred in the 1st layer. - Caused by error in `draw_panel()`: + Caused by error in `ranges_annotation()`: ! `annotation_custom()` only works with `coord_cartesian()`. # annotation_map() checks the input data diff --git a/tests/testthat/test-annotate.R b/tests/testthat/test-annotate.R index 129b5b6720..a0200a82d3 100644 --- a/tests/testthat/test-annotate.R +++ b/tests/testthat/test-annotate.R @@ -86,3 +86,32 @@ test_that("annotate() warns about `stat` or `position` arguments", { annotate("point", 1:3, 1:3, stat = "density", position = "dodge") ) }) + +test_that("annotation_custom() and annotation_raster() adhere to scale transforms", { + rast <- matrix(rainbow(10), nrow = 1) + + p <- ggplot() + + annotation_raster(rast, 1, 10, 1, 9) + + scale_x_continuous(transform = "log10", limits = c(0.1, 100), expand = FALSE) + + scale_y_continuous(limits = c(0, 10), expand = FALSE) + ann <- get_layer_grob(p)[[1]] + + expect_equal(as.numeric(ann$x), 1/3) + expect_equal(as.numeric(ann$y), 1/10) + expect_equal(as.numeric(ann$width), 1/3) + expect_equal(as.numeric(ann$height), 8/10) + + rast <- rasterGrob(rast, width = 1, height = 1) + + p <- ggplot() + + annotation_custom(rast, 1, 10, 1, 9) + + scale_x_continuous(transform = "log10", limits = c(0.1, 100), expand = FALSE) + + scale_y_continuous(limits = c(0, 10), expand = FALSE) + ann <- get_layer_grob(p)[[1]]$vp + + expect_equal(as.numeric(ann$x), 1/2) + expect_equal(as.numeric(ann$y), 1/2) + expect_equal(as.numeric(ann$width), 1/3) + expect_equal(as.numeric(ann$height), 8/10) + +}) From 083a17d2f9591dcd895f974e79c06443c072cd27 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Mon, 25 Nov 2024 09:34:30 +0100 Subject: [PATCH 162/264] Fix typos in the vignette (#6198) * Fix typos in the vignette. * Fix two other typos. --- vignettes/articles/faq-annotation.Rmd | 2 +- vignettes/articles/faq-axes.Rmd | 6 +++--- vignettes/articles/faq-reordering.Rmd | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/vignettes/articles/faq-annotation.Rmd b/vignettes/articles/faq-annotation.Rmd index a5a5c61f3c..ff382d40b3 100644 --- a/vignettes/articles/faq-annotation.Rmd +++ b/vignettes/articles/faq-annotation.Rmd @@ -206,7 +206,7 @@ mpg %>% ### How can I display proportions (relative frequencies) instead of counts on a bar plot? -Either calculate the proportions ahead of time and place them on bars using `geom_text()` or let `ggplot()` calculate them for you and then add them to the plot using `stat_coun()` with `geom = "text"`. +Either calculate the proportions ahead of time and place them on bars using `geom_text()` or let `ggplot()` calculate them for you and then add them to the plot using `stat_count()` with `geom = "text"`.
diff --git a/vignettes/articles/faq-axes.Rmd b/vignettes/articles/faq-axes.Rmd index f37195a84f..cf88240cfa 100644 --- a/vignettes/articles/faq-axes.Rmd +++ b/vignettes/articles/faq-axes.Rmd @@ -69,7 +69,7 @@ ggplot(msleep, aes(y = order, x = sleep_total)) + geom_boxplot() ``` -- Dodge axis labels: Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc., and customise the `guide` argument with the `guide_axis()` function. In this case we want to customise the x-axis, and the variable on the x-axis is discrete, so we'll use `scale_x_continuous()`. In the `guide` argument we use the `guide_axis()` and specify how many rows to dodge the labels into with `n.dodge`. This is likely a trial-and-error exercise, depending on the lengths of your labels and the width of your plot. In this case we've settled on 3 rows to render the labels. +- Dodge axis labels: Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc., and customise the `guide` argument with the `guide_axis()` function. In this case we want to customise the x-axis, and the variable on the x-axis is discrete, so we'll use `scale_x_discrete()`. In the `guide` argument we use the `guide_axis()` and specify how many rows to dodge the labels into with `n.dodge`. This is likely a trial-and-error exercise, depending on the lengths of your labels and the width of your plot. In this case we've settled on 3 rows to render the labels. ```{r} #| label: msleep-order-sleep-total-dodge @@ -115,9 +115,9 @@ Suppose we want to remove the axis labels entirely. - Remove x or y axis labels: If you want to modify just one of the axes, you can do so by modifying the components of the `theme()`, setting the elements you want to remove to `element_blank()`. You would replace `x` with `y` for applying the same update to the y-axis. Note the distinction between `axis.title` and `axis.ticks` -- `axis.title` is the name of the variable and `axis.text` is the text accompanying each of the ticks. ```{r} -#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The annotation on the x-axis -#| is abent." +#| is absent." ggplot(msleep, aes(x = order, y = sleep_total)) + geom_boxplot() + theme( diff --git a/vignettes/articles/faq-reordering.Rmd b/vignettes/articles/faq-reordering.Rmd index 3bbc180d6f..964dd6ba08 100644 --- a/vignettes/articles/faq-reordering.Rmd +++ b/vignettes/articles/faq-reordering.Rmd @@ -211,7 +211,7 @@ df <- tibble::tribble( ) ``` -By default, this is how a scatterplot of these looks. +By default, this is how a scatter plot of these looks. Note that the blue circle is partially covered by the yellow triangle since that observation comes later in the dataset. Similarly the black asterisk appears on top of the red square. From 9b07550d875386afdeaa623566ad8bd9ea2d5bd6 Mon Sep 17 00:00:00 2001 From: "Lydia Gibson, MS, GStat" Date: Mon, 25 Nov 2024 02:12:23 -0800 Subject: [PATCH 163/264] Export GeomBin2d (#6048) Fix #5791 --- DESCRIPTION | 2 +- NAMESPACE | 1 + R/geom-bin2d.R | 10 +++++++++- man/ggplot2-ggproto.Rd | 19 ++++++++++--------- 4 files changed, 21 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 585a51285a..c1570b7c4d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -135,6 +135,7 @@ Collate: 'geom-abline.R' 'geom-rect.R' 'geom-bar.R' + 'geom-tile.R' 'geom-bin2d.R' 'geom-blank.R' 'geom-boxplot.R' @@ -167,7 +168,6 @@ Collate: 'geom-smooth.R' 'geom-spoke.R' 'geom-text.R' - 'geom-tile.R' 'geom-violin.R' 'geom-vline.R' 'ggplot2-package.R' diff --git a/NAMESPACE b/NAMESPACE index 63bee440fc..67649360da 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -172,6 +172,7 @@ export(GeomAbline) export(GeomAnnotationMap) export(GeomArea) export(GeomBar) +export(GeomBin2d) export(GeomBlank) export(GeomBoxplot) export(GeomCol) diff --git a/R/geom-bin2d.R b/R/geom-bin2d.R index 2fe756dc96..5a143df51d 100644 --- a/R/geom-bin2d.R +++ b/R/geom-bin2d.R @@ -1,3 +1,6 @@ +#' @include geom-tile.R +NULL + #' Heatmap of 2d bin counts #' #' Divides the plane into rectangles, counts the number of cases in @@ -37,7 +40,7 @@ geom_bin_2d <- function(mapping = NULL, data = NULL, data = data, mapping = mapping, stat = stat, - geom = GeomTile, + geom = GeomBin2d, position = position, show.legend = show.legend, inherit.aes = inherit.aes, @@ -53,3 +56,8 @@ geom_bin_2d <- function(mapping = NULL, data = NULL, #' @usage NULL geom_bin2d <- geom_bin_2d +#' @rdname ggplot2-ggproto +#' @format NULL +#' @usage NULL +#' @export +GeomBin2d <- ggproto("GeomBin2d", GeomTile) diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd index 963df0278c..602ce35e4f 100644 --- a/man/ggplot2-ggproto.Rd +++ b/man/ggplot2-ggproto.Rd @@ -5,14 +5,14 @@ % R/coord-cartesian-.R, R/coord-fixed.R, R/coord-flip.R, R/coord-map.R, % R/coord-polar.R, R/coord-quickmap.R, R/coord-radial.R, R/coord-transform.R, % R/facet-.R, R/facet-grid-.R, R/facet-null.R, R/facet-wrap.R, R/stat-.R, -% R/geom-abline.R, R/geom-rect.R, R/geom-bar.R, R/geom-blank.R, -% R/geom-boxplot.R, R/geom-col.R, R/geom-path.R, R/geom-contour.R, -% R/geom-crossbar.R, R/geom-segment.R, R/geom-curve.R, R/geom-ribbon.R, -% R/geom-density.R, R/geom-density2d.R, R/geom-dotplot.R, R/geom-errorbar.R, -% R/geom-function.R, R/geom-hex.R, R/geom-hline.R, R/geom-label.R, -% R/geom-linerange.R, R/geom-point.R, R/geom-pointrange.R, R/geom-quantile.R, -% R/geom-rug.R, R/geom-smooth.R, R/geom-spoke.R, R/geom-text.R, -% R/geom-tile.R, R/geom-violin.R, R/geom-vline.R, R/guide-.R, R/guide-axis.R, +% R/geom-abline.R, R/geom-rect.R, R/geom-bar.R, R/geom-tile.R, R/geom-bin2d.R, +% R/geom-blank.R, R/geom-boxplot.R, R/geom-col.R, R/geom-path.R, +% R/geom-contour.R, R/geom-crossbar.R, R/geom-segment.R, R/geom-curve.R, +% R/geom-ribbon.R, R/geom-density.R, R/geom-density2d.R, R/geom-dotplot.R, +% R/geom-errorbar.R, R/geom-function.R, R/geom-hex.R, R/geom-hline.R, +% R/geom-label.R, R/geom-linerange.R, R/geom-point.R, R/geom-pointrange.R, +% R/geom-quantile.R, R/geom-rug.R, R/geom-smooth.R, R/geom-spoke.R, +% R/geom-text.R, R/geom-violin.R, R/geom-vline.R, R/guide-.R, R/guide-axis.R, % R/guide-axis-logticks.R, R/guide-axis-stack.R, R/guide-axis-theta.R, % R/guide-legend.R, R/guide-bins.R, R/guide-colorbar.R, R/guide-colorsteps.R, % R/guide-custom.R, R/guide-none.R, R/guide-old.R, R/layout.R, R/position-.R, @@ -55,6 +55,8 @@ \alias{GeomAbline} \alias{GeomRect} \alias{GeomBar} +\alias{GeomTile} +\alias{GeomBin2d} \alias{GeomBlank} \alias{GeomBoxplot} \alias{GeomCol} @@ -86,7 +88,6 @@ \alias{GeomSmooth} \alias{GeomSpoke} \alias{GeomText} -\alias{GeomTile} \alias{GeomViolin} \alias{GeomVline} \alias{Guide} From cf7ec1857c4ba6b3069e3e8dc176bd102b821a04 Mon Sep 17 00:00:00 2001 From: Hiroaki Yutani Date: Tue, 26 Nov 2024 16:21:21 +0900 Subject: [PATCH 164/264] Fix a minor deprecated warning about `trans` arg (#6202) --- tests/testthat/test-scale-binned.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-scale-binned.R b/tests/testthat/test-scale-binned.R index 1f558b6c77..527d862339 100644 --- a/tests/testthat/test-scale-binned.R +++ b/tests/testthat/test-scale-binned.R @@ -47,7 +47,7 @@ test_that("binned limits should not compute out-of-bounds breaks", { test_that("binned scales can use limits and transformations simultaneously (#6144)", { s <- scale_x_binned( limits = function(x) x + 1, - trans = transform_log10() + transform = transform_log10() ) s$train(c(0, 1)) # c(1, 10) in untransformed space out <- s$get_limits() From 3d67907396a48d68928540a51e84607ffb038ad9 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 26 Nov 2024 08:43:19 +0100 Subject: [PATCH 165/264] Deprecate `fortify()` for models (#6193) * mark deprecation in docs * add `broom` to suggests * throw deprecation warnings * highlight {broom} functions in examples * collect in single file * add news bullet --- DESCRIPTION | 4 +- NEWS.md | 4 + R/fortify-lm.R | 87 --------------------- R/fortify-models.R | 169 ++++++++++++++++++++++++++++++++++++++++ R/fortify-multcomp.R | 89 --------------------- man/fortify-multcomp.Rd | 40 ++++++---- man/fortify.lm.Rd | 63 ++++----------- 7 files changed, 215 insertions(+), 241 deletions(-) delete mode 100644 R/fortify-lm.R create mode 100644 R/fortify-models.R delete mode 100644 R/fortify-multcomp.R diff --git a/DESCRIPTION b/DESCRIPTION index c1570b7c4d..84b7e6357b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,6 +44,7 @@ Imports: vctrs (>= 0.6.0), withr (>= 2.5.0) Suggests: + broom, covr, dplyr, ggplot2movies, @@ -126,9 +127,8 @@ Collate: 'facet-grid-.R' 'facet-null.R' 'facet-wrap.R' - 'fortify-lm.R' 'fortify-map.R' - 'fortify-multcomp.R' + 'fortify-models.R' 'fortify-spatial.R' 'fortify.R' 'stat-.R' diff --git a/NEWS.md b/NEWS.md index 0c493a8f58..42b1bfaa98 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* The following methods have been deprecated: `fortify.lm()`, `fortify.glht()`, + `fortify.confint.glht()`, `fortify.summary.glht()` and `fortify.cld()`. It + is recommend to use `broom::augment()` and `broom::tidy()` instead + (@teunbrand, #3816). * Custom and raster annotation now respond to scale transformations, and can use AsIs variables for relative placement (@teunbrand based on @yutannihilation's prior work, #3120) diff --git a/R/fortify-lm.R b/R/fortify-lm.R deleted file mode 100644 index ebfb0334b2..0000000000 --- a/R/fortify-lm.R +++ /dev/null @@ -1,87 +0,0 @@ -#' Supplement the data fitted to a linear model with model fit statistics. -#' -#' If you have missing values in your model data, you may need to refit -#' the model with `na.action = na.exclude`. -#' -#' @return The original data with extra columns: -#' \item{.hat}{Diagonal of the hat matrix} -#' \item{.sigma}{Estimate of residual standard deviation when -#' corresponding observation is dropped from model} -#' \item{.cooksd}{Cooks distance, [cooks.distance()]} -#' \item{.fitted}{Fitted values of model} -#' \item{.resid}{Residuals} -#' \item{.stdresid}{Standardised residuals} -#' @param model linear model -#' @param data data set, defaults to data used to fit model -#' @param ... not used by this method -#' @keywords internal -#' @export -#' @examples -#' mod <- lm(mpg ~ wt, data = mtcars) -#' head(fortify(mod)) -#' head(fortify(mod, mtcars)) -#' -#' plot(mod, which = 1) -#' -#' ggplot(mod, aes(.fitted, .resid)) + -#' geom_point() + -#' geom_hline(yintercept = 0) + -#' geom_smooth(se = FALSE) -#' -#' ggplot(mod, aes(.fitted, .stdresid)) + -#' geom_point() + -#' geom_hline(yintercept = 0) + -#' geom_smooth(se = FALSE) -#' -#' ggplot(fortify(mod, mtcars), aes(.fitted, .stdresid)) + -#' geom_point(aes(colour = factor(cyl))) -#' -#' ggplot(fortify(mod, mtcars), aes(mpg, .stdresid)) + -#' geom_point(aes(colour = factor(cyl))) -#' -#' plot(mod, which = 2) -#' ggplot(mod) + -#' stat_qq(aes(sample = .stdresid)) + -#' geom_abline() -#' -#' plot(mod, which = 3) -#' ggplot(mod, aes(.fitted, sqrt(abs(.stdresid)))) + -#' geom_point() + -#' geom_smooth(se = FALSE) -#' -#' plot(mod, which = 4) -#' ggplot(mod, aes(seq_along(.cooksd), .cooksd)) + -#' geom_col() -#' -#' plot(mod, which = 5) -#' ggplot(mod, aes(.hat, .stdresid)) + -#' geom_vline(linewidth = 2, colour = "white", xintercept = 0) + -#' geom_hline(linewidth = 2, colour = "white", yintercept = 0) + -#' geom_point() + geom_smooth(se = FALSE) -#' -#' ggplot(mod, aes(.hat, .stdresid)) + -#' geom_point(aes(size = .cooksd)) + -#' geom_smooth(se = FALSE, linewidth = 0.5) -#' -#' plot(mod, which = 6) -#' ggplot(mod, aes(.hat, .cooksd)) + -#' geom_vline(xintercept = 0, colour = NA) + -#' geom_abline(slope = seq(0, 3, by = 0.5), colour = "white") + -#' geom_smooth(se = FALSE) + -#' geom_point() -#' -#' ggplot(mod, aes(.hat, .cooksd)) + -#' geom_point(aes(size = .cooksd / .hat)) + -#' scale_size_area() -fortify.lm <- function(model, data = model$model, ...) { - infl <- stats::influence(model, do.coef = FALSE) - data$.hat <- infl$hat - data$.sigma <- infl$sigma - data$.cooksd <- stats::cooks.distance(model, infl) - - data$.fitted <- stats::predict(model) - data$.resid <- stats::resid(model) - data$.stdresid <- stats::rstandard(model, infl) - - data -} diff --git a/R/fortify-models.R b/R/fortify-models.R new file mode 100644 index 0000000000..5a0e95199a --- /dev/null +++ b/R/fortify-models.R @@ -0,0 +1,169 @@ +#' Supplement the data fitted to a linear model with model fit statistics. +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' This method is deprecated because using `broom::augment()` is a better +#' solution to supplement data from a linear model. +#' If you have missing values in your model data, you may need to refit +#' the model with `na.action = na.exclude`. +#' +#' @return The original data with extra columns: +#' \item{.hat}{Diagonal of the hat matrix} +#' \item{.sigma}{Estimate of residual standard deviation when +#' corresponding observation is dropped from model} +#' \item{.cooksd}{Cooks distance, [cooks.distance()]} +#' \item{.fitted}{Fitted values of model} +#' \item{.resid}{Residuals} +#' \item{.stdresid}{Standardised residuals} +#' @param model linear model +#' @param data data set, defaults to data used to fit model +#' @param ... not used by this method +#' @keywords internal +#' @export +#' @examplesIf require("broom") +#' mod <- lm(mpg ~ wt, data = mtcars) +#' +#' # Show augmented model +#' head(augment(mod)) +#' head(fortify(mod)) +#' +#' # Using augment to convert model to ready-to-plot data +#' ggplot(augment(mod), aes(.fitted, .resid)) + +#' geom_point() + +#' geom_hline(yintercept = 0) + +#' geom_smooth(se = FALSE) +#' +#' # Colouring by original data not included in the model +#' ggplot(augment(mod, mtcars), aes(.fitted, .std.resid, colour = factor(cyl))) + +#' geom_point() +fortify.lm <- function(model, data = model$model, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), I("`broom::augment()`") + ) + infl <- stats::influence(model, do.coef = FALSE) + data$.hat <- infl$hat + data$.sigma <- infl$sigma + data$.cooksd <- stats::cooks.distance(model, infl) + + data$.fitted <- stats::predict(model) + data$.resid <- stats::resid(model) + data$.stdresid <- stats::rstandard(model, infl) + + data +} + +#' Fortify methods for objects produced by \pkg{multcomp} +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' This function is deprecated because using `broom::tidy()` is a better +#' solution to convert model objects. +#' +#' @param model an object of class `glht`, `confint.glht`, +#' `summary.glht` or [multcomp::cld()] +#' @param data,... other arguments to the generic ignored in this method. +#' @name fortify-multcomp +#' @keywords internal +#' @examplesIf require("multcomp") && require("broom") +#' amod <- aov(breaks ~ wool + tension, data = warpbreaks) +#' wht <- multcomp::glht(amod, linfct = multcomp::mcp(tension = "Tukey")) +#' +#' tidy(wht) # recommended +#' fortify(wht) +#' +#' ggplot(tidy(wht), aes(contrast, estimate)) + geom_point() +#' +#' ci <- confint(wht) +#' tidy(ci) # recommended +#' fortify(ci) +#' +#' ggplot(tidy(confint(wht)), +#' aes(contrast, estimate, ymin = conf.low, ymax = conf.high)) + +#' geom_pointrange() +#' +#' smry <- summary(wht) +#' tidy(smry) # recommended +#' fortify(smry) +#' +#' ggplot(mapping = aes(contrast, estimate)) + +#' geom_linerange(aes(ymin = conf.low, ymax = conf.high), data = tidy(ci)) + +#' geom_point(aes(size = adj.p.value), data = tidy(smry)) + +#' scale_size(transform = "reverse") +#' +#' cld <- multcomp::cld(wht) +#' tidy(cld) # recommended +#' fortify(cld) +NULL + +#' @method fortify glht +#' @rdname fortify-multcomp +#' @export +fortify.glht <- function(model, data, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), I("`broom::tidy()`") + ) + base::data.frame( + lhs = rownames(model$linfct), + rhs = model$rhs, + estimate = stats::coef(model), + check.names = FALSE, + stringsAsFactors = FALSE + ) +} + +#' @rdname fortify-multcomp +#' @method fortify confint.glht +#' @export +fortify.confint.glht <- function(model, data, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), I("`broom::tidy()`") + ) + coef <- model$confint + colnames(coef) <- to_lower_ascii(colnames(coef)) + + base::data.frame( + lhs = rownames(coef), + rhs = model$rhs, + coef, + check.names = FALSE, + stringsAsFactors = FALSE + ) +} + +#' @method fortify summary.glht +#' @rdname fortify-multcomp +#' @export +fortify.summary.glht <- function(model, data, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), I("`broom::tidy()`") + ) + coef <- as.data.frame( + model$test[c("coefficients", "sigma", "tstat", "pvalues")]) + names(coef) <- c("estimate", "se", "t", "p") + + base::data.frame( + lhs = rownames(coef), + rhs = model$rhs, + coef, + check.names = FALSE, + stringsAsFactors = FALSE + ) +} + + +#' @method fortify cld +#' @rdname fortify-multcomp +#' @export +fortify.cld <- function(model, data, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), I("`broom::tidy()`") + ) + base::data.frame( + lhs = names(model$mcletters$Letters), + letters = model$mcletters$Letters, + check.names = FALSE, + stringsAsFactors = FALSE + ) +} diff --git a/R/fortify-multcomp.R b/R/fortify-multcomp.R deleted file mode 100644 index 79714b2a68..0000000000 --- a/R/fortify-multcomp.R +++ /dev/null @@ -1,89 +0,0 @@ -#' Fortify methods for objects produced by \pkg{multcomp} -#' -#' @param model an object of class `glht`, `confint.glht`, -#' `summary.glht` or [multcomp::cld()] -#' @param data,... other arguments to the generic ignored in this method. -#' @name fortify-multcomp -#' @keywords internal -#' @examples -#' if (require("multcomp")) { -#' amod <- aov(breaks ~ wool + tension, data = warpbreaks) -#' wht <- glht(amod, linfct = mcp(tension = "Tukey")) -#' -#' fortify(wht) -#' ggplot(wht, aes(lhs, estimate)) + geom_point() -#' -#' CI <- confint(wht) -#' fortify(CI) -#' ggplot(CI, aes(lhs, estimate, ymin = lwr, ymax = upr)) + -#' geom_pointrange() -#' -#' fortify(summary(wht)) -#' ggplot(mapping = aes(lhs, estimate)) + -#' geom_linerange(aes(ymin = lwr, ymax = upr), data = CI) + -#' geom_point(aes(size = p), data = summary(wht)) + -#' scale_size(transform = "reverse") -#' -#' cld <- cld(wht) -#' fortify(cld) -#' } -NULL - -#' @method fortify glht -#' @rdname fortify-multcomp -#' @export -fortify.glht <- function(model, data, ...) { - base::data.frame( - lhs = rownames(model$linfct), - rhs = model$rhs, - estimate = stats::coef(model), - check.names = FALSE, - stringsAsFactors = FALSE - ) -} - -#' @rdname fortify-multcomp -#' @method fortify confint.glht -#' @export -fortify.confint.glht <- function(model, data, ...) { - coef <- model$confint - colnames(coef) <- to_lower_ascii(colnames(coef)) - - base::data.frame( - lhs = rownames(coef), - rhs = model$rhs, - coef, - check.names = FALSE, - stringsAsFactors = FALSE - ) -} - -#' @method fortify summary.glht -#' @rdname fortify-multcomp -#' @export -fortify.summary.glht <- function(model, data, ...) { - coef <- as.data.frame( - model$test[c("coefficients", "sigma", "tstat", "pvalues")]) - names(coef) <- c("estimate", "se", "t", "p") - - base::data.frame( - lhs = rownames(coef), - rhs = model$rhs, - coef, - check.names = FALSE, - stringsAsFactors = FALSE - ) -} - - -#' @method fortify cld -#' @rdname fortify-multcomp -#' @export -fortify.cld <- function(model, data, ...) { - base::data.frame( - lhs = names(model$mcletters$Letters), - letters = model$mcletters$Letters, - check.names = FALSE, - stringsAsFactors = FALSE - ) -} diff --git a/man/fortify-multcomp.Rd b/man/fortify-multcomp.Rd index a52dec001c..654e5bbe9a 100644 --- a/man/fortify-multcomp.Rd +++ b/man/fortify-multcomp.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/fortify-multcomp.R +% Please edit documentation in R/fortify-models.R \name{fortify-multcomp} \alias{fortify-multcomp} \alias{fortify.glht} @@ -23,29 +23,41 @@ \item{data, ...}{other arguments to the generic ignored in this method.} } \description{ -Fortify methods for objects produced by \pkg{multcomp} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} + +This function is deprecated because using \code{broom::tidy()} is a better +solution to convert model objects. } \examples{ -if (require("multcomp")) { +\dontshow{if (require("multcomp") && require("broom")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} amod <- aov(breaks ~ wool + tension, data = warpbreaks) -wht <- glht(amod, linfct = mcp(tension = "Tukey")) +wht <- multcomp::glht(amod, linfct = multcomp::mcp(tension = "Tukey")) +tidy(wht) # recommended fortify(wht) -ggplot(wht, aes(lhs, estimate)) + geom_point() -CI <- confint(wht) -fortify(CI) -ggplot(CI, aes(lhs, estimate, ymin = lwr, ymax = upr)) + +ggplot(tidy(wht), aes(contrast, estimate)) + geom_point() + +ci <- confint(wht) +tidy(ci) # recommended +fortify(ci) + +ggplot(tidy(confint(wht)), + aes(contrast, estimate, ymin = conf.low, ymax = conf.high)) + geom_pointrange() -fortify(summary(wht)) -ggplot(mapping = aes(lhs, estimate)) + - geom_linerange(aes(ymin = lwr, ymax = upr), data = CI) + - geom_point(aes(size = p), data = summary(wht)) + +smry <- summary(wht) +tidy(smry) # recommended +fortify(smry) + +ggplot(mapping = aes(contrast, estimate)) + + geom_linerange(aes(ymin = conf.low, ymax = conf.high), data = tidy(ci)) + + geom_point(aes(size = adj.p.value), data = tidy(smry)) + scale_size(transform = "reverse") -cld <- cld(wht) +cld <- multcomp::cld(wht) +tidy(cld) # recommended fortify(cld) -} +\dontshow{\}) # examplesIf} } \keyword{internal} diff --git a/man/fortify.lm.Rd b/man/fortify.lm.Rd index 4a994a6c56..d98b28a07f 100644 --- a/man/fortify.lm.Rd +++ b/man/fortify.lm.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/fortify-lm.R +% Please edit documentation in R/fortify-models.R \name{fortify.lm} \alias{fortify.lm} \title{Supplement the data fitted to a linear model with model fit statistics.} @@ -24,65 +24,30 @@ corresponding observation is dropped from model} \item{.stdresid}{Standardised residuals} } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} + +This method is deprecated because using \code{broom::augment()} is a better +solution to supplement data from a linear model. If you have missing values in your model data, you may need to refit the model with \code{na.action = na.exclude}. } \examples{ +\dontshow{if (require("broom")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} mod <- lm(mpg ~ wt, data = mtcars) -head(fortify(mod)) -head(fortify(mod, mtcars)) - -plot(mod, which = 1) -ggplot(mod, aes(.fitted, .resid)) + - geom_point() + - geom_hline(yintercept = 0) + - geom_smooth(se = FALSE) +# Show augmented model +head(augment(mod)) +head(fortify(mod)) -ggplot(mod, aes(.fitted, .stdresid)) + +# Using augment to convert model to ready-to-plot data +ggplot(augment(mod), aes(.fitted, .resid)) + geom_point() + geom_hline(yintercept = 0) + geom_smooth(se = FALSE) -ggplot(fortify(mod, mtcars), aes(.fitted, .stdresid)) + - geom_point(aes(colour = factor(cyl))) - -ggplot(fortify(mod, mtcars), aes(mpg, .stdresid)) + - geom_point(aes(colour = factor(cyl))) - -plot(mod, which = 2) -ggplot(mod) + - stat_qq(aes(sample = .stdresid)) + - geom_abline() - -plot(mod, which = 3) -ggplot(mod, aes(.fitted, sqrt(abs(.stdresid)))) + - geom_point() + - geom_smooth(se = FALSE) - -plot(mod, which = 4) -ggplot(mod, aes(seq_along(.cooksd), .cooksd)) + - geom_col() - -plot(mod, which = 5) -ggplot(mod, aes(.hat, .stdresid)) + - geom_vline(linewidth = 2, colour = "white", xintercept = 0) + - geom_hline(linewidth = 2, colour = "white", yintercept = 0) + - geom_point() + geom_smooth(se = FALSE) - -ggplot(mod, aes(.hat, .stdresid)) + - geom_point(aes(size = .cooksd)) + - geom_smooth(se = FALSE, linewidth = 0.5) - -plot(mod, which = 6) -ggplot(mod, aes(.hat, .cooksd)) + - geom_vline(xintercept = 0, colour = NA) + - geom_abline(slope = seq(0, 3, by = 0.5), colour = "white") + - geom_smooth(se = FALSE) + +# Colouring by original data not included in the model +ggplot(augment(mod, mtcars), aes(.fitted, .std.resid, colour = factor(cyl))) + geom_point() - -ggplot(mod, aes(.hat, .cooksd)) + - geom_point(aes(size = .cooksd / .hat)) + - scale_size_area() +\dontshow{\}) # examplesIf} } \keyword{internal} From 949d3599c52b17bb74a0dfa0d3dea1c232defa34 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 27 Nov 2024 09:31:18 +0100 Subject: [PATCH 166/264] defend against potentially missing `stroke` default (#6190) --- R/geom-sf.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/geom-sf.R b/R/geom-sf.R index dfc3926153..1d53d67499 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -231,7 +231,7 @@ GeomSf <- ggproto("GeomSf", Geom, point_size[!(is_point | is_collection)] <- data$linewidth[!(is_point | is_collection)] - stroke <- data$stroke * .stroke / 2 + stroke <- (data$stroke %||% rep(0.5, nrow(data))) * .stroke / 2 font_size <- point_size * .pt + stroke linewidth <- data$linewidth * .pt From 4193a50650af5c022616a34daf7a2c983ee28ba0 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:04:18 +0100 Subject: [PATCH 167/264] Non-orthogonal coords preserve AsIs x/y variables (#6206) * exempt some coords from transforming x/y AsIs variables * add tests * add news bullet * throw warning when only one of two variables is AsIs * update snapshot --- NEWS.md | 3 +++ R/coord-.R | 21 +++++++++++++++++++++ R/coord-polar.R | 4 ++++ R/coord-radial.R | 4 ++++ R/coord-sf.R | 4 ++++ tests/testthat/_snaps/coord-polar.md | 4 ++++ tests/testthat/test-coord-polar.R | 25 +++++++++++++++++++++++++ tests/testthat/test-coord_sf.R | 16 ++++++++++++++++ 8 files changed, 81 insertions(+) diff --git a/NEWS.md b/NEWS.md index 42b1bfaa98..65e8c9fc48 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* In non-orthogonal coordinate systems (`coord_sf()`, `coord_polar()` and + `coord_radial()`), using 'AsIs' variables escape transformation when + both `x` and `y` is an 'AsIs' variable (@teunbrand, #6205). * The following methods have been deprecated: `fortify.lm()`, `fortify.glht()`, `fortify.confint.glht()`, `fortify.summary.glht()` and `fortify.cld()`. It is recommend to use `broom::augment()` and `broom::tidy()` instead diff --git a/R/coord-.R b/R/coord-.R index 5e711cf95c..6aa113d3ff 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -284,3 +284,24 @@ check_coord_limits <- function( check_object(limits, is_vector, "a vector", arg = arg, call = call) check_length(limits, 2L, arg = arg, call = call) } + +is_transform_immune <- function(data, coord_name) { + x <- inherits(data$x, "AsIs") + y <- inherits(data$y, "AsIs") + if (!(x || y)) { + # Neither variable is AsIs, so we need to transform + return(FALSE) + } + if (x && y) { + # Both variables are AsIs, so no need to transform + return(TRUE) + } + # We're now in the `xor(x, y)` case + var <- if (x) "x" else "y" + alt <- if (x) "y" else "x" + cli::cli_warn( + "{.fn {coord_name}} cannot respect the {.cls AsIs} class of {.var {var}} \\ + when {.var {alt}} is not also {.cls AsIs}." + ) + return(FALSE) +} diff --git a/R/coord-polar.R b/R/coord-polar.R index f1c8108ddf..aa5e7c538b 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -180,6 +180,10 @@ CoordPolar <- ggproto("CoordPolar", Coord, }, transform = function(self, data, panel_params) { + if (is_transform_immune(data, snake_class(self))) { + return(data) + } + arc <- self$start + c(0, 2 * pi) dir <- self$direction data <- rename_data(self, data) diff --git a/R/coord-radial.R b/R/coord-radial.R index 3a5ccf1ee2..b028822f0e 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -275,6 +275,10 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, transform = function(self, data, panel_params) { + if (is_transform_immune(data, snake_class(self))) { + return(data) + } + data <- rename_data(self, data) bbox <- panel_params$bbox %||% list(x = c(0, 1), y = c(0, 1)) arc <- panel_params$arc %||% c(0, 2 * pi) diff --git a/R/coord-sf.R b/R/coord-sf.R index 45cc7a90fb..2a43d2e5ef 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -77,6 +77,10 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, }, transform = function(self, data, panel_params) { + if (is_transform_immune(data, snake_class(self))) { + return(data) + } + # we need to transform all non-sf data into the correct coordinate system source_crs <- panel_params$default_crs target_crs <- panel_params$crs diff --git a/tests/testthat/_snaps/coord-polar.md b/tests/testthat/_snaps/coord-polar.md index 1e43119dbe..62138ccf99 100644 --- a/tests/testthat/_snaps/coord-polar.md +++ b/tests/testthat/_snaps/coord-polar.md @@ -12,3 +12,7 @@ No appropriate placement found for `r_axis_inside`. i Axis will be placed at panel edge. +# when both x and y are AsIs, they are not transformed + + `coord_radial()` cannot respect the class of `x` when `y` is not also . + diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index da49368108..27b641f964 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -155,6 +155,31 @@ test_that("bounding box calculations are sensible", { ) }) +test_that("when both x and y are AsIs, they are not transformed", { + + p <- ggplot() + + annotate("text", x = I(0.75), y = I(0.25), label = "foo") + + scale_x_continuous(limits = c(0, 10)) + + scale_y_continuous(limits = c(0, 10)) + + grob <- get_layer_grob(p + coord_polar())[[1]] + location <- c(as.numeric(grob$x), as.numeric(grob$y)) + expect_equal(location, c(0.75, 0.25)) + + grob <- get_layer_grob(p + coord_radial())[[1]] + location <- c(as.numeric(grob$x), as.numeric(grob$y)) + expect_equal(location, c(0.75, 0.25)) + + # Check warning is thrown if only one is AsIs + p <- ggplot() + + annotate("text", x = I(0.75), y = 2.5, label = "foo") + + scale_x_continuous(limits = c(0, 10)) + + scale_y_continuous(limits = c(0, 10)) + + coord_radial() + + expect_snapshot_warning(ggplotGrob(p)) + +}) # Visual tests ------------------------------------------------------------ diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index a25d470e3b..70cdbb9d20 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -314,6 +314,22 @@ test_that("sf_transform_xy() works", { }) +test_that("when both x and y are AsIs, they are not transformed", { + + skip_if_not_installed("sf") + + p <- ggplot() + + annotate("text", x = I(0.75), y = I(0.25), label = "foo") + + scale_x_continuous(limits = c(-180, 180)) + + scale_y_continuous(limits = c(-80, 80)) + + coord_sf(default_crs = 4326, crs = 3857) + + grob <- get_layer_grob(p)[[1]] + location <- c(as.numeric(grob$x), as.numeric(grob$y)) + expect_equal(location, c(0.75, 0.25)) + +}) + test_that("coord_sf() can use function breaks and n.breaks", { polygon <- sf::st_sfc( From f9b97036ea2580ae097a26625917b437fc7a515a Mon Sep 17 00:00:00 2001 From: Max Kuhn Date: Mon, 2 Dec 2024 04:22:32 -0500 Subject: [PATCH 168/264] transparent theme (#5018) * theme_transparent * update unit tests * document * new snapshot * transparent fills -> element_blank() * move new theme * adapt theme * update tests * move news bullet * redocument * cleanup duplicated news entry --------- Co-authored-by: Teun van den Brand --- NAMESPACE | 1 + NEWS.md | 1 + R/theme-defaults.R | 35 +++++++ man/ggtheme.Rd | 11 +++ tests/testthat/_snaps/prohibited-functions.md | 4 + .../_snaps/theme/theme-transparent-large.svg | 92 +++++++++++++++++++ .../_snaps/theme/theme-transparent.svg | 92 +++++++++++++++++++ tests/testthat/test-theme.R | 6 ++ 8 files changed, 242 insertions(+) create mode 100644 tests/testthat/_snaps/theme/theme-transparent-large.svg create mode 100644 tests/testthat/_snaps/theme/theme-transparent.svg diff --git a/NAMESPACE b/NAMESPACE index 67649360da..becf512278 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -721,6 +721,7 @@ export(theme_minimal) export(theme_replace) export(theme_set) export(theme_test) +export(theme_transparent) export(theme_update) export(theme_void) export(transform_position) diff --git a/NEWS.md b/NEWS.md index 65e8c9fc48..b40ea07f25 100644 --- a/NEWS.md +++ b/NEWS.md @@ -212,6 +212,7 @@ * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). * Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) * `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052) +* Added `theme_transparent()` with transparent backgrounds (@topepo). # ggplot2 3.5.1 diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 8be7999d4d..88aa05146b 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -497,6 +497,41 @@ theme_classic <- function(base_size = 11, base_family = "", ) } +#' @export +#' @rdname ggtheme +theme_transparent <- function(base_size = 11, base_family = "", + header_family = NULL, + base_line_size = base_size / 22, + base_rect_size = base_size / 22, + ink = "black", paper = alpha(ink, 0)) { + force(ink) + # Based on theme_bw + theme_grey( + base_size = base_size, + base_family = base_family, + header_family = header_family, + base_line_size = base_line_size, + base_rect_size = base_rect_size, + ink = ink, paper = paper + ) %+replace% + theme( + panel.background = element_blank(), + plot.background = element_blank(), + legend.background = element_blank(), + legend.key = element_blank(), + # theme_bw specifications + panel.border = element_rect(fill = NA, colour = col_mix(ink, paper, 0.20)), + # make gridlines dark, same contrast with white as in theme_grey + panel.grid = element_line(colour = col_mix(ink, paper, 0.92)), + # contour strips to match panel contour + strip.background = element_rect( + fill = col_mix(ink, paper, 0.85), + colour = col_mix(ink, paper, 0.20), + ), + complete = TRUE + ) +} + #' @export #' @rdname ggtheme theme_void <- function(base_size = 11, base_family = "", diff --git a/man/ggtheme.Rd b/man/ggtheme.Rd index e86accb182..57dd519355 100644 --- a/man/ggtheme.Rd +++ b/man/ggtheme.Rd @@ -9,6 +9,7 @@ \alias{theme_dark} \alias{theme_minimal} \alias{theme_classic} +\alias{theme_transparent} \alias{theme_void} \alias{theme_test} \title{Complete themes} @@ -93,6 +94,16 @@ theme_classic( paper = "white" ) +theme_transparent( + base_size = 11, + base_family = "", + header_family = NULL, + base_line_size = base_size/22, + base_rect_size = base_size/22, + ink = "black", + paper = alpha(ink, 0) +) + theme_void( base_size = 11, base_family = "", diff --git a/tests/testthat/_snaps/prohibited-functions.md b/tests/testthat/_snaps/prohibited-functions.md index afc77c3c60..007e6521c4 100644 --- a/tests/testthat/_snaps/prohibited-functions.md +++ b/tests/testthat/_snaps/prohibited-functions.md @@ -219,6 +219,10 @@ [1] "base_size" "base_family" "header_family" "base_line_size" [5] "base_rect_size" + $theme_transparent + [1] "base_size" "base_family" "header_family" "base_line_size" + [5] "base_rect_size" + $theme_void [1] "base_size" "base_family" "header_family" "base_line_size" [5] "base_rect_size" diff --git a/tests/testthat/_snaps/theme/theme-transparent-large.svg b/tests/testthat/_snaps/theme/theme-transparent-large.svg new file mode 100644 index 0000000000..ebf6962840 --- /dev/null +++ b/tests/testthat/_snaps/theme/theme-transparent-large.svg @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1 + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + +x +y +z + + +a +b +theme_transparent_large + + diff --git a/tests/testthat/_snaps/theme/theme-transparent.svg b/tests/testthat/_snaps/theme/theme-transparent.svg new file mode 100644 index 0000000000..067326449a --- /dev/null +++ b/tests/testthat/_snaps/theme/theme-transparent.svg @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +1 + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +1.0 +1.5 +2.0 +2.5 +3.0 + + + + + +x +y +z + + +a +b +theme_transparent + + diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index cf98a1bb3f..2f7f7874f9 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -350,6 +350,7 @@ test_that("all elements in complete themes have inherit.blank=TRUE", { expect_true(inherit_blanks(theme_linedraw())) expect_true(inherit_blanks(theme_minimal())) expect_true(inherit_blanks(theme_void())) + expect_true(inherit_blanks(theme_transparent())) }) test_that("elements can be merged", { @@ -496,6 +497,9 @@ test_that("provided themes explicitly define all elements", { t <- theme_test() expect_true(all(names(t) %in% elements)) + + t <- theme_transparent() + expect_true(all(names(t) %in% elements)) }) test_that("Theme elements are checked during build", { @@ -661,6 +665,7 @@ test_that("themes don't change without acknowledgement", { expect_doppelganger("theme_light", plot + theme_light()) expect_doppelganger("theme_void", plot + theme_void()) expect_doppelganger("theme_linedraw", plot + theme_linedraw()) + expect_doppelganger("theme_transparent", plot + theme_transparent()) }) test_that("themes look decent at larger base sizes", { @@ -677,6 +682,7 @@ test_that("themes look decent at larger base sizes", { expect_doppelganger("theme_light_large", plot + theme_light(base_size = 33)) expect_doppelganger("theme_void_large", plot + theme_void(base_size = 33)) expect_doppelganger("theme_linedraw_large", plot + theme_linedraw(base_size = 33)) + expect_doppelganger("theme_transparent_large", plot + theme_transparent(base_size = 33)) }) test_that("setting 'spacing' and 'margins' affect the whole plot", { From f13d9ab2ad60476e3df2ffbc907192ef5dac1cef Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 11:04:07 +0100 Subject: [PATCH 169/264] Fix expression labels in `guide_coloursteps()` and `guide_bins()` (#6007) * cast expressions to lists * additional workaround for expressions * linearise discrete `get_labels()` logic * scales cast expressions as lists * alleviate wrangling label expressions * fix deprecated argument name * add news bullets * revert even.steps logic --- NEWS.md | 2 ++ R/guide-.R | 7 +----- R/guide-axis-theta.R | 2 +- R/guide-bins.R | 4 +-- R/scale-.R | 60 ++++++++++++++++++++------------------------ 5 files changed, 33 insertions(+), 42 deletions(-) diff --git a/NEWS.md b/NEWS.md index b40ea07f25..36ab09933e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Binned guides now accept expressions as labels (@teunbrand, #6005) +* (internal) `Scale$get_labels()` format expressions as lists. * In non-orthogonal coordinate systems (`coord_sf()`, `coord_polar()` and `coord_radial()`), using 'AsIs' variables escape transformation when both `x` and `y` is an 'AsIs' variable (@teunbrand, #6205). diff --git a/R/guide-.R b/R/guide-.R index fc002c33d2..aa2aa7b37d 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -225,13 +225,8 @@ Guide <- ggproto( mapped <- scale$map(breaks) labels <- scale$get_labels(breaks) - # {vctrs} doesn't play nice with expressions, convert to list. - # see also https://github.com/r-lib/vctrs/issues/559 - if (is.expression(labels)) { - labels <- as.list(labels) - } - key <- data_frame(mapped, .name_repair = ~ aesthetic) + key <- data_frame(!!aesthetic := mapped) key$.value <- breaks key$.label <- labels diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index 7c7b62a9d0..dc4e1b405d 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -110,7 +110,7 @@ GuideAxisTheta <- ggproto( # labels of these positions ends_apart <- (key$theta[n] - key$theta[1]) %% (2 * pi) if (n > 0 && ends_apart < 0.05 && !is.null(key$.label)) { - if (is.expression(key$.label)) { + if (is.expression(key$.label[[1]])) { combined <- substitute( paste(a, "/", b), list(a = key$.label[[1]], b = key$.label[[n]]) diff --git a/R/guide-bins.R b/R/guide-bins.R index 0124ea6052..5bc695b010 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -161,7 +161,7 @@ GuideBins <- ggproto( key$.show <- NA labels <- scale$get_labels(breaks) - if (is.character(scale$labels) || is.numeric(scale$labels)) { + if (is.character(scale$labels) || is.numeric(scale$labels) || is.expression(scale$labels)) { limit_lab <- c(NA, NA) } else { limit_lab <- scale$get_labels(limits) @@ -265,7 +265,7 @@ GuideBins <- ggproto( list(labels = flip_element_grob( elements$text, - label = key$.label, + label = validate_labels(key$.label), x = unit(key$.value, "npc"), margin_x = FALSE, margin_y = TRUE, diff --git a/R/scale-.R b/R/scale-.R index b8c03571bd..33752f9ec2 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -861,12 +861,9 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, labels[lengths(labels) == 0] <- "" # Make sure each element is scalar labels <- lapply(labels, `[`, 1) - - if (any(vapply(labels, is.language, logical(1)))) { - labels <- inject(expression(!!!labels)) - } else { - labels <- unlist(labels) - } + } + if (is.expression(labels)) { + labels <- as.list(labels) } labels @@ -1074,48 +1071,42 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, return(NULL) } - if (is.null(self$labels)) { + labels <- self$labels + if (is.null(labels)) { return(NULL) } - if (identical(self$labels, NA)) { + if (identical(labels, NA)) { cli::cli_abort( "Invalid {.arg labels} specification. Use {.code NULL}, not {.code NA}.", call = self$call ) } - if (is.waiver(self$labels)) { + if (is.waiver(labels)) { if (!is.null(names(breaks))) { - return(names(breaks)) - } - if (is.numeric(breaks)) { + labels <- names(breaks) + } else if (is.numeric(breaks)) { # Only format numbers, because on Windows, format messes up encoding - format(breaks, justify = "none") + labels <- format(breaks, justify = "none") } else { - as.character(breaks) + labels <- as.character(breaks) } - } else if (is.function(self$labels)) { - self$labels(breaks) - } else { - if (!is.null(names(self$labels))) { - # If labels have names, use them to match with breaks - labels <- breaks - - map <- match(names(self$labels), labels, nomatch = 0) - labels[map] <- self$labels[map != 0] - labels - } else { - labels <- self$labels + } else if (is.function(labels)) { + labels <- labels(breaks) + } else if (!is.null(names(labels))) { + # If labels have names, use them to match with breaks + map <- match(names(self$labels), breaks, nomatch = 0) + labels <- replace(breaks, map, labels[map != 0]) + } else if (!is.null(attr(breaks, "pos"))) { + # Need to ensure that if breaks were dropped, corresponding labels are too + labels <- labels[attr(breaks, "pos")] + } - # Need to ensure that if breaks were dropped, corresponding labels are too - pos <- attr(breaks, "pos") - if (!is.null(pos)) { - labels <- labels[pos] - } - labels - } + if (is.expression(labels)) { + labels <- as.list(labels) } + labels }, clone = function(self) { @@ -1351,6 +1342,9 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, call = self$call ) } + if (is.expression(labels)) { + labels <- as.list(labels) + } labels }, From 1bb923099e5d44b21615431f07bb99894e7a7dfd Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 11:14:57 +0100 Subject: [PATCH 170/264] Scale palettes from theme (#5946) * add palette theme elements * set palettes * expand options for numeric palettes * backward compatibility for `options()` default scales * use explicit scales in tests * standard colour scales have `palette = NULL` * document * properly document this time * misc fixes * more palettes in theme * use binned versions of discrete palettes for continuous linetype/shape * Set default palettes to `NULL` * tweak test to populate palettes * try registered theme palettes * document * remove redundant call to `plot_theme()` * simplify `fallback_palette()` args * Put in shims for scales/#427 * Streamline `ScalesList$set_palettes()` method * try to match first non-null aesthetic * add news bullet --- NEWS.md | 3 + R/geom-text.R | 2 +- R/plot-build.R | 1 + R/scale-.R | 1 + R/scale-alpha.R | 35 +-- R/scale-colour.R | 216 ++++++++++-------- R/scale-hue.R | 57 ++--- R/scale-linetype.R | 4 +- R/scale-linewidth.R | 35 +-- R/scale-shape.R | 8 +- R/scale-size.R | 38 +-- R/scales-.R | 33 +++ R/theme-elements.R | 15 ++ R/utilities.R | 62 ++++- man/geom_text.Rd | 2 +- man/scale_alpha.Rd | 8 +- man/scale_colour_continuous.Rd | 45 +++- man/scale_colour_discrete.Rd | 20 +- man/scale_linewidth.Rd | 4 +- man/scale_shape.Rd | 2 +- man/scale_size.Rd | 4 +- .../_snaps/scale-colour-continuous.md | 2 - tests/testthat/_snaps/scale-discrete.md | 8 +- tests/testthat/test-guide-colorbar.R | 2 +- tests/testthat/test-guide-legend.R | 13 +- tests/testthat/test-scales.R | 24 ++ 26 files changed, 427 insertions(+), 217 deletions(-) diff --git a/NEWS.md b/NEWS.md index 36ab09933e..2bd655a5c1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -215,6 +215,9 @@ * Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) * `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052) * Added `theme_transparent()` with transparent backgrounds (@topepo). +* New theme elements `palette.{aes}.discrete` and `palette.{aes}.continuous`. + Theme palettes replace palettes in scales where `palette = NULL`, which is + the new default in many scales (@teunbrand, #4696). # ggplot2 3.5.1 diff --git a/R/geom-text.R b/R/geom-text.R index ed378734ba..78e601f8f9 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -95,7 +95,7 @@ #' # Add aesthetic mappings #' p + geom_text(aes(colour = factor(cyl))) #' p + geom_text(aes(colour = factor(cyl))) + -#' scale_colour_discrete(l = 40) +#' scale_colour_hue(l = 40) #' p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") #' #' # Scale size of text, and change legend key glyph from a to point diff --git a/R/plot-build.R b/R/plot-build.R index 873f79a32c..b55c599198 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -106,6 +106,7 @@ ggplot_build.ggplot <- function(plot) { # Train and map non-position scales and guides npscales <- scales$non_position_scales() if (npscales$n() > 0) { + npscales$set_palettes(plot$theme) lapply(data, npscales$train_df) plot$guides <- plot$guides$build(npscales, plot$layers, plot$labels, data, plot$theme) data <- lapply(data, npscales$map_df) diff --git a/R/scale-.R b/R/scale-.R index 33752f9ec2..f345310e4b 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -528,6 +528,7 @@ Scale <- ggproto("Scale", NULL, if (empty(df)) { return() } + self$palette <- self$palette %||% fallback_palette(self) aesthetics <- intersect(self$aesthetics, names(df)) names(aesthetics) <- aesthetics diff --git a/R/scale-alpha.R b/R/scale-alpha.R index 53344f23be..5e22937e88 100644 --- a/R/scale-alpha.R +++ b/R/scale-alpha.R @@ -31,8 +31,9 @@ #' #' # Changing the title #' p + scale_alpha("cylinders") -scale_alpha <- function(name = waiver(), ..., range = c(0.1, 1)) { - continuous_scale("alpha", name = name, palette = pal_rescale(range), ...) +scale_alpha <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_rescale(range) else NULL + continuous_scale("alpha", name = name, palette = palette, ...) } #' @rdname scale_alpha @@ -41,8 +42,9 @@ scale_alpha_continuous <- scale_alpha #' @rdname scale_alpha #' @export -scale_alpha_binned <- function(name = waiver(), ..., range = c(0.1, 1)) { - binned_scale("alpha", name = name, palette = pal_rescale(range), ...) +scale_alpha_binned <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_rescale(range) else NULL + binned_scale("alpha", name = name, palette = palette, ...) } #' @rdname scale_alpha @@ -56,32 +58,33 @@ scale_alpha_discrete <- function(...) { #' @rdname scale_alpha #' @export -scale_alpha_ordinal <- function(name = waiver(), ..., range = c(0.1, 1)) { - discrete_scale( - "alpha", name = name, - palette = function(n) seq(range[1], range[2], length.out = n), - ... - ) +scale_alpha_ordinal <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) { + function(n) seq(range[1], range[2], length.out = n) + } else { + NULL + } + discrete_scale("alpha", name = name, palette = palette, ...) } #' @rdname scale_alpha #' @export #' @usage NULL -scale_alpha_datetime <- function(name = waiver(), ..., range = c(0.1, 1)) { +scale_alpha_datetime <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( aesthetics = "alpha", transform = "time", name = name, - palette = pal_rescale(range), - ... + palette = palette, ... ) } #' @rdname scale_alpha #' @export #' @usage NULL -scale_alpha_date <- function(name = waiver(), ..., range = c(0.1, 1)){ +scale_alpha_date <- function(name = waiver(), ..., range = NULL){ + palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( aesthetics = "alpha", transform = "date", name = name, - palette = pal_rescale(range), - ... + palette = palette, ... ) } diff --git a/R/scale-colour.R b/R/scale-colour.R index 19cdda1396..a17d872dbe 100644 --- a/R/scale-colour.R +++ b/R/scale-colour.R @@ -27,6 +27,7 @@ #' you want to manually set the colors of a scale, consider using #' [scale_colour_gradient()] or [scale_colour_steps()]. #' +#' @inheritParams continuous_scale #' @param ... Additional parameters passed on to the scale type #' @param type One of the following: #' * "gradient" (the default) @@ -77,122 +78,81 @@ #' v #' options(ggplot2.continuous.fill = tmp) # restore previous setting #' @export -scale_colour_continuous <- function(..., +scale_colour_continuous <- function(..., aesthetics = "colour", + guide = "colourbar", na.value = "grey50", type = getOption("ggplot2.continuous.colour")) { - type <- type %||% "gradient" - args <- list2(...) - args$call <- args$call %||% current_call() - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type(exec(type, !!!args), "scale_colour_continuous", "colour") - } else if (identical(type, "gradient")) { - exec(scale_colour_gradient, !!!args) - } else if (identical(type, "viridis")) { - exec(scale_colour_viridis_c, !!!args) - } else { - cli::cli_abort(c( - "Unknown scale type: {.val {type}}", - "i" = "Use either {.val gradient} or {.val viridis}." - )) + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., guide = guide, na.value = na.value, scale = type, + aesthetic = "colour", type = "continuous" + ) + return(scale) } + + continuous_scale( + aesthetics, palette = NULL, guide = guide, na.value = na.value, + ... + ) } #' @rdname scale_colour_continuous #' @export -scale_fill_continuous <- function(..., +scale_fill_continuous <- function(..., aesthetics = "fill", guide = "colourbar", + na.value = "grey50", type = getOption("ggplot2.continuous.fill")) { - type <- type %||% "gradient" - args <- list2(...) - args$call <- args$call %||% current_call() - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type(exec(type, !!!args), "scale_fill_continuous", "fill") - } else if (identical(type, "gradient")) { - exec(scale_fill_gradient, !!!args) - } else if (identical(type, "viridis")) { - exec(scale_fill_viridis_c, !!!args) - } else { - cli::cli_abort(c( - "Unknown scale type: {.val {type}}", - "i" = "Use either {.val gradient} or {.val viridis}." - )) + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., guide = guide, na.value = na.value, scale = type, + aesthetic = "fill", type = "continuous" + ) + return(scale) } + + continuous_scale( + aesthetics, palette = NULL, guide = guide, na.value = na.value, + ... + ) } #' @export #' @rdname scale_colour_continuous -scale_colour_binned <- function(..., +scale_colour_binned <- function(..., aesthetics = "colour", guide = "coloursteps", + na.value = "grey50", type = getOption("ggplot2.binned.colour")) { - args <- list2(...) - args$call <- args$call %||% current_call() - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type(exec(type, !!!args), "scale_colour_binned", "colour") - } else { - type_fallback <- getOption("ggplot2.continuous.colour", default = "gradient") - # don't use fallback from scale_colour_continuous() if it is - # a function, since that would change the type of the color - # scale from binned to continuous - if (is.function(type_fallback)) { - type_fallback <- "gradient" - } - type <- type %||% type_fallback - - if (identical(type, "gradient")) { - exec(scale_colour_steps, !!!args) - } else if (identical(type, "viridis")) { - exec(scale_colour_viridis_b, !!!args) - } else { - cli::cli_abort(c( - "Unknown scale type: {.val {type}}", - "i" = "Use either {.val gradient} or {.val viridis}." - )) - } + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., guide = guide, na.value = na.value, scale = type, + aesthetic = "colour", type = "binned" + ) + return(scale) } + + binned_scale( + aesthetics, palette = NULL, guide = guide, na.value = na.value, + ... + ) } #' @export #' @rdname scale_colour_continuous -scale_fill_binned <- function(..., +scale_fill_binned <- function(..., aesthetics = "fill", guide = "coloursteps", + na.value = "grey50", type = getOption("ggplot2.binned.fill")) { - args <- list2(...) - args$call <- args$call %||% current_call() - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type(exec(type, !!!args), "scale_fill_binned", "fill") - } else { - type_fallback <- getOption("ggplot2.continuous.fill", default = "gradient") - # don't use fallback from scale_colour_continuous() if it is - # a function, since that would change the type of the color - # scale from binned to continuous - if (is.function(type_fallback)) { - type_fallback <- "gradient" - } - type <- type %||% type_fallback - - if (identical(type, "gradient")) { - exec(scale_fill_steps, !!!args) - } else if (identical(type, "viridis")) { - exec(scale_fill_viridis_b, !!!args) - } else { - cli::cli_abort(c( - "Unknown scale type: {.val {type}}", - "i" = "Use either {.val gradient} or {.val viridis}." - )) - } + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., guide = guide, na.value = na.value, scale = type, + aesthetic = "fill", type = "binned" + ) + return(scale) } -} + binned_scale( + aesthetics, palette = NULL, guide = guide, na.value = na.value, + ... + ) +} # helper function to make sure that the provided scale is of the correct # type (i.e., is continuous and works with the provided aesthetic) @@ -222,3 +182,73 @@ check_scale_type <- function(scale, name, aesthetic, scale_is_discrete = FALSE, scale } + +# helper function for backwards compatibility through setting defaults +# scales through `options()` instead of `theme()`. +scale_backward_compatibility <- function(..., scale, aesthetic, type) { + aesthetic <- standardise_aes_names(aesthetic[1]) + + args <- list2(...) + args$call <- args$call %||% caller_call() %||% current_call() + + if (type == "binned") { + fallback <- getOption( + paste("ggplot2", type, aesthetic, sep = "."), + default = "gradient" + ) + if (is.function(fallback)) { + fallback <- "gradient" + } + scale <- scale %||% fallback + } + + if (is_bare_string(scale)) { + if (scale == "continuous") { + scale <- "gradient" + } + if (scale == "discrete") { + scale <- "hue" + } + if (scale == "viridis") { + scale <- switch( + type, discrete = "viridis_d", binned = "viridis_b", "viridis_c" + ) + } + + candidates <- paste("scale", aesthetic, scale, sep = "_") + for (candi in candidates) { + f <- find_global(candi, env = caller_env(), mode = "function") + if (!is.null(f)) { + scale <- f + break + } + } + } + + if (!is.function(scale) && type == "discrete") { + args$type <- scale + scale <- switch( + aesthetic, + colour = scale_colour_qualitative, + fill = scale_fill_qualitative + ) + } + + if (is.function(scale)) { + if (!any(c("...", "call") %in% fn_fmls_names(scale))) { + args$call <- NULL + } + if (!"..." %in% fn_fmls_names(scale)) { + args <- args[intersect(names(args), fn_fmls_names(scale))] + } + scale <- check_scale_type( + exec(scale, !!!args), + paste("scale", aesthetic, type, sep = "_"), + aesthetic, + scale_is_discrete = type == "discrete" + ) + return(scale) + } + + cli::cli_abort("Unknown scale type: {.val {scale}}") +} diff --git a/R/scale-hue.R b/R/scale-hue.R index 414f10864e..b95938ceb6 100644 --- a/R/scale-hue.R +++ b/R/scale-hue.R @@ -86,6 +86,7 @@ scale_fill_hue <- function(name = waiver(), ..., h = c(0, 360) + 15, c = 100, #' is specified. #' #' @param ... Additional parameters passed on to the scale type, +#' @inheritParams discrete_scale #' @param type One of the following: #' * A character vector of color codes. The codes are used for a 'manual' color #' scale as long as the number of codes exceeds the number of data levels @@ -134,48 +135,36 @@ scale_fill_hue <- function(name = waiver(), ..., h = c(0, 360) + 15, c = 100, #' print(cty_by_var(fl)) #' }) #' -scale_colour_discrete <- function(..., type = getOption("ggplot2.discrete.colour")) { - # TODO: eventually `type` should default to a set of colour-blind safe color codes (e.g. Okabe-Ito) - type <- type %||% scale_colour_hue - args <- list2(...) - args$call <- args$call %||% current_call() - - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type( - exec(type, !!!args), - "scale_colour_discrete", - "colour", - scale_is_discrete = TRUE +scale_colour_discrete <- function(..., aesthetics = "colour", na.value = "grey50", + type = getOption("ggplot2.discrete.colour")) { + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., na.value = na.value, scale = type, + aesthetic = "colour", type = "discrete" ) - } else { - exec(scale_colour_qualitative, !!!args, type = type) + return(scale) } + discrete_scale( + aesthetics, palette = NULL, na.value = na.value, + ... + ) } #' @rdname scale_colour_discrete #' @export -scale_fill_discrete <- function(..., type = getOption("ggplot2.discrete.fill")) { - # TODO: eventually `type` should default to a set of colour-blind safe color codes (e.g. Okabe-Ito) - type <- type %||% scale_fill_hue - args <- list2(...) - args$call <- args$call %||% current_call() - - if (is.function(type)) { - if (!any(c("...", "call") %in% fn_fmls_names(type))) { - args$call <- NULL - } - check_scale_type( - exec(type, !!!args), - "scale_fill_discrete", - "fill", - scale_is_discrete = TRUE +scale_fill_discrete <- function(..., aesthetics = "fill", na.value = "grey50", + type = getOption("ggplot2.discrete.fill")) { + if (!is.null(type)) { + scale <- scale_backward_compatibility( + ..., na.value = na.value, scale = type, + aesthetic = "fill", type = "discrete" ) - } else { - exec(scale_fill_qualitative, !!!args, type = type) + return(scale) } + discrete_scale( + aesthetics, palette = NULL, na.value = na.value, + ... + ) } scale_colour_qualitative <- function(name = waiver(), ..., type = NULL, diff --git a/R/scale-linetype.R b/R/scale-linetype.R index d4ea6df26d..8f8c62e30e 100644 --- a/R/scale-linetype.R +++ b/R/scale-linetype.R @@ -38,7 +38,7 @@ scale_linetype <- function(name = waiver(), ..., na.value = NA) { discrete_scale( "linetype", name = name, - palette = pal_linetype(), + palette = NULL, na.value = na.value, ... ) @@ -49,7 +49,7 @@ scale_linetype <- function(name = waiver(), ..., na.value = NA) { scale_linetype_binned <- function(name = waiver(), ..., na.value = NA) { binned_scale( "linetype", name = name, - palette = pal_binned(pal_linetype()), + palette = NULL, na.value = na.value, ... ) diff --git a/R/scale-linewidth.R b/R/scale-linewidth.R index 801df22b3a..9bf05b3913 100644 --- a/R/scale-linewidth.R +++ b/R/scale-linewidth.R @@ -31,10 +31,11 @@ NULL #' @usage NULL scale_linewidth_continuous <- function(name = waiver(), breaks = waiver(), labels = waiver(), limits = NULL, - range = c(1, 6), transform = "identity", + range = NULL, transform = "identity", trans = deprecated(), guide = "legend") { - continuous_scale("linewidth", palette = pal_rescale(range), name = name, + palette <- if (!is.null(range)) pal_rescale(range) else NULL + continuous_scale("linewidth", palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, guide = guide) } @@ -46,10 +47,11 @@ scale_linewidth <- scale_linewidth_continuous #' @rdname scale_linewidth #' @export scale_linewidth_binned <- function(name = waiver(), breaks = waiver(), labels = waiver(), - limits = NULL, range = c(1, 6), n.breaks = NULL, + limits = NULL, range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", trans = deprecated(), guide = "bins") { - binned_scale("linewidth", palette = pal_rescale(range), name = name, + palette <- if (!is.null(range)) pal_rescale(range) else NULL + binned_scale("linewidth", palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, n.breaks = n.breaks, nice.breaks = nice.breaks, guide = guide) @@ -68,32 +70,33 @@ scale_linewidth_discrete <- function(...) { #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_ordinal <- function(name = waiver(), ..., range = c(2, 6)) { - force(range) - - discrete_scale( - "linewidth", name = name, - palette = function(n) seq(range[1], range[2], length.out = n), - ... - ) +scale_linewidth_ordinal <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) { + function(n) seq(range[1], range[2], length.out = n) + } else { + NULL + } + discrete_scale("linewidth", name = name, palette = palette, ...) } #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_datetime <- function(name = waiver(), ..., range = c(1, 6)) { +scale_linewidth_datetime <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( "linewidth", transform = "time", name = name, - palette = pal_rescale(range), ... + palette = palette, ... ) } #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_date <- function(name = waiver(), ..., range = c(1, 6)) { +scale_linewidth_date <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( "linewidth", transform = "date", name = name, - palette = pal_rescale(range), ... + palette = palette, ... ) } diff --git a/R/scale-shape.R b/R/scale-shape.R index ecb8a2a2a1..effa0a0b2f 100644 --- a/R/scale-shape.R +++ b/R/scale-shape.R @@ -42,14 +42,16 @@ #' scale_shape_identity() + #' facet_wrap(~shape) + #' theme_void() -scale_shape <- function(name = waiver(), ..., solid = TRUE) { - discrete_scale("shape", name = name, palette = pal_shape(solid), ...) +scale_shape <- function(name = waiver(), ..., solid = NULL) { + palette <- if (!is.null(solid)) pal_shape(solid) else NULL + discrete_scale("shape", name = name, palette = palette, ...) } #' @rdname scale_shape #' @export scale_shape_binned <- function(name = waiver(), ..., solid = TRUE) { - binned_scale("shape", name = name, palette = pal_binned(pal_shape(solid)), ...) + palette <- if (!is.null(solid)) pal_binned(pal_shape(solid)) else NULL + binned_scale("shape", name = name, palette = palette, ...) } #' @rdname scale_shape diff --git a/R/scale-size.R b/R/scale-size.R index 33f14d4834..525f378e15 100644 --- a/R/scale-size.R +++ b/R/scale-size.R @@ -52,11 +52,12 @@ NULL #' @export #' @usage NULL scale_size_continuous <- function(name = waiver(), breaks = waiver(), labels = waiver(), - limits = NULL, range = c(1, 6), + limits = NULL, range = NULL, transform = "identity", trans = deprecated(), guide = "legend") { - continuous_scale("size", palette = pal_area(range), name = name, + palette <- if (!is.null(range)) pal_area(range) else NULL + continuous_scale("size", palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, guide = guide) } @@ -79,10 +80,11 @@ scale_radius <- function(name = waiver(), breaks = waiver(), labels = waiver(), #' @rdname scale_size #' @export scale_size_binned <- function(name = waiver(), breaks = waiver(), labels = waiver(), - limits = NULL, range = c(1, 6), n.breaks = NULL, + limits = NULL, range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", trans = deprecated(), guide = "bins") { - binned_scale("size", palette = pal_area(range), name = name, + palette <- if (!is.null(range)) pal_area(range) else NULL + binned_scale("size", palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, n.breaks = n.breaks, nice.breaks = nice.breaks, guide = guide) @@ -101,17 +103,13 @@ scale_size_discrete <- function(...) { #' @rdname scale_size #' @export #' @usage NULL -scale_size_ordinal <- function(name = waiver(), ..., range = c(2, 6)) { - force(range) - - discrete_scale( - "size", name = name, - palette = function(n) { - area <- seq(range[1] ^ 2, range[2] ^ 2, length.out = n) - sqrt(area) - }, - ... - ) +scale_size_ordinal <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) { + function(n) sqrt(seq(range[1]^2, range[2]^2, length.out = n)) + } else { + NULL + } + discrete_scale("size", name = name, palette = palette, ...) } #' @inheritDotParams continuous_scale -aesthetics -scale_name -palette -rescaler -expand -position @@ -139,13 +137,15 @@ scale_size_binned_area <- function(name = waiver(), ..., max_size = 6) { #' @rdname scale_size #' @export #' @usage NULL -scale_size_datetime <- function(name = waiver(), ..., range = c(1, 6)) { - datetime_scale("size", "time", name = name, palette = pal_area(range), ...) +scale_size_datetime <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_area(range) else NULL + datetime_scale("size", "time", name = name, palette = palette, ...) } #' @rdname scale_size #' @export #' @usage NULL -scale_size_date <- function(name = waiver(), ..., range = c(1, 6)) { - datetime_scale("size", "date", name = name, palette = pal_area(range), ...) +scale_size_date <- function(name = waiver(), ..., range = NULL) { + palette <- if (!is.null(range)) pal_area(range) else NULL + datetime_scale("size", "date", name = name, palette = palette, ...) } diff --git a/R/scales-.R b/R/scales-.R index e62eb0e8cb..769613a2d8 100644 --- a/R/scales-.R +++ b/R/scales-.R @@ -168,6 +168,39 @@ ScalesList <- ggproto("ScalesList", NULL, scale_name <- paste("scale", aes, "continuous", sep = "_") self$add(find_global(scale_name, env, mode = "function")()) } + }, + + set_palettes = function(self, theme) { + for (scale in self$scales) { + if (!is.null(scale$palette)) { + next + } + + # Resolve palette theme setting for this scale + type <- if (scale$is_discrete()) "discrete" else "continuous" + elem <- paste0("palette.", scale$aesthetics, ".", type) + elem <- compact(lapply(elem, calc_element, theme))[1][[1]] + + # Resolve the palette itself + elem <- elem %||% fallback_palette(scale) + palette <- switch( + type, + discrete = as_discrete_pal(elem), + continuous = as_continuous_pal(elem) + ) + if (!is.function(palette)) { + cli::cli_warn( + "Failed to find palette for {.field {scale$aesthetics[1]}} scale." + ) + } + + # Set palette to scale + # Note: while direct assignment is not ideal, we've already cloned the + # scale at the beginning of the plot build method, so it doesn't affect + # other plots + scale$palette <- palette + invisible() + } } ) diff --git a/R/theme-elements.R b/R/theme-elements.R index fb3341bf49..c51134216f 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -666,6 +666,21 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { plot.tag.location = el_def("character"), plot.margin = el_def(c("margin", "unit", "rel"), "margins"), + palette.colour.discrete = el_def(c("character", "function")), + palette.colour.continuous = el_def(c("character", "function")), + palette.fill.discrete = el_def(c("character", "function"), "palette.colour.discrete"), + palette.fill.continuous = el_def(c("character", "function"), "palette.colour.continuous"), + palette.alpha.discrete = el_def(c("character", "numeric", "integer", "function")), + palette.alpha.continuous = el_def(c("character", "numeric", "integer", "function")), + palette.linewidth.discrete = el_def(c("character", "numeric", "integer", "function")), + palette.linewidth.continuous = el_def(c("character", "numeric", "integer", "function")), + palette.size.discrete = el_def(c("character", "numeric", "integer", "function")), + palette.size.continuous = el_def(c("character", "numeric", "integer", "function")), + palette.shape.discrete = el_def(c("character", "numeric", "integer", "function")), + palette.shape.continuous = el_def(c("character", "numeric", "integer", "function")), + palette.linetype.discrete = el_def(c("character", "numeric", "integer", "function")), + palette.linetype.continuous = el_def(c("character", "numeric", "integer", "function")), + aspect.ratio = el_def(c("numeric", "integer")) ) diff --git a/R/utilities.R b/R/utilities.R index 039376f4df..cbb403da4e 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -781,6 +781,34 @@ as_unordered_factor <- function(x) { x } +fallback_palette <- function(scale) { + aes <- scale$aesthetics[1] + discrete <- scale$is_discrete() + if (discrete) { + pal <- switch( + aes, + colour = , fill = pal_hue(), + alpha = function(n) seq(0.1, 1, length.out = n), + linewidth = function(n) seq(2, 6, length.out = n), + linetype = pal_linetype(), + shape = pal_shape(), + size = function(n) sqrt(seq(4, 36, length.out = n)), + ggplot_global$theme_default[[paste0("palette.", aes, ".discrete")]] + ) + return(pal) + } + switch( + aes, + colour = , fill = pal_seq_gradient("#132B43", "#56B1F7"), + alpha = pal_rescale(c(0.1, 1)), + linewidth = pal_rescale(c(1, 6)), + linetype = pal_binned(pal_linetype()), + shape = pal_binned(pal_shape()), + size = pal_area(), + ggplot_global$theme_default[[paste0("palette.", aes, ".continuous")]] + ) +} + warn_dots_used <- function(env = caller_env(), call = caller_env()) { check_dots_used( env = env, call = call, @@ -793,6 +821,8 @@ warn_dots_used <- function(env = caller_env(), call = caller_env()) { ) } +# TODO: delete shims when {scales} releases >1.3.0.9000 +# and bump {scales} version requirements # Shim for scales/#424 col_mix <- function(a, b, amount = 0.5) { input <- vec_recycle_common(a = a, b = b, amount = amount) @@ -805,10 +835,40 @@ col_mix <- function(a, b, amount = 0.5) { ) } +# Shim for scales/#427 +as_discrete_pal <- function(x, ...) { + if (is.function(x)) { + return(x) + } + pal_manual(x) +} + +# Shim for scales/#427 +as_continuous_pal <- function(x, ...) { + if (is.function(x)) { + return(x) + } + is_color <- grepl("^#(([[:xdigit:]]{2}){3,4}|([[:xdigit:]]){3,4})$", x) | + x %in% grDevices::colours() + if (all(is_color)) { + colour_ramp(x) + } else { + approxfun(seq(0, 1, length.out = length(x)), x) + } +} + +# Replace shims by actual scales function when available on_load({ - if ("col_mix" %in% getNamespaceExports("scales")) { + nse <- getNamespaceExports("scales") + if ("col_mix" %in% nse) { col_mix <- scales::col_mix } + if ("as_discrete_pal" %in% nse) { + as_discrete_pal <- scales::as_discrete_pal + } + if ("as_continuous_pal" %in% nse) { + as_continuous_pal <- scales::as_continuous_pal + } }) # TODO: Replace me if rlang/#1730 gets implemented diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 1b06e73ae1..e88e45a0e1 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -246,7 +246,7 @@ p + # Add aesthetic mappings p + geom_text(aes(colour = factor(cyl))) p + geom_text(aes(colour = factor(cyl))) + - scale_colour_discrete(l = 40) + scale_colour_hue(l = 40) p + geom_label(aes(fill = factor(cyl)), colour = "white", fontface = "bold") # Scale size of text, and change legend key glyph from a to point diff --git a/man/scale_alpha.Rd b/man/scale_alpha.Rd index 28defef0de..6833a08002 100644 --- a/man/scale_alpha.Rd +++ b/man/scale_alpha.Rd @@ -10,15 +10,15 @@ \alias{scale_alpha_date} \title{Alpha transparency scales} \usage{ -scale_alpha(name = waiver(), ..., range = c(0.1, 1)) +scale_alpha(name = waiver(), ..., range = NULL) -scale_alpha_continuous(name = waiver(), ..., range = c(0.1, 1)) +scale_alpha_continuous(name = waiver(), ..., range = NULL) -scale_alpha_binned(name = waiver(), ..., range = c(0.1, 1)) +scale_alpha_binned(name = waiver(), ..., range = NULL) scale_alpha_discrete(...) -scale_alpha_ordinal(name = waiver(), ..., range = c(0.1, 1)) +scale_alpha_ordinal(name = waiver(), ..., range = NULL) } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If diff --git a/man/scale_colour_continuous.Rd b/man/scale_colour_continuous.Rd index 36f3427746..d88a74f399 100644 --- a/man/scale_colour_continuous.Rd +++ b/man/scale_colour_continuous.Rd @@ -9,17 +9,48 @@ \alias{scale_color_binned} \title{Continuous and binned colour scales} \usage{ -scale_colour_continuous(..., type = getOption("ggplot2.continuous.colour")) - -scale_fill_continuous(..., type = getOption("ggplot2.continuous.fill")) - -scale_colour_binned(..., type = getOption("ggplot2.binned.colour")) - -scale_fill_binned(..., type = getOption("ggplot2.binned.fill")) +scale_colour_continuous( + ..., + aesthetics = "colour", + guide = "colourbar", + na.value = "grey50", + type = getOption("ggplot2.continuous.colour") +) + +scale_fill_continuous( + ..., + aesthetics = "fill", + guide = "colourbar", + na.value = "grey50", + type = getOption("ggplot2.continuous.fill") +) + +scale_colour_binned( + ..., + aesthetics = "colour", + guide = "coloursteps", + na.value = "grey50", + type = getOption("ggplot2.binned.colour") +) + +scale_fill_binned( + ..., + aesthetics = "fill", + guide = "coloursteps", + na.value = "grey50", + type = getOption("ggplot2.binned.fill") +) } \arguments{ \item{...}{Additional parameters passed on to the scale type} +\item{aesthetics}{The names of the aesthetics that this scale works with.} + +\item{guide}{A function used to create a guide or its name. See +\code{\link[=guides]{guides()}} for more information.} + +\item{na.value}{Missing values will be replaced with this value.} + \item{type}{One of the following: \itemize{ \item "gradient" (the default) diff --git a/man/scale_colour_discrete.Rd b/man/scale_colour_discrete.Rd index 0c7883fb6e..ff8fe3f9e7 100644 --- a/man/scale_colour_discrete.Rd +++ b/man/scale_colour_discrete.Rd @@ -6,13 +6,29 @@ \alias{scale_color_discrete} \title{Discrete colour scales} \usage{ -scale_colour_discrete(..., type = getOption("ggplot2.discrete.colour")) +scale_colour_discrete( + ..., + aesthetics = "colour", + na.value = "grey50", + type = getOption("ggplot2.discrete.colour") +) -scale_fill_discrete(..., type = getOption("ggplot2.discrete.fill")) +scale_fill_discrete( + ..., + aesthetics = "fill", + na.value = "grey50", + type = getOption("ggplot2.discrete.fill") +) } \arguments{ \item{...}{Additional parameters passed on to the scale type,} +\item{aesthetics}{The names of the aesthetics that this scale works with.} + +\item{na.value}{If \code{na.translate = TRUE}, what aesthetic value should the +missing values be displayed as? Does not apply to position scales +where \code{NA} is always placed at the far right.} + \item{type}{One of the following: \itemize{ \item A character vector of color codes. The codes are used for a 'manual' color diff --git a/man/scale_linewidth.Rd b/man/scale_linewidth.Rd index 275f860582..5c9a842da9 100644 --- a/man/scale_linewidth.Rd +++ b/man/scale_linewidth.Rd @@ -15,7 +15,7 @@ scale_linewidth( breaks = waiver(), labels = waiver(), limits = NULL, - range = c(1, 6), + range = NULL, transform = "identity", trans = deprecated(), guide = "legend" @@ -26,7 +26,7 @@ scale_linewidth_binned( breaks = waiver(), labels = waiver(), limits = NULL, - range = c(1, 6), + range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index 8c8b8320fc..85b991fd9a 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -8,7 +8,7 @@ \alias{scale_shape_continuous} \title{Scales for shapes, aka glyphs} \usage{ -scale_shape(name = waiver(), ..., solid = TRUE) +scale_shape(name = waiver(), ..., solid = NULL) scale_shape_binned(name = waiver(), ..., solid = TRUE) } diff --git a/man/scale_size.Rd b/man/scale_size.Rd index 753ecfa790..2ba6a1e295 100644 --- a/man/scale_size.Rd +++ b/man/scale_size.Rd @@ -18,7 +18,7 @@ scale_size( breaks = waiver(), labels = waiver(), limits = NULL, - range = c(1, 6), + range = NULL, transform = "identity", trans = deprecated(), guide = "legend" @@ -40,7 +40,7 @@ scale_size_binned( breaks = waiver(), labels = waiver(), limits = NULL, - range = c(1, 6), + range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", diff --git a/tests/testthat/_snaps/scale-colour-continuous.md b/tests/testthat/_snaps/scale-colour-continuous.md index a5410a8799..14d6e6a95d 100644 --- a/tests/testthat/_snaps/scale-colour-continuous.md +++ b/tests/testthat/_snaps/scale-colour-continuous.md @@ -21,10 +21,8 @@ --- Unknown scale type: "abc" - i Use either "gradient" or "viridis". --- Unknown scale type: "abc" - i Use either "gradient" or "viridis". diff --git a/tests/testthat/_snaps/scale-discrete.md b/tests/testthat/_snaps/scale-discrete.md index a3251c4c4e..6a49fa9fdf 100644 --- a/tests/testthat/_snaps/scale-discrete.md +++ b/tests/testthat/_snaps/scale-discrete.md @@ -3,7 +3,7 @@ Code scale_colour_discrete(type = scale_colour_gradient) Condition - Error in `scale_colour_discrete()`: + Error in `scale_backward_compatibility()`: ! The `type` argument must return a discrete scale for the colour aesthetic. x The provided scale is continuous. @@ -12,7 +12,7 @@ Code scale_fill_discrete(type = scale_fill_gradient) Condition - Error in `scale_fill_discrete()`: + Error in `scale_backward_compatibility()`: ! The `type` argument must return a discrete scale for the fill aesthetic. x The provided scale is continuous. @@ -21,7 +21,7 @@ Code scale_colour_discrete(type = scale_fill_hue) Condition - Error in `scale_colour_discrete()`: + Error in `scale_backward_compatibility()`: ! The `type` argument must return a continuous scale for the colour aesthetic. x The provided scale works with the following aesthetics: fill. @@ -30,7 +30,7 @@ Code scale_fill_discrete(type = scale_colour_hue) Condition - Error in `scale_fill_discrete()`: + Error in `scale_backward_compatibility()`: ! The `type` argument must return a continuous scale for the fill aesthetic. x The provided scale works with the following aesthetics: colour. diff --git a/tests/testthat/test-guide-colorbar.R b/tests/testthat/test-guide-colorbar.R index 9f44adb371..7cfd96a2f1 100644 --- a/tests/testthat/test-guide-colorbar.R +++ b/tests/testthat/test-guide-colorbar.R @@ -2,7 +2,7 @@ skip_on_cran() # This test suite is long-running (on cran) and is skipped test_that("colourbar trains without labels", { g <- guide_colorbar() - sc <- scale_colour_continuous(limits = c(0, 4), labels = NULL) + sc <- scale_colour_gradient(limits = c(0, 4), labels = NULL) out <- g$train(scale = sc) expect_named(out$key, c("colour", ".value")) diff --git a/tests/testthat/test-guide-legend.R b/tests/testthat/test-guide-legend.R index ff79bd7aa7..d4a47c145e 100644 --- a/tests/testthat/test-guide-legend.R +++ b/tests/testthat/test-guide-legend.R @@ -38,6 +38,7 @@ test_that("guide merging for guide_legend() works as expected", { scales <- scales_list() scales$add(scale1) scales$add(scale2) + scales$set_palettes(NULL) scales <- scales$scales aesthetics <- lapply(scales, `[[`, "aesthetics") @@ -52,34 +53,34 @@ test_that("guide merging for guide_legend() works as expected", { } different_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c", "d")), + scale_colour_hue(limits = c("a", "b", "c", "d")), scale_linetype_discrete(limits = c("a", "b", "c")) ) expect_length(different_limits, 2) same_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c")), + scale_colour_hue(limits = c("a", "b", "c")), scale_linetype_discrete(limits = c("a", "b", "c")) ) expect_length(same_limits, 1) expect_equal(same_limits[[1]]$key$.label, c("a", "b", "c")) same_labels_different_limits <- merge_test_guides( - scale_colour_discrete(limits = c("a", "b", "c")), + scale_colour_hue(limits = c("a", "b", "c")), scale_linetype_discrete(limits = c("one", "two", "three"), labels = c("a", "b", "c")) ) expect_length(same_labels_different_limits, 1) expect_equal(same_labels_different_limits[[1]]$key$.label, c("a", "b", "c")) same_labels_different_scale <- merge_test_guides( - scale_colour_continuous(limits = c(0, 4), breaks = 1:3, labels = c("a", "b", "c")), + scale_colour_gradient(limits = c(0, 4), breaks = 1:3, labels = c("a", "b", "c")), scale_linetype_discrete(limits = c("a", "b", "c")) ) expect_length(same_labels_different_scale, 1) expect_equal(same_labels_different_scale[[1]]$key$.label, c("a", "b", "c")) repeated_identical_labels <- merge_test_guides( - scale_colour_discrete(limits = c("one", "two", "three"), labels = c("label1", "label1", "label2")), + scale_colour_hue(limits = c("one", "two", "three"), labels = c("label1", "label1", "label2")), scale_linetype_discrete(limits = c("1", "2", "3"), labels = c("label1", "label1", "label2")) ) expect_length(repeated_identical_labels, 1) @@ -99,7 +100,7 @@ test_that("size = NA doesn't throw rendering errors", { test_that("legend reverse argument reverses the key", { - scale <- scale_colour_discrete() + scale <- scale_colour_hue() scale$train(LETTERS[1:4]) guides <- guides_list(NULL) diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index d9286b513f..514cb392a3 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -734,6 +734,30 @@ test_that("continuous scales warn about faulty `limits`", { expect_snapshot(scale_x_continuous(limits = 1:3), error = TRUE) }) +test_that("populating palettes works", { + + scl <- scales_list() + scl$add(scale_colour_discrete(aesthetics = c("colour", "fill"))) + + my_theme <- theme( + palette.colour.discrete = c("white", "black"), + palette.fill.discrete = c("red", "blue") + ) + + scl$set_palettes(my_theme) + expect_equal(scl$scales[[1]]$palette(2), c("white", "black")) + + # Scales with >1 aesthetic + scl <- scales_list() + scl$add(scale_colour_discrete(aesthetics = c("colour", "fill"))) + + my_theme$palette.colour.discrete <- NULL + + scl$set_palettes(my_theme) + expect_equal(scl$scales[[1]]$palette(2), c("red", "blue")) + +}) + test_that("discrete scales work with NAs in arbitrary positions", { # Prevents intermediate caching of palettes map <- function(x, limits) { From f52de1c3bbddd7912adf0d839a66acf9f9725398 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 12:08:08 +0100 Subject: [PATCH 171/264] Discard out-of-bounds binned breaks after generating labels (#6061) * scales don't discard oob breaks * guides deal with NA-breaks better * `parse_binned_breaks()` preserves break length * add test * add news bullet * choose non-default scale for test --- NEWS.md | 1 + R/guide-bins.R | 14 ++++++++++---- R/guide-colorsteps.R | 4 +++- R/scale-.R | 3 --- tests/testthat/test-guides.R | 14 ++++++++++++++ 5 files changed, 28 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index 2bd655a5c1..6e3896e061 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Fixed bug in out-of-bounds binned breaks (@teunbrand, #6054) * Binned guides now accept expressions as labels (@teunbrand, #6005) * (internal) `Scale$get_labels()` format expressions as lists. * In non-orthogonal coordinate systems (`coord_sf()`, `coord_polar()` and diff --git a/R/guide-bins.R b/R/guide-bins.R index 5bc695b010..c0344bbbe0 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -161,6 +161,9 @@ GuideBins <- ggproto( key$.show <- NA labels <- scale$get_labels(breaks) + labels <- labels[!is.na(breaks)] + breaks <- breaks[!is.na(breaks)] + if (is.character(scale$labels) || is.numeric(scale$labels) || is.expression(scale$labels)) { limit_lab <- c(NA, NA) } else { @@ -335,19 +338,22 @@ GuideBins <- ggproto( parse_binned_breaks <- function(scale, breaks = scale$get_breaks()) { - breaks <- breaks[!is.na(breaks)] + if (is.waiver(scale$labels) || is.function(scale$labels)) { + breaks <- breaks[!is.na(breaks)] + } if (length(breaks) == 0) { return(NULL) } if (is.numeric(breaks)) { - breaks <- sort(breaks) limits <- scale$get_limits() if (!is.numeric(scale$breaks)) { - breaks <- breaks[!breaks %in% limits] + breaks[breaks %in% limits] <- NA } - breaks <- oob_discard(breaks, limits) + breaks <- oob_censor(breaks, limits) all_breaks <- unique0(c(limits[1], breaks, limits[2])) + # Sorting drops NAs on purpose here + all_breaks <- sort(all_breaks, na.last = NA) bin_at <- all_breaks[-1] - diff(all_breaks) / 2 } else { bin_at <- breaks diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index 54cd89a948..240a1e607c 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -112,11 +112,13 @@ GuideColoursteps <- ggproto( key <- data_frame0(!!aesthetic := scale$map(breaks)) if (even.steps) { - key$.value <- seq_along(breaks) + key$.value <- NA_integer_ + key$.value[!is.na(breaks)] <- seq_along(breaks[!is.na(breaks)]) } else { key$.value <- breaks } key$.label <- scale$get_labels(breaks) + key <- vec_slice(key, !is.na(breaks)) if (breaks[1] %in% limits) { key$.value <- key$.value - 1L diff --git a/R/scale-.R b/R/scale-.R index f345310e4b..6732e22ba3 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -1307,9 +1307,6 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, breaks <- self$breaks } - # Breaks must be within limits - breaks <- oob_discard(breaks, sort(limits)) - self$breaks <- breaks transformation$transform(breaks) diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 5904676541..03848b85f2 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -190,6 +190,20 @@ test_that("bins can be parsed by guides for all scale types", { ) }) +test_that("binned breaks can have hardcoded labels when oob", { + + sc <- scale_colour_steps(breaks = 1:3, labels = as.character(1:3)) + sc$train(c(1, 2)) + + g <- guide_bins() + key <- g$train(scale = sc, aesthetic = "colour")$key + expect_equal(key$.label, c("1", "2")) + + g <- guide_coloursteps() + key <- g$train(scale = sc, aesthetic = "colour")$key + expect_equal(key$.label, c("1", "2")) +}) + # Visual tests ------------------------------------------------------------ test_that("guides are positioned correctly", { From 3be5d6c1bfb3a684e9de90989dc14b4309e605e7 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 12:17:50 +0100 Subject: [PATCH 172/264] No ticks no space (#6071) * no space for blank ticks * preserve axis text spacing for `theme_minimal()` * add news bullet --- NEWS.md | 2 ++ R/guide-axis.R | 6 ++++++ R/theme-defaults.R | 6 +++++- 3 files changed, 13 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 6e3896e061..c0097b2de4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -219,6 +219,8 @@ * New theme elements `palette.{aes}.discrete` and `palette.{aes}.continuous`. Theme palettes replace palettes in scales where `palette = NULL`, which is the new default in many scales (@teunbrand, #4696). +* `guide_axis()` no longer reserves space for blank ticks + (@teunbrand, #4722, #6069). # ggplot2 3.5.1 diff --git a/R/guide-axis.R b/R/guide-axis.R index bc2a2e1596..70ac3da43f 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -256,6 +256,12 @@ GuideAxis <- ggproto( override_elements = function(params, elements, theme) { elements$text <- label_angle_heuristic(elements$text, params$position, params$angle) + if (inherits(elements$ticks, "element_blank")) { + elements$major_length <- unit(0, "cm") + } + if (inherits(elements$minor, "element_blank") || isFALSE(params$minor.ticks)) { + elements$minor_length <- unit(0, "cm") + } return(elements) }, diff --git a/R/theme-defaults.R b/R/theme-defaults.R index 88aa05146b..ac8c5ecb51 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -451,7 +451,11 @@ theme_minimal <- function(base_size = 11, base_family = "", ink = ink, paper = paper ) %+replace% theme( - axis.ticks = element_blank(), + axis.ticks = element_blank(), # Extra margins due to absence ticks + axis.text.x.bottom = element_text(margin = margin(t = 0.45 * base_size)), + axis.text.x.top = element_text(margin = margin(b = 0.45 * base_size)), + axis.text.y.left = element_text(margin = margin(r = 0.45 * base_size)), + axis.text.y.right = element_text(margin = margin(l = 0.45 * base_size)), legend.background = element_blank(), legend.key = element_blank(), panel.background = element_blank(), From 918821a7ac377cd8710935a425d9c774529cdf6b Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 14:09:24 +0100 Subject: [PATCH 173/264] replace confusing wording in vignette (#6075) --- vignettes/ggplot2-in-packages.Rmd | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/vignettes/ggplot2-in-packages.Rmd b/vignettes/ggplot2-in-packages.Rmd index 06c6a30eec..fb40d8ba44 100644 --- a/vignettes/ggplot2-in-packages.Rmd +++ b/vignettes/ggplot2-in-packages.Rmd @@ -194,15 +194,11 @@ theme_custom <- function(...) { mpg_drv_summary() + theme_custom() ``` -It is important that the theme be calculated after the package is loaded. If not, the theme object is stored in the compiled bytecode of the built package, which may or may not align with the installed version of ggplot2! If your package has a default theme for its visualizations, the correct way to load it is to have a function that returns the default theme: +It is important that the theme be calculated after the package is loaded. If not, a theme object —stored as a variable in the built package— may or may not align with the installed version of ggplot2! If your package has a default theme for its visualizations, the correct way to apply this theme is by calling the constructor: ```{r} -default_theme <- function() { - theme_custom() -} - mpg_drv_summary2 <- function() { - mpg_drv_summary() + default_theme() + mpg_drv_summary() + theme_custom() } ``` From 4af509ef825fec8551ac69e8cf1da0f06139009c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 2 Dec 2024 14:44:58 +0100 Subject: [PATCH 174/264] Label dictionary (#6077) * first implementation of `labs(dict)` * add test * add news bullet * rename dict --> dictionary * `revalue` was removed --- NEWS.md | 2 ++ R/labels.R | 26 ++++++++++++++++++++++++-- man/labs.Rd | 14 ++++++++++++++ tests/testthat/test-labels.R | 25 +++++++++++++++++++++++++ 4 files changed, 65 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index c0097b2de4..ebbcf92e02 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* New argument `labs(dictionary)` to label based on variable name rather than + based on aesthetic (@teunbrand, #5178) * Fixed bug in out-of-bounds binned breaks (@teunbrand, #6054) * Binned guides now accept expressions as labels (@teunbrand, #6005) * (internal) `Scale$get_labels()` format expressions as lists. diff --git a/R/labels.R b/R/labels.R index 050d42829e..14d7f32a41 100644 --- a/R/labels.R +++ b/R/labels.R @@ -84,6 +84,15 @@ setup_plot_labels <- function(plot, layers, data) { )) } + dict <- plot_labels$dictionary + if (length(dict) > 0) { + labels <- lapply(labels, function(x) { + dict <- dict[names(dict) %in% x] + x[match(names(dict), x)] <- dict + x + }) + } + defaults(plot_labels, labels) } @@ -114,6 +123,10 @@ setup_plot_labels <- function(plot, layers, data) { #' bottom-right of the plot by default. #' @param tag The text for the tag label which will be displayed at the #' top-left of the plot by default. +#' @param dictionary A named character vector to serve as dictionary. +#' Automatically derived labels, such as those based on variables will +#' be matched with `names(dictionary)` and replaced by the matching +#' entry in `dictionary`. #' @param alt,alt_insight Text used for the generation of alt-text for the plot. #' See [get_alt_text] for examples. `alt` can also be a function that #' takes the plot as input and returns text as output. `alt` also accepts @@ -128,6 +141,14 @@ setup_plot_labels <- function(plot, layers, data) { #' p + labs(colour = "Cylinders") #' p + labs(x = "New x label") #' +#' # Set labels by variable name instead of aesthetic +#' p + labs(dict = c( +#' disp = "Displacment", # Not in use +#' cyl = "Number of cylinders", +#' mpg = "Miles per gallon", +#' wt = "Weight (1000 lbs)" +#' )) +#' #' # The plot title appears at the top-left, with the subtitle #' # display in smaller text underneath it #' p + labs(title = "New plot title") @@ -146,11 +167,12 @@ setup_plot_labels <- function(plot, layers, data) { #' labs(title = "title") + #' labs(title = NULL) labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), - tag = waiver(), alt = waiver(), alt_insight = waiver()) { + tag = waiver(), dictionary = waiver(), alt = waiver(), + alt_insight = waiver()) { # .ignore_empty = "all" is needed to allow trailing commas, which is NOT a trailing comma for dots_list() as it's in ... args <- dots_list(..., title = title, subtitle = subtitle, caption = caption, tag = tag, alt = allow_lambda(alt), alt_insight = alt_insight, - .ignore_empty = "all") + dictionary = dictionary, .ignore_empty = "all") is_waive <- vapply(args, is.waiver, logical(1)) args <- args[!is_waive] diff --git a/man/labs.Rd b/man/labs.Rd index 5d6fb93b52..18cd7690f6 100644 --- a/man/labs.Rd +++ b/man/labs.Rd @@ -14,6 +14,7 @@ labs( subtitle = waiver(), caption = waiver(), tag = waiver(), + dictionary = waiver(), alt = waiver(), alt_insight = waiver() ) @@ -40,6 +41,11 @@ bottom-right of the plot by default.} \item{tag}{The text for the tag label which will be displayed at the top-left of the plot by default.} +\item{dictionary}{A named character vector to serve as dictionary. +Automatically derived labels, such as those based on variables will +be matched with \code{names(dictionary)} and replaced by the matching +entry in \code{dictionary}.} + \item{alt, alt_insight}{Text used for the generation of alt-text for the plot. See \link{get_alt_text} for examples. \code{alt} can also be a function that takes the plot as input and returns text as output. \code{alt} also accepts @@ -75,6 +81,14 @@ p <- ggplot(mtcars, aes(mpg, wt, colour = cyl)) + geom_point() p + labs(colour = "Cylinders") p + labs(x = "New x label") +# Set labels by variable name instead of aesthetic +p + labs(dict = c( + disp = "Displacment", # Not in use + cyl = "Number of cylinders", + mpg = "Miles per gallon", + wt = "Weight (1000 lbs)" +)) + # The plot title appears at the top-left, with the subtitle # display in smaller text underneath it p + labs(title = "New plot title") diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index b8b002a3db..0b1fc5df50 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -246,6 +246,31 @@ test_that("moving guide positions lets titles follow", { expect_identical(labs[names(expect)], expect) }) +test_that("label dictionaries work", { + + p <- ggplot(mtcars, aes(disp, mpg, shape = factor(cyl), size = drat)) + + geom_point() + + labs(dictionary = c( + disp = "Displacement", + mpg = "Miles per gallon", + `factor(cyl)` = "Number of cylinders", + drat = "Rear axle ratio" + )) + p <- ggplot_build(p) + + x <- p$layout$resolve_label(p$layout$panel_scales_x[[1]], p$plot$labels) + expect_equal(x$primary, "Displacement") + + y <- p$layout$resolve_label(p$layout$panel_scales_y[[1]], p$plot$labels) + expect_equal(y$primary, "Miles per gallon") + + shape <- p$plot$guides$get_params("shape")$title + expect_equal(shape, "Number of cylinders") + + size <- p$plot$guides$get_params("size")$title + expect_equal(size, "Rear axle ratio") +}) + # Visual tests ------------------------------------------------------------ test_that("tags are drawn correctly", { From 73f6bffb991978cb5398a6db21c0665472d9f480 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 08:33:46 +0100 Subject: [PATCH 175/264] Clipping in `geom_abline()` (#6109) * clip `geom_abline()` in y-direction * add test * accept visual changes * add news bullet --- NEWS.md | 2 ++ R/geom-abline.R | 12 ++++++++---- .../cartesian-lines-intersect-mid-bars.svg | 2 +- .../flipped-lines-intersect-mid-bars.svg | 2 +- .../polar-lines-intersect-mid-bars.svg | 2 +- tests/testthat/test-geom-hline-vline-abline.R | 19 +++++++++++++++++++ 6 files changed, 32 insertions(+), 7 deletions(-) diff --git a/NEWS.md b/NEWS.md index ebbcf92e02..8b999863b2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -223,6 +223,8 @@ the new default in many scales (@teunbrand, #4696). * `guide_axis()` no longer reserves space for blank ticks (@teunbrand, #4722, #6069). +* `geom_abline()` clips to the panel range in the vertical direction too + (@teunbrand, #6086). # ggplot2 3.5.1 diff --git a/R/geom-abline.R b/R/geom-abline.R index e9775e33fb..825d45faf8 100644 --- a/R/geom-abline.R +++ b/R/geom-abline.R @@ -132,12 +132,16 @@ GeomAbline <- ggproto("GeomAbline", Geom, # Ensure the line extends well outside the panel to avoid visible line # ending for thick lines ranges$x <- ranges$x + c(-1, 1) * diff(ranges$x) + ranges$y <- ranges$y + c(-1, 1) * diff(ranges$y) } - data$x <- ranges$x[1] - data$xend <- ranges$x[2] - data$y <- ranges$x[1] * data$slope + data$intercept - data$yend <- ranges$x[2] * data$slope + data$intercept + # Restrict 'x' to where 'y' is in range: x = (y - intercept) / slope + x <- sweep(outer(ranges$y, data$intercept, FUN = "-"), 2, data$slope, FUN = "/") + + data$x <- pmax(ranges$x[1], pmin(x[1, ], x[2, ])) + data$xend <- pmin(ranges$x[2], pmax(x[1, ], x[2, ])) + data$y <- data$x * data$slope + data$intercept + data$yend <- data$xend * data$slope + data$intercept GeomSegment$draw_panel(unique0(data), panel_params, coord, lineend = lineend) }, diff --git a/tests/testthat/_snaps/geom-hline-vline-abline/cartesian-lines-intersect-mid-bars.svg b/tests/testthat/_snaps/geom-hline-vline-abline/cartesian-lines-intersect-mid-bars.svg index f76c20a281..163e6973da 100644 --- a/tests/testthat/_snaps/geom-hline-vline-abline/cartesian-lines-intersect-mid-bars.svg +++ b/tests/testthat/_snaps/geom-hline-vline-abline/cartesian-lines-intersect-mid-bars.svg @@ -39,7 +39,7 @@ - + diff --git a/tests/testthat/_snaps/geom-hline-vline-abline/flipped-lines-intersect-mid-bars.svg b/tests/testthat/_snaps/geom-hline-vline-abline/flipped-lines-intersect-mid-bars.svg index bdda8286d6..cd136306cc 100644 --- a/tests/testthat/_snaps/geom-hline-vline-abline/flipped-lines-intersect-mid-bars.svg +++ b/tests/testthat/_snaps/geom-hline-vline-abline/flipped-lines-intersect-mid-bars.svg @@ -39,7 +39,7 @@ - + diff --git a/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg b/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg index c6f3b60763..2f67080988 100644 --- a/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg +++ b/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg @@ -48,7 +48,7 @@ - + A B C diff --git a/tests/testthat/test-geom-hline-vline-abline.R b/tests/testthat/test-geom-hline-vline-abline.R index b637cd0a2f..8a324dcf4c 100644 --- a/tests/testthat/test-geom-hline-vline-abline.R +++ b/tests/testthat/test-geom-hline-vline-abline.R @@ -43,6 +43,25 @@ test_that("curved lines in map projections", { ) }) +test_that("geom_abline is clipped to x/y ranges", { + + df <- data.frame(slope = c(-0.2, -1, -5, 5, 1, 0.2)) + + p <- ggplot(df) + + geom_abline(aes(slope = slope, intercept = 0)) + + scale_x_continuous(limits = c(-1, 1), expand = FALSE) + + scale_y_continuous(limits = c(-1, 1), expand = FALSE) + + coord_cartesian(clip = "off") + + data <- layer_grob(p)[[1]] + + x <- c(as.numeric(data$x0), as.numeric(data$x1)) + expect_true(all(x >= 0 & x <= 1)) + + y <- c(as.numeric(data$y0), as.numeric(data$y1)) + expect_true(all(y >= 0 & y <= 1)) +}) + # Warning tests ------------------------------------------------------------ test_that("warnings are thrown when parameters cause mapping and data to be ignored", { From 4c5bb24ab9edc915e872b820a5114b00c52102a6 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 08:34:08 +0100 Subject: [PATCH 176/264] Partial margins (#6116) * inheritance of NA-margins * add `part_margin()` function * setup merge method for margins * add test * add news bullet * rename `part_margin()` to `margin_part()` * rename `part_margin()` to `margin_part()` * new `margin_auto()` * use `margin_auto()` where appropriate * fix mistake in issue id --- NAMESPACE | 3 +++ NEWS.md | 3 +++ R/geom-rug.R | 2 +- R/legend-draw.R | 2 +- R/margins.R | 12 ++++++++++++ R/theme-defaults.R | 20 ++++++++++---------- R/theme-elements.R | 5 +++-- R/theme.R | 29 +++++++++++++++++++++++++++-- man/element.Rd | 11 +++++++++-- man/geom_rug.Rd | 2 +- man/merge_element.Rd | 3 +++ man/theme.Rd | 4 ++-- tests/testthat/test-theme.R | 16 ++++++++++++++++ 13 files changed, 91 insertions(+), 21 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index becf512278..8f4f9c5856 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -94,6 +94,7 @@ S3method(makeContext,dotstackGrob) S3method(merge_element,default) S3method(merge_element,element) S3method(merge_element,element_blank) +S3method(merge_element,margin) S3method(pattern_alpha,GridPattern) S3method(pattern_alpha,GridTilingPattern) S3method(pattern_alpha,default) @@ -494,6 +495,8 @@ export(layer_sf) export(lims) export(map_data) export(margin) +export(margin_auto) +export(margin_part) export(max_height) export(max_width) export(mean_cl_boot) diff --git a/NEWS.md b/NEWS.md index 8b999863b2..077cce4c15 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* Theme margins can have NA-units to inherit from parent elements. The new + function `margin_part()` has NA-units as default (@teunbrand, #6115) +* New `margin_auto()` specification for theme margins. * New argument `labs(dictionary)` to label based on variable name rather than based on aesthetic (@teunbrand, #5178) * Fixed bug in out-of-bounds binned breaks (@teunbrand, #6054) diff --git a/R/geom-rug.R b/R/geom-rug.R index d675474f43..ffc761b91c 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -45,7 +45,7 @@ #' p + #' geom_rug(outside = TRUE, sides = "tr") + #' coord_cartesian(clip = "off") + -#' theme(plot.margin = margin(1, 1, 1, 1, "cm")) +#' theme(plot.margin = margin_auto(1, unit = "cm")) #' #' # increase the line length and #' # expand axis to avoid overplotting diff --git a/R/legend-draw.R b/R/legend-draw.R index 0f734f8fea..d08c6c6c93 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -320,7 +320,7 @@ draw_key_text <- function(data, params, size) { fontface = data$fontface %||% 1, fontsize = (data$size %||% 3.88) * .pt ), - margin = margin(0.1, 0.1, 0.1, 0.1, unit = "lines"), + margin = margin_auto(0.1, unit = "lines"), margin_x = TRUE, margin_y = TRUE ) attr(grob, "width") <- convertWidth(grobWidth(grob), "cm", valueOnly = TRUE) diff --git a/R/margins.R b/R/margins.R index 7104a7d330..61ea1dab43 100644 --- a/R/margins.R +++ b/R/margins.R @@ -9,6 +9,18 @@ margin <- function(t = 0, r = 0, b = 0, l = 0, unit = "pt") { u } +#' @rdname element +#' @export +margin_part <- function(t = NA, r = NA, b = NA, l = NA, unit = "pt") { + margin(t = t, r = r, b = b, l = l, unit = unit) +} + +#' @rdname element +#' @export +margin_auto <- function(t = 0, r = t, b = t, l = r, unit = "pt") { + margin(t = t, r = r, b = b, l = l, unit) +} + #' @export #' @rdname is_tests is.margin <- function(x) inherits(x, "margin") diff --git a/R/theme-defaults.R b/R/theme-defaults.R index ac8c5ecb51..e6efd2a783 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -143,7 +143,7 @@ theme_grey <- function(base_size = 11, base_family = "", title = element_text(family = header_family), spacing = unit(half_line, "pt"), - margins = margin(half_line, half_line, half_line, half_line), + margins = margin_auto(half_line), geom = element_geom( ink = ink, paper = paper, accent = "#3366FF", @@ -226,7 +226,7 @@ theme_grey <- function(base_size = 11, base_family = "", strip.text = element_text( colour = col_mix(ink, paper, 0.105), size = rel(0.8), - margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) + margin = margin_auto(0.8 * half_line) ), strip.text.x = NULL, strip.text.y = element_text(angle = -90), @@ -341,7 +341,7 @@ theme_linedraw <- function(base_size = 11, base_family = "", strip.text = element_text( colour = paper, size = rel(0.8), - margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) + margin = margin_auto(0.8 * half_line) ), complete = TRUE @@ -384,7 +384,7 @@ theme_light <- function(base_size = 11, base_family = "", strip.text = element_text( colour = paper, size = rel(0.8), - margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) + margin = margin_auto(0.8 * half_line) ), complete = TRUE @@ -427,7 +427,7 @@ theme_dark <- function(base_size = 11, base_family = "", strip.text = element_text( colour = col_mix(ink, paper, 0.9), size = rel(0.8), - margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) + margin = margin_auto(0.8 * half_line) ), complete = TRUE @@ -557,7 +557,7 @@ theme_void <- function(base_size = 11, base_family = "", ), title = element_text(family = header_family), spacing = unit(half_line, "pt"), - margins = margin(half_line, half_line, half_line, half_line), + margins = margin_auto(half_line), axis.text = element_blank(), axis.title = element_blank(), axis.ticks.length = rel(0), @@ -641,7 +641,7 @@ theme_test <- function(base_size = 11, base_family = "", ), title = element_text(family = header_family), spacing = unit(half_line, "pt"), - margins = margin(half_line, half_line, half_line, half_line), + margins = margin_auto(half_line), geom = element_geom( ink = ink, paper = paper, accent = "#3366FF", linewidth = base_line_size, borderwidth = base_line_size, @@ -690,7 +690,7 @@ theme_test <- function(base_size = 11, base_family = "", legend.spacing = rel(2), legend.spacing.x = NULL, legend.spacing.y = NULL, - legend.margin = margin(0, 0, 0, 0, "cm"), + legend.margin = margin_auto(0, unit = "cm"), legend.key = NULL, legend.key.size = unit(1.2, "lines"), legend.key.height = NULL, @@ -705,7 +705,7 @@ theme_test <- function(base_size = 11, base_family = "", legend.direction = NULL, legend.justification = "center", legend.box = NULL, - legend.box.margin = margin(0, 0, 0, 0, "cm"), + legend.box.margin = margin_auto(0, unit = "cm"), legend.box.background = element_blank(), legend.box.spacing = rel(2), @@ -726,7 +726,7 @@ theme_test <- function(base_size = 11, base_family = "", strip.text = element_text( colour = col_mix(ink, paper, 0.105), size = rel(0.8), - margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line) + margin = margin_auto(0.8 * half_line) ), strip.text.x = NULL, strip.text.y = element_text(angle = -90), diff --git a/R/theme-elements.R b/R/theme-elements.R index c51134216f..b1cb67b046 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -11,7 +11,8 @@ #' - `element_geom()`: defaults for drawing layers. #' #' `rel()` is used to specify sizes relative to the parent, -#' `margin()` is used to specify the margins of elements. +#' `margin()`, `margin_part()` and `margin_auto()` are all used to specify the +#' margins of elements. #' #' @param fill Fill colour. #' @param colour,color Line/border colour. Color is an alias for colour. @@ -42,7 +43,7 @@ #' #' plot + theme( #' panel.background = element_rect(fill = "white"), -#' plot.margin = margin(2, 2, 2, 2, "cm"), +#' plot.margin = margin_auto(2, unit = "cm"), #' plot.background = element_rect( #' fill = "grey90", #' colour = "black", diff --git a/R/theme.R b/R/theme.R index 2eecc13253..04ab2edf98 100644 --- a/R/theme.R +++ b/R/theme.R @@ -281,14 +281,14 @@ #' legend.position.inside = c(.95, .95), #' legend.justification = c("right", "top"), #' legend.box.just = "right", -#' legend.margin = margin(6, 6, 6, 6) +#' legend.margin = margin_auto(6) #' ) #' #' # The legend.box properties work similarly for the space around #' # all the legends #' p2 + theme( #' legend.box.background = element_rect(), -#' legend.box.margin = margin(6, 6, 6, 6) +#' legend.box.margin = margin_auto(6) #' ) #' #' # You can also control the display of the keys @@ -835,6 +835,18 @@ merge_element.element <- function(new, old) { new } +#' @rdname merge_element +#' @export +merge_element.margin <- function(new, old) { + if (is.null(old) || inherits(old, "element_blank")) { + return(new) + } + if (anyNA(new)) { + new[is.na(new)] <- old[is.na(new)] + } + new +} + #' Combine the properties of two elements #' #' @param e1 An element object @@ -868,6 +880,15 @@ combine_elements <- function(e1, e2) { return(e1) } + if (inherits(e1, "margin") && inherits(e2, "margin")) { + if (anyNA(e2)) { + e2[is.na(e2)] <- unit(0, "pt") + } + if (anyNA(e1)) { + e1[is.na(e1)] <- e2[is.na(e1)] + } + } + # If neither of e1 or e2 are element_* objects, return e1 if (!inherits(e1, "element") && !inherits(e2, "element")) { return(e1) @@ -897,6 +918,10 @@ combine_elements <- function(e1, e2) { e1$linewidth <- e2$linewidth * unclass(e1$linewidth) } + if (inherits(e1, "element_text")) { + e1$margin <- combine_elements(e1$margin, e2$margin) + } + # If e2 is 'richer' than e1, fill e2 with e1 parameters is_subclass <- !any(inherits(e2, class(e1), which = TRUE) == 0) is_subclass <- is_subclass && length(setdiff(class(e2), class(e1)) > 0) diff --git a/man/element.Rd b/man/element.Rd index adb1b7eb22..c43fadfed2 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -8,6 +8,8 @@ \alias{element_geom} \alias{rel} \alias{margin} +\alias{margin_part} +\alias{margin_auto} \title{Theme elements} \usage{ element_blank() @@ -66,6 +68,10 @@ element_geom( rel(x) margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") + +margin_part(t = NA, r = NA, b = NA, l = NA, unit = "pt") + +margin_auto(t = 0, r = t, b = t, l = r, unit = "pt") } \arguments{ \item{fill}{Fill colour.} @@ -145,7 +151,8 @@ specify the display of how non-data components of the plot are drawn. } \code{rel()} is used to specify sizes relative to the parent, -\code{margin()} is used to specify the margins of elements. +\code{margin()}, \code{margin_part()} and \code{margin_auto()} are all used to specify the +margins of elements. } \examples{ plot <- ggplot(mpg, aes(displ, hwy)) + geom_point() @@ -165,7 +172,7 @@ plot + theme( plot + theme( panel.background = element_rect(fill = "white"), - plot.margin = margin(2, 2, 2, 2, "cm"), + plot.margin = margin_auto(2, unit = "cm"), plot.background = element_rect( fill = "grey90", colour = "black", diff --git a/man/geom_rug.Rd b/man/geom_rug.Rd index 1cc10e785a..b6508c7f9a 100644 --- a/man/geom_rug.Rd +++ b/man/geom_rug.Rd @@ -170,7 +170,7 @@ p + p + geom_rug(outside = TRUE, sides = "tr") + coord_cartesian(clip = "off") + - theme(plot.margin = margin(1, 1, 1, 1, "cm")) + theme(plot.margin = margin_auto(1, unit = "cm")) # increase the line length and # expand axis to avoid overplotting diff --git a/man/merge_element.Rd b/man/merge_element.Rd index 4071e6c69a..ca993eeec3 100644 --- a/man/merge_element.Rd +++ b/man/merge_element.Rd @@ -5,6 +5,7 @@ \alias{merge_element.default} \alias{merge_element.element_blank} \alias{merge_element.element} +\alias{merge_element.margin} \title{Merge a parent element into a child element} \usage{ merge_element(new, old) @@ -14,6 +15,8 @@ merge_element(new, old) \method{merge_element}{element_blank}(new, old) \method{merge_element}{element}(new, old) + +\method{merge_element}{margin}(new, old) } \arguments{ \item{new}{The child element in the theme hierarchy} diff --git a/man/theme.Rd b/man/theme.Rd index 829254ecdf..869e45ea71 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -469,14 +469,14 @@ p2 + theme( legend.position.inside = c(.95, .95), legend.justification = c("right", "top"), legend.box.just = "right", - legend.margin = margin(6, 6, 6, 6) + legend.margin = margin_auto(6) ) # The legend.box properties work similarly for the space around # all the legends p2 + theme( legend.box.background = element_rect(), - legend.box.margin = margin(6, 6, 6, 6) + legend.box.margin = margin_auto(6) ) # You can also control the display of the keys diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 2f7f7874f9..a1b656dbab 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -617,6 +617,22 @@ test_that("complete_theme completes a theme", { reset_theme_settings() }) +test_that("margin_part() mechanics work as expected", { + + t <- theme_gray() + + theme(plot.margin = margin_part(b = 11)) + + test <- calc_element("plot.margin", t) + expect_equal(as.numeric(test), c(5.5, 5.5, 11, 5.5)) + + t <- theme_gray() + + theme(margins = margin_part(b = 11)) + + test <- calc_element("plot.margin", t) + expect_equal(as.numeric(test), c(5.5, 5.5, 11, 5.5)) + +}) + # Visual tests ------------------------------------------------------------ test_that("aspect ratio is honored", { From cc98fd1f39450a64a52da0259b437cf98a48f2b5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 08:42:02 +0100 Subject: [PATCH 177/264] Enable 2D structures as aesthetics (#6076) * replace `lengths()` with `list_sizes()` * unname via `vec_set_names()` * add test * add news bullet * use slicing as subsetting * deduplicate label validation efforts * comparise sizes * use `is_finite()` helper in `check_transformation()` --- NEWS.md | 2 ++ R/geom-.R | 2 +- R/guide-.R | 5 +++-- R/layer.R | 4 ++-- R/layout.R | 2 +- R/scale-.R | 7 ++++--- R/utilities.R | 10 ++++++++++ tests/testthat/test-layer.R | 17 +++++++++++++++++ 8 files changed, 40 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index 077cce4c15..e512f0b707 100644 --- a/NEWS.md +++ b/NEWS.md @@ -219,6 +219,8 @@ `labs()` and several guides (@teunbrand, #3196). * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). * Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) +* (internal) removed barriers for using 2D structures as aesthetics + (@teunbrand, #4189). * `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052) * Added `theme_transparent()` with transparent backgrounds (@topepo). * New theme elements `palette.{aes}.discrete` and `palette.{aes}.continuous`. diff --git a/R/geom-.R b/R/geom-.R index dae3027e1b..50bdeb66a6 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -270,7 +270,7 @@ NULL .stroke <- 96 / 25.4 check_aesthetics <- function(x, n) { - ns <- lengths(x) + ns <- list_sizes(x) good <- ns == 1L | ns == n if (all(good)) { diff --git a/R/guide-.R b/R/guide-.R index aa2aa7b37d..c700329cb3 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -525,11 +525,12 @@ opposite_position <- function(position) { # Ensure that labels aren't a list of expressions, but proper expressions validate_labels <- function(labels) { - if (!is.list(labels)) { + if (!obj_is_list(labels)) { return(labels) } + labels[lengths(labels) == 0L] <- "" if (any(vapply(labels, is.language, logical(1)))) { - do.call(expression, labels) + inject(expression(!!!labels)) } else { unlist(labels) } diff --git a/R/layer.R b/R/layer.R index 639fece4af..d2355a46ba 100644 --- a/R/layer.R +++ b/R/layer.R @@ -327,7 +327,7 @@ Layer <- ggproto("Layer", NULL, } n <- nrow(data) - aes_n <- lengths(evaled) + aes_n <- list_sizes(evaled) if (n == 0) { # No data, so look at longest evaluated aesthetic if (length(evaled) == 0) { @@ -352,7 +352,7 @@ Layer <- ggproto("Layer", NULL, } else { evaled$PANEL <- data$PANEL } - evaled <- lapply(evaled, unname) + evaled <- lapply(evaled, vec_set_names, names = NULL) evaled <- as_gg_data_frame(evaled) evaled <- add_group(evaled) evaled diff --git a/R/layout.R b/R/layout.R index 25088798b1..5954031d20 100644 --- a/R/layout.R +++ b/R/layout.R @@ -318,7 +318,7 @@ scale_apply <- function(data, vars, method, scale_id, scales) { lapply(vars, function(var) { pieces <- lapply(seq_along(scales), function(i) { - scales[[i]][[method]](data[[var]][scale_index[[i]]]) + scales[[i]][[method]](vec_slice(data[[var]], scale_index[[i]])) }) # Remove empty vectors to avoid coercion issues with vctrs pieces[lengths(pieces) == 0] <- NULL diff --git a/R/scale-.R b/R/scale-.R index 6732e22ba3..53c9f4ee66 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -851,13 +851,14 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, labels <- self$labels } - if (length(labels) != length(breaks)) { + if (!identical(size0(labels), size0(breaks))) { cli::cli_abort( "{.arg breaks} and {.arg labels} have different lengths.", call = self$call ) } - if (is.list(labels)) { + + if (obj_is_list(labels)) { # Guard against list with empty elements labels[lengths(labels) == 0] <- "" # Make sure each element is scalar @@ -1386,7 +1387,7 @@ scale_flip_position <- function(scale) { } check_transformation <- function(x, transformed, name, arg = NULL, call = NULL) { - if (!any(is.finite(x) != is.finite(transformed))) { + if (!any(is_finite(x) != is_finite(transformed))) { return(invisible()) } if (is.null(arg)) { diff --git a/R/utilities.R b/R/utilities.R index cbb403da4e..54087eba68 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -781,6 +781,16 @@ as_unordered_factor <- function(x) { x } +size0 <- function(x) { + if (obj_is_vector(x)) { + vec_size(x) + } else if (is.vector(x)) { + length(x) + } else { + NULL + } +} + fallback_palette <- function(scale) { aes <- scale$aesthetics[1] discrete <- scale$is_discrete() diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 964211a4ee..225cedd947 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -182,3 +182,20 @@ test_that("layer_data returns a data.frame", { l <- geom_point(data = nrow) expect_snapshot_error(l$layer_data(mtcars)) }) + +test_that("data.frames and matrix aesthetics survive the build stage", { + df <- data_frame0( + x = 1:2, + g = matrix(1:4, 2), + f = data_frame0(a = 1:2, b = c("c", "d")) + ) + + p <- layer_data( + ggplot(df, aes(x, x, colour = g, shape = f)) + + geom_point() + + scale_colour_identity() + + scale_shape_identity() + ) + expect_vector(p$colour, matrix(NA_integer_, nrow = 0, ncol = 2), size = 2) + expect_vector(p$shape, data_frame0(a = integer(), b = character()), size = 2) +}) From e57d6b851d05b7c5e28774514361900ca0d263d5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 09:17:41 +0100 Subject: [PATCH 178/264] Reversal of coordinates (#6070) * remove vestigial code * reverse mechanism for cartesian coords * reverse mechanism for sf coord * simplify `guide_axis_theta()` decor stuff * replace `direction` with `reverse = "theta"` * swap `inner_radius` when `reverse = "r"` * reverse for coord_transform * rewrite `guide_grid()` to work with coord transforms * new ViewScale methods for mapped (but not rescaled) breaks * adopt new `guide_grid()` * accept that `coord_radial()` now renders minor r gridlines * document * internally sort ranges * add tests * scales sort limits upon construction * add news bullet * fix merge misstep --- NEWS.md | 7 + R/coord-.R | 9 +- R/coord-cartesian-.R | 24 ++-- R/coord-fixed.R | 4 +- R/coord-radial.R | 129 ++++++------------ R/coord-sf.R | 48 ++++--- R/coord-transform.R | 21 ++- R/guide-axis-theta.R | 26 ++-- R/guides-grid.R | 74 ++++++---- R/scale-.R | 25 ++-- R/scale-expansion.R | 4 +- R/scale-view.R | 13 ++ man/coord_cartesian.Rd | 8 +- man/coord_fixed.Rd | 14 +- man/coord_polar.Rd | 10 +- man/coord_trans.Rd | 8 +- man/ggsf.Rd | 8 +- .../bottom-half-circle-with-rotated-text.svg | 22 +-- ...with-axes-placed-at-90-and-225-degrees.svg | 23 ++-- .../inner-radius-with-all-axes.svg | 33 +++-- .../coord-polar/partial-with-all-axes.svg | 34 +++-- ...xis-theta-with-angle-adapting-to-theta.svg | 87 ++++++------ .../_snaps/guide-axis/stacked-radial-axes.svg | 24 ++-- tests/testthat/test-coord-cartesian.R | 13 ++ tests/testthat/test-coord-polar.R | 17 +++ tests/testthat/test-coord-transform.R | 14 ++ tests/testthat/test-coord_sf.R | 14 ++ tests/testthat/test-scale-expansion.R | 4 +- 28 files changed, 421 insertions(+), 296 deletions(-) diff --git a/NEWS.md b/NEWS.md index e512f0b707..8214635e8c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,12 @@ # ggplot2 (development version) +* Reversal of a dimension, typically 'x' or 'y', is now controlled by the + `reverse` argument in `coord_cartesian()`, `coord_fixed()`, `coord_radial()` + and `coord_sf()`. In `coord_radial()`, this replaces the older `direction` + argument (#4021, @teunbrand). +* `coord_radial()` displays minor gridlines now (@teunbrand). +* (internal) `continuous_scale()` and `binned_scale()` sort the `limits` + argument internally (@teunbrand). * Theme margins can have NA-units to inherit from parent elements. The new function `margin_part()` has NA-units as default (@teunbrand, #6115) * New `margin_auto()` specification for theme margins. diff --git a/R/coord-.R b/R/coord-.R index 6aa113d3ff..6b0470e39e 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -59,6 +59,9 @@ Coord <- ggproto("Coord", # "on" = yes, "off" = no clip = "on", + # Should any of the scales be reversed? + reverse = "none", + aspect = function(ranges) NULL, labels = function(self, labels, panel_params) { @@ -185,11 +188,7 @@ Coord <- ggproto("Coord", is_free = function() FALSE, setup_params = function(self, data) { - list( - guide_default = guide_axis(), - guide_missing = guide_none(), - expand = parse_coord_expand(self$expand %||% TRUE) - ) + list(expand = parse_coord_expand(self$expand %||% TRUE)) }, setup_data = function(data, params = list()) { diff --git a/R/coord-cartesian-.R b/R/coord-cartesian-.R index 1b13d9c6c0..23e237583c 100644 --- a/R/coord-cartesian-.R +++ b/R/coord-cartesian-.R @@ -25,6 +25,10 @@ #' limits are set via `xlim` and `ylim` and some data points fall outside those #' limits, then those data points may show up in places such as the axes, the #' legend, the plot title, or the plot margins. +#' @param reverse A string giving which directions to reverse. `"none"` +#' (default) keeps directions as is. `"x"` and `"y"` can be used to reverse +#' their respective directions. `"xy"` can be used to reverse both +#' directions. #' @export #' @examples #' # There are two ways of zooming the plot display: with scales or @@ -64,11 +68,12 @@ #' # displayed bigger #' d + coord_cartesian(xlim = c(0, 1)) coord_cartesian <- function(xlim = NULL, ylim = NULL, expand = TRUE, - default = FALSE, clip = "on") { + default = FALSE, clip = "on", reverse = "none") { check_coord_limits(xlim) check_coord_limits(ylim) ggproto(NULL, CoordCartesian, limits = list(x = xlim, y = ylim), + reverse = reverse, expand = expand, default = default, clip = clip @@ -97,8 +102,11 @@ CoordCartesian <- ggproto("CoordCartesian", Coord, self$range(panel_params) }, - transform = function(data, panel_params) { - data <- transform_position(data, panel_params$x$rescale, panel_params$y$rescale) + transform = function(self, data, panel_params) { + reverse <- self$reverse %||% "none" + x <- panel_params$x[[switch(reverse, xy = , x = "reverse", "rescale")]] + y <- panel_params$y[[switch(reverse, xy = , y = "reverse", "rescale")]] + data <- transform_position(data, x, y) transform_position(data, squish_infinite, squish_infinite) }, @@ -109,14 +117,8 @@ CoordCartesian <- ggproto("CoordCartesian", Coord, ) }, - render_bg = function(panel_params, theme) { - guide_grid( - theme, - panel_params$x$break_positions_minor(), - panel_params$x$break_positions(), - panel_params$y$break_positions_minor(), - panel_params$y$break_positions() - ) + render_bg = function(self, panel_params, theme) { + guide_grid(theme, panel_params, self) }, render_axis_h = function(panel_params, theme) { diff --git a/R/coord-fixed.R b/R/coord-fixed.R index a942fbb28b..d48824cfc4 100644 --- a/R/coord-fixed.R +++ b/R/coord-fixed.R @@ -22,13 +22,15 @@ #' p + coord_fixed(xlim = c(15, 30)) #' #' # Resize the plot to see that the specified aspect ratio is maintained -coord_fixed <- function(ratio = 1, xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") { +coord_fixed <- function(ratio = 1, xlim = NULL, ylim = NULL, expand = TRUE, + clip = "on", reverse = "none") { check_coord_limits(xlim) check_coord_limits(ylim) ggproto(NULL, CoordFixed, limits = list(x = xlim, y = ylim), ratio = ratio, expand = expand, + reverse = reverse, clip = clip ) } diff --git a/R/coord-radial.R b/R/coord-radial.R index b028822f0e..de3bac2d00 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -19,7 +19,11 @@ #' in accordance with the computed `theta` position. If `FALSE` (default), #' no such transformation is performed. Can be useful to rotate text geoms in #' alignment with the coordinates. -#' @param inner.radius A `numeric` between 0 and 1 setting the size of a inner.radius hole. +#' @param inner.radius A `numeric` between 0 and 1 setting the size of a +#' inner radius hole. +#' @param reverse A string giving which directions to reverse. `"none"` +#' (default) keep directions as is. `"theta"` reverses the angle and `"r"` +#' reverses the radius. `"thetar"` reverses both the angle and the radius. #' @param r_axis_inside,rotate_angle `r lifecycle::badge("deprecated")` #' #' @note @@ -39,11 +43,12 @@ coord_radial <- function(theta = "x", start = 0, end = NULL, expand = TRUE, - direction = 1, + direction = deprecated(), clip = "off", r.axis.inside = NULL, rotate.angle = FALSE, inner.radius = 0, + reverse = "none", r_axis_inside = deprecated(), rotate_angle = deprecated()) { @@ -59,34 +64,46 @@ coord_radial <- function(theta = "x", ) rotate.angle <- rotate_angle } + if (lifecycle::is_present(direction)) { + deprecate_warn0( + "3.5.2", "coord_radial(direction)", "coord_radial(reverse)" + ) + reverse <- switch(reverse, "r" = "thetar", "theta") + } theta <- arg_match0(theta, c("x", "y")) r <- if (theta == "x") "y" else "x" if (!is.numeric(r.axis.inside)) { check_bool(r.axis.inside, allow_null = TRUE) } + reverse <- arg_match0(reverse, c("theta", "thetar", "r", "none")) check_bool(rotate.angle) check_number_decimal(start, allow_infinite = FALSE) check_number_decimal(end, allow_infinite = FALSE, allow_null = TRUE) check_number_decimal(inner.radius, min = 0, max = 1, allow_infinite = FALSE) - end <- end %||% (start + 2 * pi) - if (start > end) { - n_rotate <- ((start - end) %/% (2 * pi)) + 1 - start <- start - n_rotate * 2 * pi + arc <- c(start, end %||% (start + 2 * pi)) + if (arc[1] > arc[2]) { + n_rotate <- ((arc[1] - arc[2]) %/% (2 * pi)) + 1 + arc[1] <- arc[1] - n_rotate * 2 * pi } - r.axis.inside <- r.axis.inside %||% !(abs(end - start) >= 1.999 * pi) + arc <- switch(reverse, thetar = , theta = rev(arc), arc) + + r.axis.inside <- r.axis.inside %||% !(abs(arc[2] - arc[1]) >= 1.999 * pi) + + inner.radius <- c(inner.radius, 1) * 0.4 + inner.radius <- switch(reverse, thetar = , r = rev, identity)(inner.radius) ggproto(NULL, CoordRadial, theta = theta, r = r, - arc = c(start, end), + arc = arc, expand = expand, - direction = sign(direction), + reverse = reverse, r_axis_inside = r.axis.inside, rotate_angle = rotate.angle, - inner_radius = c(inner.radius, 1) * 0.4, + inner_radius = inner.radius, clip = clip ) } @@ -107,16 +124,10 @@ CoordRadial <- ggproto("CoordRadial", Coord, arc <- details$arc %||% c(0, 2 * pi) if (self$theta == "x") { r <- rescale(y, from = details$r.range, to = self$inner_radius / 0.4) - theta <- theta_rescale_no_clip( - x, details$theta.range, - arc, self$direction - ) + theta <- theta_rescale_no_clip(x, details$theta.range, arc) } else { r <- rescale(x, from = details$r.range, to = self$inner_radius / 0.4) - theta <- theta_rescale_no_clip( - y, details$theta.range, - arc, self$direction - ) + theta <- theta_rescale_no_clip(y, details$theta.range, arc) } dist_polar(r, theta) @@ -200,10 +211,10 @@ CoordRadial <- ggproto("CoordRadial", Coord, r_position <- c("left", "right") # If both opposite direction and opposite position, don't flip - if (xor(self$direction == -1, opposite_r)) { + if (xor(self$reverse %in% c("thetar", "theta"), opposite_r)) { r_position <- rev(r_position) } - arc <- rad2deg(panel_params$axis_rotation) * self$direction + arc <- rad2deg(panel_params$axis_rotation) if (opposite_r) { arc <- rev(arc) } @@ -284,10 +295,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, arc <- panel_params$arc %||% c(0, 2 * pi) data$r <- r_rescale(data$r, panel_params$r.range, panel_params$inner_radius) - data$theta <- theta_rescale( - data$theta, panel_params$theta.range, - arc, self$direction - ) + data$theta <- theta_rescale(data$theta, panel_params$theta.range, arc) data$x <- rescale(data$r * sin(data$theta) + 0.5, from = bbox$x) data$y <- rescale(data$r * cos(data$theta) + 0.5, from = bbox$y) @@ -313,70 +321,12 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, render_bg = function(self, panel_params, theme) { - - bbox <- panel_params$bbox %||% list(x = c(0, 1), y = c(0, 1)) - arc <- panel_params$arc %||% c(0, 2 * pi) - dir <- self$direction - inner_radius <- panel_params$inner_radius - - theta_lim <- panel_params$theta.range - theta_maj <- panel_params$theta.major - theta_min <- setdiff(panel_params$theta.minor, theta_maj) - - if (length(theta_maj) > 0) { - theta_maj <- theta_rescale(theta_maj, theta_lim, arc, dir) - } - if (length(theta_min) > 0) { - theta_min <- theta_rescale(theta_min, theta_lim, arc, dir) - } - - theta_fine <- theta_rescale(seq(0, 1, length.out = 100), c(0, 1), arc, dir) - r_fine <- r_rescale(panel_params$r.major, panel_params$r.range, - panel_params$inner_radius) - - # This gets the proper theme element for theta and r grid lines: - # panel.grid.major.x or .y - grid_elems <- paste( - c("panel.grid.major.", "panel.grid.minor.", "panel.grid.major."), - c(self$theta, self$theta, self$r), sep = "" + panel_params <- switch( + self$theta, + x = rename(panel_params, c(theta = "x", r = "y")), + y = rename(panel_params, c(theta = "y", r = "x")) ) - grid_elems <- lapply(grid_elems, calc_element, theme = theme) - majortheta <- paste("panel.grid.major.", self$theta, sep = "") - minortheta <- paste("panel.grid.minor.", self$theta, sep = "") - majorr <- paste("panel.grid.major.", self$r, sep = "") - - bg_element <- calc_element("panel.background", theme) - if (!inherits(bg_element, "element_blank")) { - background <- data_frame0( - x = c(Inf, Inf, -Inf, -Inf), - y = c(Inf, -Inf, -Inf, Inf) - ) - background <- coord_munch(self, background, panel_params, is_closed = TRUE) - bg_gp <- gg_par( - lwd = bg_element$linewidth, - col = bg_element$colour, fill = bg_element$fill, - lty = bg_element$linetype - ) - background <- polygonGrob( - x = background$x, y = background$y, - gp = bg_gp - ) - } else { - background <- zeroGrob() - } - - ggname("grill", grobTree( - background, - theta_grid(theta_maj, grid_elems[[1]], inner_radius, bbox), - theta_grid(theta_min, grid_elems[[2]], inner_radius, bbox), - element_render( - theme, majorr, name = "radius", - x = rescale(outer(sin(theta_fine), r_fine) + 0.5, from = bbox$x), - y = rescale(outer(cos(theta_fine), r_fine) + 0.5, from = bbox$y), - id.lengths = rep(length(theta_fine), length(r_fine)), - default.units = "native" - ) - )) + guide_grid(theme, panel_params, self, square = FALSE) }, render_fg = function(self, panel_params, theme) { @@ -395,8 +345,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, bbox <- panel_params$bbox dir <- self$direction rot <- panel_params$axis_rotation - rot <- if (dir == 1) rot else rev(rot) - rot <- dir * rad2deg(-rot) + rot <- switch(self$reverse, thetar = , theta = rev(rot), rot) + rot <- rad2deg(-rot) left <- panel_guides_grob(panel_params$guides, position = "left", theme) left <- rotate_r_axis(left, rot[1], bbox, "left") @@ -540,6 +490,7 @@ polar_bbox <- function(arc, margin = c(0.05, 0.05, 0.05, 0.05), if (abs(diff(arc)) >= 2 * pi) { return(list(x = c(0, 1), y = c(0, 1))) } + arc <- sort(arc) # X and Y position of the sector arc ends xmax <- 0.5 * sin(arc) + 0.5 diff --git a/R/coord-sf.R b/R/coord-sf.R index 2a43d2e5ef..3f96ff6aaf 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -85,18 +85,22 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, source_crs <- panel_params$default_crs target_crs <- panel_params$crs + # CoordSf doesn't use the viewscale rescaling, so we just flip ranges + reverse <- self$reverse %||% "none" + x_range <- switch(reverse, xy = , x = rev, identity)(panel_params$x_range) + y_range <- switch(reverse, xy = , y = rev, identity)(panel_params$y_range) + # normalize geometry data, it should already be in the correct crs here data[[ geom_column(data) ]] <- sf_rescale01( data[[ geom_column(data) ]], - panel_params$x_range, - panel_params$y_range + x_range, y_range ) # transform and normalize regular position data data <- transform_position( sf_transform_xy(data, target_crs, source_crs), - function(x) rescale(x, from = panel_params$x_range), - function(x) rescale(x, from = panel_params$y_range) + function(x) rescale(x, from = x_range), + function(x) rescale(x, from = y_range) ) transform_position(data, squish_infinite, squish_infinite) @@ -259,21 +263,17 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, ) ) - # Rescale graticule for panel grid - sf::st_geometry(graticule) <- sf_rescale01(sf::st_geometry(graticule), x_range, y_range) - graticule$x_start <- rescale(graticule$x_start, from = x_range) - graticule$x_end <- rescale(graticule$x_end, from = x_range) - graticule$y_start <- rescale(graticule$y_start, from = y_range) - graticule$y_end <- rescale(graticule$y_end, from = y_range) - - list2( + panel_params <- list2( x_range = x_range, y_range = y_range, - graticule = graticule, crs = params$crs, default_crs = params$default_crs, !!!viewscales ) + + # Rescale graticule for panel grid + panel_params$graticule <- self$transform(graticule, panel_params) + panel_params }, train_panel_guides = function(self, panel_params, layers, params = list()) { @@ -408,12 +408,26 @@ sf_transform_xy <- function(data, target_crs, source_crs, authority_compliant = ## helper functions to normalize geometry and position data # normalize geometry data (variable x is geometry column) +# this is a wrapper for `sf::st_normalize()`, but deals with empty input and +# reversed ranges too sf_rescale01 <- function(x, x_range, y_range) { if (is.null(x)) { return(x) } - - sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) + mult <- cbind(1, 1) + if (isTRUE(x_range[1] > x_range[2])) { + x_range <- sort(x_range) + mult[1] <- -1 + } + if (isTRUE(y_range[1] > y_range[2])) { + y_range <- sort(y_range) + mult[2] <- -1 + } + x <- sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) + if (all(mult == 1)) { + return(x) + } + x * mult + pmax(-mult, 0) } # different limits methods @@ -536,7 +550,8 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, datum = sf::st_crs(4326), label_graticule = waiver(), label_axes = waiver(), lims_method = "cross", - ndiscr = 100, default = FALSE, clip = "on") { + ndiscr = 100, default = FALSE, clip = "on", + reverse = "none") { if (is.waiver(label_graticule) && is.waiver(label_axes)) { # if both `label_graticule` and `label_axes` are set to waive then we @@ -576,6 +591,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, label_axes = label_axes, label_graticule = label_graticule, ndiscr = ndiscr, + reverse = reverse, expand = expand, default = default, clip = clip diff --git a/R/coord-transform.R b/R/coord-transform.R index 1253529fdd..18230a1742 100644 --- a/R/coord-transform.R +++ b/R/coord-transform.R @@ -78,7 +78,8 @@ #' plot + coord_trans(x = "sqrt") #' } coord_trans <- function(x = "identity", y = "identity", xlim = NULL, ylim = NULL, - limx = deprecated(), limy = deprecated(), clip = "on", expand = TRUE) { + limx = deprecated(), limy = deprecated(), clip = "on", + expand = TRUE, reverse = "none") { if (lifecycle::is_present(limx)) { deprecate_warn0("3.3.0", "coord_trans(limx)", "coord_trans(xlim)") xlim <- limx @@ -99,6 +100,7 @@ coord_trans <- function(x = "identity", y = "identity", xlim = NULL, ylim = NULL trans = list(x = x, y = y), limits = list(x = xlim, y = ylim), expand = expand, + reverse = reverse, clip = clip ) } @@ -132,14 +134,17 @@ CoordTrans <- ggproto("CoordTrans", Coord, transform = function(self, data, panel_params) { # trans_x() and trans_y() needs to keep Inf values because this can be called # in guide_transform.axis() + reverse <- self$reverse %||% "none" + x_range <- switch(reverse, xy = , x = rev, identity)(panel_params$x.range) + y_range <- switch(reverse, xy = , y = rev, identity)(panel_params$y.range) trans_x <- function(data) { idx <- !is.infinite(data) - data[idx] <- transform_value(self$trans$x, data[idx], panel_params$x.range) + data[idx] <- transform_value(self$trans$x, data[idx], x_range) data } trans_y <- function(data) { idx <- !is.infinite(data) - data[idx] <- transform_value(self$trans$y, data[idx], panel_params$y.range) + data[idx] <- transform_value(self$trans$y, data[idx], y_range) data } @@ -158,14 +163,8 @@ CoordTrans <- ggproto("CoordTrans", Coord, ) }, - render_bg = function(panel_params, theme) { - guide_grid( - theme, - panel_params$x.minor, - panel_params$x.major, - panel_params$y.minor, - panel_params$y.major - ) + render_bg = function(self, panel_params, theme) { + guide_grid(theme, panel_params, self) }, render_axis_h = function(panel_params, theme) { diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index dc4e1b405d..7f4c3c9246 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -61,26 +61,18 @@ guide_axis_theta <- function(title = waiver(), theme = NULL, angle = waiver(), GuideAxisTheta <- ggproto( "GuideAxisTheta", GuideAxis, - extract_decor = function(scale, aesthetic, key, cap = "none", position, ...) { - # For theta position, we pretend we're left/right because that will put - # the correct opposite aesthetic as the line coordinates. - position <- switch(position, theta = "left", theta.sec = "right", position) - - GuideAxis$extract_decor( - scale = scale, aesthetic = aesthetic, - position = position, key = key, cap = cap - ) - }, - transform = function(params, coord, panel_params) { + opposite_var <- setdiff(c("x", "y"), params$aesthetic) + opposite_value <- switch(params$position, top = , right = , theta.sec = -Inf, Inf) + if (is.unsorted(panel_params$inner_radius %||% NA)) { + opposite_value <- -opposite_value + } if (nrow(params$key) > 0) { - opposite <- setdiff(c("x", "y"), params$aesthetic) - params$key[[opposite]] <- switch(params$position, - theta.sec = -Inf, - top = -Inf, - right = -Inf, - Inf) + params$key[[opposite_var]] <- opposite_value + } + if (nrow(params$decor) > 0) { + params$decor[[opposite_var]] <- opposite_value } params <- GuideAxis$transform(params, coord, panel_params) diff --git a/R/guides-grid.R b/R/guides-grid.R index 9ae79a19a9..6b8f116a24 100644 --- a/R/guides-grid.R +++ b/R/guides-grid.R @@ -3,32 +3,54 @@ # be converted to `'native'` units by polylineGrob() downstream # # Any minor lines coinciding with major lines will be removed -guide_grid <- function(theme, x.minor, x.major, y.minor, y.major) { +guide_grid <- function(theme, panel_params, coord, square = TRUE) { - x.minor <- setdiff(x.minor, x.major) - y.minor <- setdiff(y.minor, y.major) + x_major <- panel_params$x$mapped_breaks() + x_minor <- setdiff(panel_params$x$mapped_breaks_minor(), x_major) - ggname("grill", grobTree( - element_render(theme, "panel.background"), - if (length(y.minor) > 0) element_render( - theme, "panel.grid.minor.y", - x = rep(0:1, length(y.minor)), y = rep(y.minor, each = 2), - id.lengths = rep(2, length(y.minor)) - ), - if (length(x.minor) > 0) element_render( - theme, "panel.grid.minor.x", - x = rep(x.minor, each = 2), y = rep(0:1, length(x.minor)), - id.lengths = rep(2, length(x.minor)) - ), - if (length(y.major) > 0) element_render( - theme, "panel.grid.major.y", - x = rep(0:1, length(y.major)), y = rep(y.major, each = 2), - id.lengths = rep(2, length(y.major)) - ), - if (length(x.major) > 0) element_render( - theme, "panel.grid.major.x", - x = rep(x.major, each = 2), y = rep(0:1, length(x.major)), - id.lengths = rep(2, length(x.major)) - ) - )) + y_major <- panel_params$y$mapped_breaks() + y_minor <- setdiff(panel_params$y$mapped_breaks_minor(), y_major) + + transform <- if (isTRUE(square)) { + function(x) coord$transform(x, panel_params) + } else { + function(x) coord_munch(coord, x, panel_params) + } + + grill <- Map( + f = breaks_as_grid, + var = list(y_minor, x_minor, y_major, x_major), + type = c("minor.y", "minor.x", "major.y", "major.x"), + MoreArgs = list(theme = theme, transform = transform) + ) + grill <- compact(grill) + + background <- element_render(theme, "panel.background") + if (!isTRUE(square) && !is.zero(background)) { + gp <- background$gp + background <- data_frame0(x = c(1, 1, -1, -1), y = c(1, -1, -1, 1)) * Inf + background <- coord_munch(coord, background, panel_params, is_closed = TRUE) + background <- polygonGrob(x = background$x, y = background$y, gp = gp) + } + + ggname("grill", inject(grobTree(background, !!!grill))) +} + +breaks_as_grid <- function(var, type, transform, theme) { + n <- length(var) + if (n < 1) { + return(NULL) + } + df <- data_frame0( + var = rep(var, each = 2), + alt = rep(c(-Inf, Inf), n), + group = rep(seq_along(var), each = 2) + ) + colnames(df)[1:2] <- + switch(type, major.y = , minor.y = c("y", "x"), c("x", "y")) + df <- transform(df) + element_render( + theme, paste0("panel.grid.", type), x = df$x, y = df$y, + id.lengths = vec_unrep(df$group)$times + ) } diff --git a/R/scale-.R b/R/scale-.R index 53c9f4ee66..4bf54328b3 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -128,20 +128,23 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam } transform <- as.transform(transform) - limits <- allow_lambda(limits) - - if (!is.null(limits) && !is.function(limits)) { - limits <- transform$transform(limits) - } - check_continuous_limits(limits, call = call) # Convert formula to function if appropriate + limits <- allow_lambda(limits) breaks <- allow_lambda(breaks) labels <- allow_lambda(labels) rescaler <- allow_lambda(rescaler) oob <- allow_lambda(oob) minor_breaks <- allow_lambda(minor_breaks) + if (!is.null(limits) && !is.function(limits)) { + limits <- transform$transform(limits) + if (!anyNA(limits)) { + limits <- sort(limits) + } + } + check_continuous_limits(limits, call = call) + ggproto(NULL, super, call = call, @@ -321,9 +324,6 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name = } transform <- as.transform(transform) - if (!is.null(limits) && !is.function(limits)) { - limits <- transform$transform(limits) - } # Convert formula input to function if appropriate limits <- allow_lambda(limits) @@ -332,6 +332,13 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name = rescaler <- allow_lambda(rescaler) oob <- allow_lambda(oob) + if (!is.null(limits) && !is.function(limits)) { + limits <- transform$transform(limits) + if (!anyNA(limits)) { + limits <- sort(limits) + } + } + ggproto(NULL, super, call = call, diff --git a/R/scale-expansion.R b/R/scale-expansion.R index 0edb01f1b8..a132f5cd22 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -206,8 +206,8 @@ expand_limits_continuous_trans <- function(limits, expand = expansion(0, 0), continuous_range <- ifelse(is.finite(final_scale_limits), final_scale_limits, limits) list( - continuous_range_coord = continuous_range_coord, - continuous_range = continuous_range + continuous_range_coord = sort(continuous_range_coord), + continuous_range = sort(continuous_range) ) } diff --git a/R/scale-view.R b/R/scale-view.R index 510f99f837..350d27e9c0 100644 --- a/R/scale-view.R +++ b/R/scale-view.R @@ -117,6 +117,9 @@ ViewScale <- ggproto("ViewScale", NULL, rescale = function(self, x) { self$scale$rescale(x, self$limits, self$continuous_range) }, + reverse = function(self, x) { + self$scale$rescale(x, rev(self$limits), rev(self$continuous_range)) + }, map = function(self, x) { if (self$is_discrete()) { self$scale$map(x, self$limits) @@ -127,6 +130,16 @@ ViewScale <- ggproto("ViewScale", NULL, make_title = function(self, title) { self$scale$make_title(title) }, + mapped_breaks = function(self) { + self$map(self$get_breaks()) + }, + mapped_breaks_minor = function(self) { + b <- self$get_breaks_minor() + if (is.null(b)) { + return(NULL) + } + self$map(b) + }, break_positions = function(self) { self$rescale(self$get_breaks()) }, diff --git a/man/coord_cartesian.Rd b/man/coord_cartesian.Rd index 20987083a5..15afad523a 100644 --- a/man/coord_cartesian.Rd +++ b/man/coord_cartesian.Rd @@ -9,7 +9,8 @@ coord_cartesian( ylim = NULL, expand = TRUE, default = FALSE, - clip = "on" + clip = "on", + reverse = "none" ) } \arguments{ @@ -36,6 +37,11 @@ drawing of data points anywhere on the plot, including in the plot margins. If limits are set via \code{xlim} and \code{ylim} and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.} + +\item{reverse}{A string giving which directions to reverse. \code{"none"} +(default) keeps directions as is. \code{"x"} and \code{"y"} can be used to reverse +their respective directions. \code{"xy"} can be used to reverse both +directions.} } \description{ The Cartesian coordinate system is the most familiar, and common, type of diff --git a/man/coord_fixed.Rd b/man/coord_fixed.Rd index 8877019a91..a3d8d358b7 100644 --- a/man/coord_fixed.Rd +++ b/man/coord_fixed.Rd @@ -5,7 +5,14 @@ \alias{coord_equal} \title{Cartesian coordinates with fixed "aspect ratio"} \usage{ -coord_fixed(ratio = 1, xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") +coord_fixed( + ratio = 1, + xlim = NULL, + ylim = NULL, + expand = TRUE, + clip = "on", + reverse = "none" +) } \arguments{ \item{ratio}{aspect ratio, expressed as \code{y / x}} @@ -28,6 +35,11 @@ drawing of data points anywhere on the plot, including in the plot margins. If limits are set via \code{xlim} and \code{ylim} and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.} + +\item{reverse}{A string giving which directions to reverse. \code{"none"} +(default) keeps directions as is. \code{"x"} and \code{"y"} can be used to reverse +their respective directions. \code{"xy"} can be used to reverse both +directions.} } \description{ A fixed scale coordinate system forces a specified ratio between the diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index aadbd9b00f..12957c2fd9 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -12,11 +12,12 @@ coord_radial( start = 0, end = NULL, expand = TRUE, - direction = 1, + direction = deprecated(), clip = "off", r.axis.inside = NULL, rotate.angle = FALSE, inner.radius = 0, + reverse = "none", r_axis_inside = deprecated(), rotate_angle = deprecated() ) @@ -57,7 +58,12 @@ in accordance with the computed \code{theta} position. If \code{FALSE} (default) no such transformation is performed. Can be useful to rotate text geoms in alignment with the coordinates.} -\item{inner.radius}{A \code{numeric} between 0 and 1 setting the size of a inner.radius hole.} +\item{inner.radius}{A \code{numeric} between 0 and 1 setting the size of a +inner radius hole.} + +\item{reverse}{A string giving which directions to reverse. \code{"none"} +(default) keep directions as is. \code{"theta"} reverses the angle and \code{"r"} +reverses the radius. \code{"thetar"} reverses both the angle and the radius.} \item{r_axis_inside, rotate_angle}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} } diff --git a/man/coord_trans.Rd b/man/coord_trans.Rd index d1f46dc1ee..0d9d2d6f79 100644 --- a/man/coord_trans.Rd +++ b/man/coord_trans.Rd @@ -12,7 +12,8 @@ coord_trans( limx = deprecated(), limy = deprecated(), clip = "on", - expand = TRUE + expand = TRUE, + reverse = "none" ) } \arguments{ @@ -38,6 +39,11 @@ Giving a logical vector will separately control the expansion for the four directions (top, left, bottom and right). The \code{expand} argument will be recycled to length 4 if necessary. Alternatively, can be a named logical vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} + +\item{reverse}{A string giving which directions to reverse. \code{"none"} +(default) keeps directions as is. \code{"x"} and \code{"y"} can be used to reverse +their respective directions. \code{"xy"} can be used to reverse both +directions.} } \description{ \code{coord_trans()} is different to scale transformations in that it occurs after diff --git a/man/ggsf.Rd b/man/ggsf.Rd index 7424d4107f..1fee9f59bb 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -25,7 +25,8 @@ coord_sf( lims_method = "cross", ndiscr = 100, default = FALSE, - clip = "on" + clip = "on", + reverse = "none" ) geom_sf( @@ -179,6 +180,11 @@ limits are set via \code{xlim} and \code{ylim} and some data points fall outside limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.} +\item{reverse}{A string giving which directions to reverse. \code{"none"} +(default) keeps directions as is. \code{"x"} and \code{"y"} can be used to reverse +their respective directions. \code{"xy"} can be used to reverse both +directions.} + \item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}}. If specified and \code{inherit.aes = TRUE} (the default), it is combined with the default mapping at the top level of the plot. You must supply \code{mapping} if there is no plot diff --git a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg index caa297b3f5..c01f91abbc 100644 --- a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg +++ b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg @@ -29,17 +29,17 @@ - - - - - - - - - - - + + + + + + + + + + + cat strawberry cake diff --git a/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg index 59e7973b41..497db8dcf4 100644 --- a/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg +++ b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg @@ -29,16 +29,19 @@ - - - - - - - - - - + + + + + + + + + + + + + 0 diff --git a/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg b/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg index 212100c87c..b75d829d47 100644 --- a/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg +++ b/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg @@ -29,20 +29,25 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg b/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg index bc58f6429b..03d06791cf 100644 --- a/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg +++ b/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg @@ -29,21 +29,25 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg b/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg index b6cfa798fc..48b903c6f3 100644 --- a/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg +++ b/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg @@ -29,47 +29,52 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg b/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg index 18609a9a74..9b4cf580e7 100644 --- a/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg +++ b/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg @@ -29,16 +29,20 @@ - - - - - - - - - - + + + + + + + + + + + + + + diff --git a/tests/testthat/test-coord-cartesian.R b/tests/testthat/test-coord-cartesian.R index 23bed331ae..5bb16c4cd1 100644 --- a/tests/testthat/test-coord-cartesian.R +++ b/tests/testthat/test-coord-cartesian.R @@ -22,6 +22,19 @@ test_that("cartesian coords throws error when limits are badly specified", { expect_snapshot_error(ggplot() + coord_cartesian(ylim=1:3)) }) +test_that("cartesian coords can be reversed", { + p <- ggplot(data_frame0(x = c(0, 2), y = c(0, 2))) + + aes(x = x, y = y) + + geom_point() + + coord_cartesian( + xlim = c(-1, 3), ylim = c(-1, 3), expand = FALSE, + reverse = "xy" + ) + grob <- layer_grob(p)[[1]] + expect_equal(as.numeric(grob$x), c(0.75, 0.25)) + expect_equal(as.numeric(grob$y), c(0.75, 0.25)) +}) + # Visual tests ------------------------------------------------------------ diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index 27b641f964..2b07d96b21 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -181,6 +181,23 @@ test_that("when both x and y are AsIs, they are not transformed", { }) +test_that("radial coords can be reversed", { + p <- ggplot(data_frame0(x = c(0, 2), y = c(0, 2))) + + aes(x = x, y = y) + + geom_point() + + scale_x_continuous(limits = c(-1, 3), expand = c(0, 0)) + + scale_y_continuous(limits = c(-1, 3), expand = c(0, 0)) + fwd <- coord_radial(start = 0.5 * pi, end = 1.5 * pi, reverse = "none") + rev <- coord_radial(start = 0.5 * pi, end = 1.5 * pi, reverse = "thetar") + + fwd <- layer_grob(p + fwd)[[1]] + rev <- layer_grob(p + rev)[[1]] + + expect_equal(as.numeric(fwd$x), rev(as.numeric(rev$x))) + expect_equal(as.numeric(fwd$y), rev(as.numeric(rev$y))) +}) + + # Visual tests ------------------------------------------------------------ #TODO: Once {vdiffr} supports non-rectangular clipping paths, we should add a diff --git a/tests/testthat/test-coord-transform.R b/tests/testthat/test-coord-transform.R index f3dd4a6b00..7621f5ed9c 100644 --- a/tests/testthat/test-coord-transform.R +++ b/tests/testthat/test-coord-transform.R @@ -131,3 +131,17 @@ test_that("coord_trans() throws error when limits are badly specified", { # throws error when limit's length is different than two expect_snapshot_error(ggplot() + coord_trans(ylim=1:3)) }) + +test_that("transformed coords can be reversed", { + p <- ggplot(data_frame0(x = c(1, 100), y = c(1, 100))) + + aes(x = x, y = y) + + geom_point() + + coord_trans( + x = "log10", y = "log10", + xlim = c(0.1, 1000), ylim = c(0.1, 1000), expand = FALSE, + reverse = "xy" + ) + grob <- layer_grob(p)[[1]] + expect_equal(as.numeric(grob$x), c(0.75, 0.25)) + expect_equal(as.numeric(grob$y), c(0.75, 0.25)) +}) diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index 70cdbb9d20..516d2fa9ec 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -388,6 +388,20 @@ test_that("coord_sf() throws error when limits are badly specified", { expect_snapshot_error(ggplot() + coord_sf(ylim=1:3)) }) +test_that("sf coords can be reversed", { + skip_if_not_installed("sf") + + p <- ggplot(sf::st_multipoint(cbind(c(0, 2), c(0, 2)))) + + geom_sf() + + coord_sf( + xlim = c(-1, 3), ylim = c(-1, 3), expand = FALSE, + reverse = "xy" + ) + grob <- layer_grob(p)[[1]] + expect_equal(as.numeric(grob$x), c(0.75, 0.25)) + expect_equal(as.numeric(grob$y), c(0.75, 0.25)) +}) + test_that("coord_sf() can render with empty graticules", { skip_if_not_installed("sf") diff --git a/tests/testthat/test-scale-expansion.R b/tests/testthat/test-scale-expansion.R index 378742de8c..41bd9430e7 100644 --- a/tests/testthat/test-scale-expansion.R +++ b/tests/testthat/test-scale-expansion.R @@ -65,7 +65,7 @@ test_that("expand_limits_discrete() can override limits with an empty range", { test_that("expand_limits_discrete() can override limits with a discrete range", { expect_identical(expand_limits_discrete(c("one", "two"), coord_limits = c(NA, NA)), c(1, 2)) expect_identical(expand_limits_discrete(c("one", "two"), coord_limits = c(NA, 3)), c(1, 3)) - expect_identical(expand_limits_discrete(c("one", "two"), coord_limits = c(3, NA)), c(3, 2)) + expect_identical(expand_limits_discrete(c("one", "two"), coord_limits = c(3, NA)), c(2, 3)) }) test_that("expand_limits_discrete() can override limits with a continuous range", { @@ -106,7 +106,7 @@ test_that("expand_limits_continuous_trans() works with inverted transformations" ) expect_identical(limit_info$continuous_range, c(0, 3)) - expect_identical(limit_info$continuous_range_coord, c(0, -3)) + expect_identical(limit_info$continuous_range_coord, c(-3, 0)) }) test_that("expand_limits_scale_discrete() begrudgingly handles numeric limits", { From c00a154d22c42054fe4393a18d2c849ffa047135 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:43:47 +0100 Subject: [PATCH 179/264] Manual stat (#6103) * write `stat_manual()` * document * add test * add news bullet * fix examples with double point layers * add to pkgdown index * document `geom` slot --- DESCRIPTION | 1 + NAMESPACE | 2 + NEWS.md | 1 + R/stat-manual.R | 131 ++++++++++++++++++++ _pkgdown.yml | 1 + man/ggplot2-ggproto.Rd | 16 +-- man/stat_manual.Rd | 199 ++++++++++++++++++++++++++++++ tests/testthat/test-stat-manual.R | 18 +++ 8 files changed, 362 insertions(+), 7 deletions(-) create mode 100644 R/stat-manual.R create mode 100644 man/stat_manual.Rd create mode 100644 tests/testthat/test-stat-manual.R diff --git a/DESCRIPTION b/DESCRIPTION index 84b7e6357b..978cbf725c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -254,6 +254,7 @@ Collate: 'stat-ellipse.R' 'stat-function.R' 'stat-identity.R' + 'stat-manual.R' 'stat-qq-line.R' 'stat-qq.R' 'stat-quantilemethods.R' diff --git a/NAMESPACE b/NAMESPACE index 8f4f9c5856..391f435b30 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -265,6 +265,7 @@ export(StatEcdf) export(StatEllipse) export(StatFunction) export(StatIdentity) +export(StatManual) export(StatQq) export(StatQqLine) export(StatQuantile) @@ -691,6 +692,7 @@ export(stat_ecdf) export(stat_ellipse) export(stat_function) export(stat_identity) +export(stat_manual) export(stat_qq) export(stat_qq_line) export(stat_quantile) diff --git a/NEWS.md b/NEWS.md index 8214635e8c..42a34453ec 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* New stat: `stat_manual()` for arbitrary computations (@teunbrand, #3501) * Reversal of a dimension, typically 'x' or 'y', is now controlled by the `reverse` argument in `coord_cartesian()`, `coord_fixed()`, `coord_radial()` and `coord_sf()`. In `coord_radial()`, this replaces the older `direction` diff --git a/R/stat-manual.R b/R/stat-manual.R new file mode 100644 index 0000000000..994c8d622e --- /dev/null +++ b/R/stat-manual.R @@ -0,0 +1,131 @@ + +#' Manually compute transformations +#' +#' `stat_manual()` takes a function that computes a data transformation for +#' every group. +#' +#' @inheritParams layer +#' @inheritParams geom_point +#' @param fun Function that takes a data frame as input and returns a data +#' frame or data frame-like list as output. The default (`identity()`) returns +#' the data unchanged. +#' @param args A list of arguments to pass to the function given in `fun`. +#' +#' @eval rd_aesthetics("stat", "manual") +#' @section Aesthetics: +#' Input aesthetics are determined by the `fun` argument. Output aesthetics must +#' include those required by `geom`. Any aesthetic that is constant within a +#' group will be preserved even if dropped by `fun`. +#' +#' @export +#' +#' @examples +#' # A standard scatterplot +#' p <- ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + +#' geom_point() +#' +#' # The default just displays points as-is +#' p + stat_manual() +#' +#' # Using a custom function +#' make_hull <- function(data) { +#' hull <- chull(x = data$x, y = data$y) +#' data.frame(x = data$x[hull], y = data$y[hull]) +#' } +#' +#' p + stat_manual( +#' geom = "polygon", +#' fun = make_hull, +#' fill = NA +#' ) +#' +#' # Using the `with` function with quoting +#' p + stat_manual( +#' fun = with, +#' args = list(expr = quote({ +#' hull <- chull(x, y) +#' list(x = x[hull], y = y[hull]) +#' })), +#' geom = "polygon", fill = NA +#' ) +#' +#' # Using the `transform` function with quoting +#' p + stat_manual( +#' geom = "segment", +#' fun = transform, +#' args = list( +#' xend = quote(mean(x)), +#' yend = quote(mean(y)) +#' ) +#' ) +#' +#' # Using dplyr verbs with `vars()` +#' if (requireNamespace("dplyr", quietly = TRUE)) { +#' +#' # Get centroids with `summarise()` +#' p + stat_manual( +#' size = 10, shape = 21, +#' fun = dplyr::summarise, +#' args = vars(x = mean(x), y = mean(y)) +#' ) +#' +#' # Connect to centroid with `mutate` +#' p + stat_manual( +#' geom = "segment", +#' fun = dplyr::mutate, +#' args = vars(xend = mean(x), yend = mean(y)) +#' ) +#' +#' # Computing hull with `reframe()` +#' p + stat_manual( +#' geom = "polygon", fill = NA, +#' fun = dplyr::reframe, +#' args = vars(hull = chull(x, y), x = x[hull], y = y[hull]) +#' ) +#' } +stat_manual <- function( + mapping = NULL, + data = NULL, + geom = "point", + position = "identity", + ..., + fun = identity, + args = list(), + na.rm = FALSE, + show.legend = NA, + inherit.aes = TRUE) { + + layer( + data = data, + mapping = mapping, + stat = StatManual, + geom = geom, + position = position, + show.legend = show.legend, + inherit.aes = inherit.aes, + params = list2( + na.rm = na.rm, + fun = fun, + args = args, + ... + ) + ) +} + +#' @rdname ggplot2-ggproto +#' @format NULL +#' @usage NULL +#' @export +StatManual <- ggproto( + "StatManual", Stat, + + setup_params = function(data, params) { + params$fun <- allow_lambda(params$fun) + check_function(params$fun, arg = "fun") + params + }, + + compute_group = function(data, scales, fun = identity, args = list()) { + as_gg_data_frame(inject(fun(data, !!!args))) + } +) diff --git a/_pkgdown.yml b/_pkgdown.yml index 1e4ea6a727..593f015590 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -68,6 +68,7 @@ reference: - stat_summary_bin - stat_unique - stat_sf_coordinates + - stat_manual - after_stat - subtitle: Position adjustment diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd index 602ce35e4f..ea01c29996 100644 --- a/man/ggplot2-ggproto.Rd +++ b/man/ggplot2-ggproto.Rd @@ -19,13 +19,14 @@ % R/position-dodge.R, R/position-dodge2.R, R/position-identity.R, % R/position-jitter.R, R/position-jitterdodge.R, R/position-nudge.R, % R/position-stack.R, R/scale-.R, R/scale-binned.R, R/scale-continuous.R, -% R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, R/stat-align.R, -% R/stat-bin.R, R/stat-bin2d.R, R/stat-bindot.R, R/stat-binhex.R, -% R/stat-boxplot.R, R/stat-contour.R, R/stat-count.R, R/stat-density-2d.R, -% R/stat-density.R, R/stat-ecdf.R, R/stat-ellipse.R, R/stat-function.R, -% R/stat-identity.R, R/stat-qq-line.R, R/stat-qq.R, R/stat-quantilemethods.R, -% R/stat-smooth.R, R/stat-sum.R, R/stat-summary-2d.R, R/stat-summary-bin.R, -% R/stat-summary-hex.R, R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R +% R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, +% R/stat-align.R, R/stat-bin.R, R/stat-bin2d.R, R/stat-bindot.R, +% R/stat-binhex.R, R/stat-boxplot.R, R/stat-contour.R, R/stat-count.R, +% R/stat-density-2d.R, R/stat-density.R, R/stat-ecdf.R, R/stat-ellipse.R, +% R/stat-function.R, R/stat-identity.R, R/stat-manual.R, R/stat-qq-line.R, +% R/stat-qq.R, R/stat-quantilemethods.R, R/stat-smooth.R, R/stat-sum.R, +% R/stat-summary-2d.R, R/stat-summary-bin.R, R/stat-summary-hex.R, +% R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R \docType{data} \name{ggplot2-ggproto} \alias{ggplot2-ggproto} @@ -139,6 +140,7 @@ \alias{StatEllipse} \alias{StatFunction} \alias{StatIdentity} +\alias{StatManual} \alias{StatQqLine} \alias{StatQq} \alias{StatQuantile} diff --git a/man/stat_manual.Rd b/man/stat_manual.Rd new file mode 100644 index 0000000000..f19a03128e --- /dev/null +++ b/man/stat_manual.Rd @@ -0,0 +1,199 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/stat-manual.R +\name{stat_manual} +\alias{stat_manual} +\title{Manually compute transformations} +\usage{ +stat_manual( + mapping = NULL, + data = NULL, + geom = "point", + position = "identity", + ..., + fun = identity, + args = list(), + na.rm = FALSE, + show.legend = NA, + inherit.aes = TRUE +) +} +\arguments{ +\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}}. If specified and +\code{inherit.aes = TRUE} (the default), it is combined with the default mapping +at the top level of the plot. You must supply \code{mapping} if there is no plot +mapping.} + +\item{data}{The data to be displayed in this layer. There are three +options: + +If \code{NULL}, the default, the data is inherited from the plot +data as specified in the call to \code{\link[=ggplot]{ggplot()}}. + +A \code{data.frame}, or other object, will override the plot +data. All objects will be fortified to produce a data frame. See +\code{\link[=fortify]{fortify()}} for which variables will be created. + +A \code{function} will be called with a single argument, +the plot data. The return value must be a \code{data.frame}, and +will be used as the layer data. A \code{function} can be created +from a \code{formula} (e.g. \code{~ head(.x, 10)}).} + +\item{geom}{The geometric object to use to display the data for this layer. +When using a \verb{stat_*()} function to construct a layer, the \code{geom} argument +can be used to override the default coupling between stats and geoms. The +\code{geom} argument accepts the following: +\itemize{ +\item A \code{Geom} ggproto subclass, for example \code{GeomPoint}. +\item A string naming the geom. To give the geom as a string, strip the +function name of the \code{geom_} prefix. For example, to use \code{geom_point()}, +give the geom as \code{"point"}. +\item For more information and other ways to specify the geom, see the +\link[=layer_geoms]{layer geom} documentation. +}} + +\item{position}{A position adjustment to use on the data for this layer. This +can be used in various ways, including to prevent overplotting and +improving the display. The \code{position} argument accepts the following: +\itemize{ +\item The result of calling a position function, such as \code{position_jitter()}. +This method allows for passing extra arguments to the position. +\item A string naming the position adjustment. To give the position as a +string, strip the function name of the \code{position_} prefix. For example, +to use \code{position_jitter()}, give the position as \code{"jitter"}. +\item For more information and other ways to specify the position, see the +\link[=layer_positions]{layer position} documentation. +}} + +\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}'s \code{params} argument. These +arguments broadly fall into one of 4 categories below. Notably, further +arguments to the \code{position} argument, or aesthetics that are required +can \emph{not} be passed through \code{...}. Unknown arguments that are not part +of the 4 categories below are ignored. +\itemize{ +\item Static aesthetics that are not mapped to a scale, but are at a fixed +value and apply to the layer as a whole. For example, \code{colour = "red"} +or \code{linewidth = 3}. The geom's documentation has an \strong{Aesthetics} +section that lists the available options. The 'required' aesthetics +cannot be passed on to the \code{params}. Please note that while passing +unmapped aesthetics as vectors is technically possible, the order and +required length is not guaranteed to be parallel to the input data. +\item When constructing a layer using +a \verb{stat_*()} function, the \code{...} argument can be used to pass on +parameters to the \code{geom} part of the layer. An example of this is +\code{stat_density(geom = "area", outline.type = "both")}. The geom's +documentation lists which parameters it can accept. +\item Inversely, when constructing a layer using a +\verb{geom_*()} function, the \code{...} argument can be used to pass on parameters +to the \code{stat} part of the layer. An example of this is +\code{geom_area(stat = "density", adjust = 0.5)}. The stat's documentation +lists which parameters it can accept. +\item The \code{key_glyph} argument of \code{\link[=layer]{layer()}} may also be passed on through +\code{...}. This can be one of the functions described as +\link[=draw_key]{key glyphs}, to change the display of the layer in the legend. +}} + +\item{fun}{Function that takes a data frame as input and returns a data +frame or data frame-like list as output. The default (\code{identity()}) returns +the data unchanged.} + +\item{args}{A list of arguments to pass to the function given in \code{fun}.} + +\item{na.rm}{If \code{FALSE}, the default, missing values are removed with +a warning. If \code{TRUE}, missing values are silently removed.} + +\item{show.legend}{logical. Should this layer be included in the legends? +\code{NA}, the default, includes if any aesthetics are mapped. +\code{FALSE} never includes, and \code{TRUE} always includes. +It can also be a named logical vector to finely select the aesthetics to +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} + +\item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics, +rather than combining with them. This is most useful for helper functions +that define both data and aesthetics and shouldn't inherit behaviour from +the default plot specification, e.g. \code{\link[=borders]{borders()}}.} +} +\description{ +\code{stat_manual()} takes a function that computes a data transformation for +every group. +} +\section{Aesthetics}{ + +\code{stat_manual()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \code{\link[=aes_group_order]{group}} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. + + +Input aesthetics are determined by the \code{fun} argument. Output aesthetics must +include those required by \code{geom}. Any aesthetic that is constant within a +group will be preserved even if dropped by \code{fun}. +} + +\examples{ +# A standard scatterplot +p <- ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + + geom_point() + +# The default just displays points as-is +p + stat_manual() + +# Using a custom function +make_hull <- function(data) { + hull <- chull(x = data$x, y = data$y) + data.frame(x = data$x[hull], y = data$y[hull]) +} + +p + stat_manual( + geom = "polygon", + fun = make_hull, + fill = NA +) + +# Using the `with` function with quoting +p + stat_manual( + fun = with, + args = list(expr = quote({ + hull <- chull(x, y) + list(x = x[hull], y = y[hull]) + })), + geom = "polygon", fill = NA +) + +# Using the `transform` function with quoting +p + stat_manual( + geom = "segment", + fun = transform, + args = list( + xend = quote(mean(x)), + yend = quote(mean(y)) + ) +) + +# Using dplyr verbs with `vars()` +if (requireNamespace("dplyr", quietly = TRUE)) { + + # Get centroids with `summarise()` + p + stat_manual( + size = 10, shape = 21, + fun = dplyr::summarise, + args = vars(x = mean(x), y = mean(y)) + ) + + # Connect to centroid with `mutate` + p + stat_manual( + geom = "segment", + fun = dplyr::mutate, + args = vars(xend = mean(x), yend = mean(y)) + ) + + # Computing hull with `reframe()` + p + stat_manual( + geom = "polygon", fill = NA, + fun = dplyr::reframe, + args = vars(hull = chull(x, y), x = x[hull], y = y[hull]) + ) +} +} diff --git a/tests/testthat/test-stat-manual.R b/tests/testthat/test-stat-manual.R new file mode 100644 index 0000000000..5e2ca54376 --- /dev/null +++ b/tests/testthat/test-stat-manual.R @@ -0,0 +1,18 @@ +test_that("stat_manual can take a function", { + + centroid <- function(data) data.frame(x = mean(data$x), y = mean(data$y)) + + layer <- get_layer_data( + ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + + stat_manual(fun = centroid, size = 5, shape = 21) + ) + + expect_equal( + layer$x, + vapply(split(mtcars$disp, mtcars$cyl), mean, numeric(1), USE.NAMES = FALSE) + ) + expect_equal( + layer$y, + vapply(split(mtcars$mpg, mtcars$cyl), mean, numeric(1), USE.NAMES = FALSE) + ) +}) From 73b41194b036776a12d3ec7d5adaeda5d4f81a33 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:50:00 +0100 Subject: [PATCH 180/264] Setting panel sizes in `theme()` (#6094) * add panel.widths/panel.heights theme elements * add `set_panel_size()` method to layout * add test * document * add aspect ratio warning * turn off respect * `set_panel_size()` is a Facet method --- NEWS.md | 1 + R/facet-.R | 47 +++++++++++++++++++++++++++++++++++++ R/layout.R | 2 +- R/theme-elements.R | 2 ++ R/theme.R | 5 ++++ man/theme.Rd | 6 +++++ tests/testthat/test-theme.R | 42 ++++++++++++++++++++++++++++++++- 7 files changed, 103 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 42a34453ec..b7563b0dee 100644 --- a/NEWS.md +++ b/NEWS.md @@ -238,6 +238,7 @@ (@teunbrand, #4722, #6069). * `geom_abline()` clips to the panel range in the vertical direction too (@teunbrand, #6086). +* Added `panel.widths` and `panel.heights` to `theme()` (#5338, @teunbrand). # ggplot2 3.5.1 diff --git a/R/facet-.R b/R/facet-.R index def19f221a..b124b54872 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -263,6 +263,53 @@ Facet <- ggproto("Facet", NULL, }, format_strip_labels = function(layout, params) { return() + }, + set_panel_size = function(table, theme) { + + new_widths <- calc_element("panel.widths", theme) + new_heights <- calc_element("panel.heights", theme) + + if (is.null(new_widths) && is.null(new_heights)) { + return(table) + } + + if (isTRUE(table$respect)) { + args <- !c(is.null(new_widths), is.null(new_heights)) + args <- c("panel.widths", "panel.heights")[args] + cli::cli_warn( + "Aspect ratios are overruled by {.arg {args}} theme element{?s}." + ) + table$respect <- FALSE + } + + rows <- panel_rows(table) + cols <- panel_cols(table) + + if (length(new_widths) == 1L && nrow(cols) > 1L) { + # Get total size of non-panel widths in between panels + extra <- setdiff(seq(min(cols$l), max(cols$r)), union(cols$l, cols$r)) + extra <- unit(sum(width_cm(table$widths[extra])), "cm") + # Distribute width proportionally + relative <- as.numeric(table$widths[cols$l]) # assumed to be simple units + new_widths <- (new_widths - extra) * (relative / sum(relative)) + } + if (!is.null(new_widths)) { + table$widths[cols$l] <- rep(new_widths, length.out = nrow(cols)) + } + + if (length(new_heights) == 1L && nrow(rows) > 1L) { + # Get total size of non-panel heights in between panels + extra <- setdiff(seq(min(rows$t), max(rows$t)), union(rows$t, rows$b)) + extra <- unit(sum(height_cm(table$heights[extra])), "cm") + # Distribute height proportionally + relative <- as.numeric(table$heights[rows$t]) # assumed to be simple units + new_heights <- (new_heights - extra) * (relative / sum(relative)) + } + if (!is.null(new_heights)) { + table$heights[rows$t] <- rep(new_heights, length.out = nrow(rows)) + } + + table } ) diff --git a/R/layout.R b/R/layout.R index 5954031d20..d3cad0ffeb 100644 --- a/R/layout.R +++ b/R/layout.R @@ -94,6 +94,7 @@ Layout <- ggproto("Layout", NULL, theme, self$facet_params ) + plot_table <- self$facet$set_panel_size(plot_table, theme) # Draw individual labels, then add to gtable labels <- self$coord$labels( @@ -300,7 +301,6 @@ Layout <- ggproto("Layout", NULL, } ) - # Helpers ----------------------------------------------------------------- # Function for applying scale method to multiple variables in a given diff --git a/R/theme-elements.R b/R/theme-elements.R index b1cb67b046..947e4e0af3 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -639,6 +639,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { panel.grid.minor.x = el_def("element_line", "panel.grid.minor"), panel.grid.minor.y = el_def("element_line", "panel.grid.minor"), panel.ontop = el_def("logical"), + panel.widths = el_def("unit"), + panel.heights = el_def("unit"), strip.background = el_def("element_rect", "rect"), strip.background.x = el_def("element_rect", "strip.background"), diff --git a/R/theme.R b/R/theme.R index 04ab2edf98..2ebd892f62 100644 --- a/R/theme.R +++ b/R/theme.R @@ -143,6 +143,9 @@ #' and x axis grid lines are vertical. `panel.grid.*.*` inherits from #' `panel.grid.*` which inherits from `panel.grid`, which in turn inherits #' from `line` +#' @param panel.widths,panel.heights Sizes for panels (`units`). Can be a +#' single unit to set the total size for the panel area, or a unit vector to +#' set the size of individual panels. #' @param panel.ontop option to place the panel (background, gridlines) over #' the data layers (`logical`). Usually used with a transparent or blank #' `panel.background`. @@ -427,6 +430,8 @@ theme <- function(..., panel.grid.minor.x, panel.grid.minor.y, panel.ontop, + panel.widths, + panel.heights, plot.background, plot.title, plot.title.position, diff --git a/man/theme.Rd b/man/theme.Rd index 869e45ea71..d28c10b149 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -121,6 +121,8 @@ theme( panel.grid.minor.x, panel.grid.minor.y, panel.ontop, + panel.widths, + panel.heights, plot.background, plot.title, plot.title.position, @@ -311,6 +313,10 @@ from \code{line}} the data layers (\code{logical}). Usually used with a transparent or blank \code{panel.background}.} +\item{panel.widths, panel.heights}{Sizes for panels (\code{units}). Can be a +single unit to set the total size for the panel area, or a unit vector to +set the size of individual panels.} + \item{plot.background}{background of the entire plot (\code{\link[=element_rect]{element_rect()}}; inherits from \code{rect})} diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index a1b656dbab..ef358b10b6 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -617,6 +617,47 @@ test_that("complete_theme completes a theme", { reset_theme_settings() }) +test_that("panel.widths and panel.heights works with free-space panels", { + + df <- data.frame(x = c(1, 1, 2, 1, 3), g = c("A", "B", "B", "C", "C")) + + p <- ggplotGrob( + ggplot(df, aes(x, x)) + + geom_point() + + scale_x_continuous(expand = expansion(add = 1)) + + facet_grid(~ g, scales = "free_x", space = "free_x") + + theme( + panel.widths = unit(11, "cm"), + panel.spacing.x = unit(1, "cm") + ) + ) + + idx <- range(panel_cols(p)$l) + expect_equal(as.numeric(p$widths[seq(idx[1], idx[2])]), c(2, 1, 3, 1, 4)) + + p <- ggplotGrob( + ggplot(df, aes(x, x)) + + geom_point() + + scale_y_continuous(expand = expansion(add = 1)) + + facet_grid(g ~ ., scales = "free_y", space = "free_y") + + theme( + panel.heights = unit(11, "cm"), + panel.spacing.y = unit(1, "cm") + ) + ) + + idx <- range(panel_rows(p)$t) + expect_equal(as.numeric(p$heights[seq(idx[1], idx[2])]), c(2, 1, 3, 1, 4)) + +}) + +test_that("panel.widths and panel.heights appropriately warn about aspect override", { + p <- ggplot(mpg, aes(displ, hwy)) + + geom_point() + + theme(aspect.ratio = 1, panel.widths = unit(4, "cm")) + expect_warning(ggplotGrob(p), "Aspect ratios are overruled") +}) + test_that("margin_part() mechanics work as expected", { t <- theme_gray() + @@ -630,7 +671,6 @@ test_that("margin_part() mechanics work as expected", { test <- calc_element("plot.margin", t) expect_equal(as.numeric(test), c(5.5, 5.5, 11, 5.5)) - }) # Visual tests ------------------------------------------------------------ From 23ab4922c5e7e1293cd0c772eae38c37d9c6766c Mon Sep 17 00:00:00 2001 From: Yunuuuu Date: Thu, 5 Dec 2024 15:52:55 +0800 Subject: [PATCH 181/264] multiple inside guide box with different position (#6210) * multiple inside guide box with different position * merge guide legends depend on `legend.position.inside` only * fix inside legend justification * no inside guide box if no inside guide legends * add `guide-box-index` when there is no inside legends * fix inside guide box area * manage position in `Guides$assemble()` * revert * revert * revert * fix inside legend coordinates * fix test error * no need to prepare inside legends when empty * allow set the inside justification for each legend * test multiple inside legends with different positions * fix R CMD check error * code notes * Update R/guides-.R Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * apply suggestion Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * avoid modify package_box * accept snapshot * Update R/guides-.R Co-authored-by: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> * accept the suggestion * new bullet * try to linearise logic * tweak formatting --- NEWS.md | 4 + R/guides-.R | 100 ++++++++++++++---- .../legend-inside-plot-multiple-positions.svg | 85 +++++++++++++++ tests/testthat/test-guides.R | 23 +++- 4 files changed, 187 insertions(+), 25 deletions(-) create mode 100644 tests/testthat/_snaps/guides/legend-inside-plot-multiple-positions.svg diff --git a/NEWS.md b/NEWS.md index b7563b0dee..dd574ac1aa 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* `guide_*()` can now accept two inside legend theme elements: + `legend.position.inside` and `legend.justification.inside`, allowing inside + legends to be placed at different positions. Only inside legends with the same + position and justification will be merged (@Yunuuuu, #6210). * New stat: `stat_manual()` for arbitrary computations (@teunbrand, #3501) * Reversal of a dimension, typically 'x' or 'y', is now controlled by the `reverse` argument in `coord_cartesian()`, `coord_fixed()`, `coord_radial()` diff --git a/R/guides-.R b/R/guides-.R index d250c78025..debb99237e 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -471,7 +471,7 @@ Guides <- ggproto( # for every position, collect all individual guides and arrange them # into a guide box which will be inserted into the main gtable # Combining multiple guides in a guide box - assemble = function(self, theme) { + assemble = function(self, theme, params = self$params, guides = self$guides) { if (length(self$guides) < 1) { return(zeroGrob()) @@ -485,42 +485,95 @@ Guides <- ggproto( return(zeroGrob()) } + # extract the guide position + positions <- vapply( + params, + function(p) p$position[1] %||% default_position, + character(1), USE.NAMES = FALSE + ) + # Populate key sizes theme$legend.key.width <- calc_element("legend.key.width", theme) theme$legend.key.height <- calc_element("legend.key.height", theme) - grobs <- self$draw(theme, default_position, theme$legend.direction) + grobs <- self$draw(theme, positions, theme$legend.direction) + keep <- !vapply(grobs, is.zero, logical(1), USE.NAMES = FALSE) + grobs <- grobs[keep] if (length(grobs) < 1) { return(zeroGrob()) } - grobs <- grobs[order(names(grobs))] + + # prepare the position of inside legends + default_inside_just <- calc_element("legend.justification.inside", theme) + default_inside_position <- calc_element("legend.position.inside", theme) + + groups <- data_frame0( + positions = positions, + justs = list(NULL), + coords = list(NULL) + ) + + # we grouped the legends by the positions, for inside legends, they'll be + # splitted by the actual inside coordinate + for (i in which(positions == "inside")) { + # the actual inside position and justification can be set in each guide + # by `theme` argument, here, we won't use `calc_element()` which will + # use inherits from `legend.justification` or `legend.position`, we only + # follow the inside elements from the guide theme + just <- params[[i]]$theme[["legend.justification.inside"]] + just <- valid.just(just %||% default_inside_just) + coord <- params[[i]]$theme[["legend.position.inside"]] + coord <- coord %||% default_inside_position %||% just + + groups$justs[[i]] <- just + groups$coord[[i]] <- coord + } + + groups <- vec_group_loc(vec_slice(groups, keep)) + grobs <- vec_chop(grobs, indices = groups$loc) + names(grobs) <- groups$key$positions # Set spacing theme$legend.spacing <- theme$legend.spacing %||% unit(0.5, "lines") theme$legend.spacing.y <- calc_element("legend.spacing.y", theme) theme$legend.spacing.x <- calc_element("legend.spacing.x", theme) - Map( - grobs = grobs, - position = names(grobs), - self$package_box, - MoreArgs = list(theme = theme) - ) + # prepare output + for (i in vec_seq_along(groups)) { + adjust <- NULL + position <- groups$key$position[i] + if (position == "inside") { + adjust <- theme( + legend.position.inside = groups$key$coord[[i]], + legend.justification.inside = groups$key$justs[[i]] + ) + } + grobs[[i]] <- self$package_box(grobs[[i]], position, theme + adjust) + } + + # merge inside grobs into single gtable + is_inside <- names(grobs) == "inside" + if (sum(is_inside) > 1) { + inside <- gtable(unit(1, "npc"), unit(1, "npc")) + inside <- gtable_add_grob( + inside, grobs[is_inside], + t = 1, l = 1, clip = "off", + name = paste0("guide-box-inside-", seq_len(sum(is_inside))) + ) + grobs <- grobs[!is_inside] + grobs$inside <- inside + } + + # fill in missing guides + grobs[setdiff(c(.trbl, "inside"), names(grobs))] <- list(zeroGrob()) + + grobs }, # Render the guides into grobs - draw = function(self, theme, - default_position = "right", - direction = NULL, + draw = function(self, theme, positions, direction = NULL, params = self$params, guides = self$guides) { - positions <- vapply( - params, - function(p) p$position[1] %||% default_position, - character(1) - ) - positions <- factor(positions, levels = c(.trbl, "inside")) - directions <- rep(direction %||% "vertical", length(positions)) if (is.null(direction)) { directions[positions %in% c("top", "bottom")] <- "horizontal" @@ -529,14 +582,16 @@ Guides <- ggproto( grobs <- vector("list", length(guides)) for (i in seq_along(grobs)) { grobs[[i]] <- guides[[i]]$draw( - theme = theme, position = as.character(positions[i]), + theme = theme, position = positions[i], direction = directions[i], params = params[[i]] ) } - keep <- !vapply(grobs, is.zero, logical(1)) - split(grobs[keep], positions[keep]) + grobs }, + # here, we put `inside_position` and `inside_just` in the last, so that it + # won't break current implement of patchwork, which depends on the top three + # arguments to collect guides package_box = function(grobs, position, theme) { if (is.zero(grobs) || length(grobs) == 0) { @@ -699,7 +754,6 @@ Guides <- ggproto( guides$name <- "guide-box" guides }, - ## Utilities ----------------------------------------------------------------- print = function(self) { diff --git a/tests/testthat/_snaps/guides/legend-inside-plot-multiple-positions.svg b/tests/testthat/_snaps/guides/legend-inside-plot-multiple-positions.svg new file mode 100644 index 0000000000..22481fa7cf --- /dev/null +++ b/tests/testthat/_snaps/guides/legend-inside-plot-multiple-positions.svg @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + +A +B +C +x +y + +x + + + + + + +A +B +C + +1:3 + + + + + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +legend inside plot, multiple positions + + diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 03848b85f2..31ce6c8b98 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -156,10 +156,10 @@ test_that("empty guides are dropped", { expect_equal(nrow(gd), 0) # Draw guides - guides <- p$plot$guides$draw(theme_gray(), direction = "vertical") + guides <- p$plot$guides$assemble(theme_gray()) # All guide-boxes should be empty - expect_equal(lengths(guides, use.names = FALSE), rep(0, 5)) + expect_true(is.zero(guides)) }) test_that("bins can be parsed by guides for all scale types", { @@ -282,6 +282,25 @@ test_that("guides are positioned correctly", { expect_doppelganger("legend inside plot, bottom left of legend at center", p2 + theme(legend.justification = c(0,0), legend.position.inside = c(0.5,0.5)) ) + expect_doppelganger("legend inside plot, multiple positions", + p2 + + guides( + colour = guide_colourbar( + position = "inside", + theme = theme( + legend.position.inside = c(0, 1), + legend.justification.inside = c(0, 1) + ) + ), + fill = guide_legend( + position = "inside", + theme = theme( + legend.position.inside = c(1, 0), + legend.justification.inside = c(1, 0) + ) + ) + ) + ) }) test_that("guides title and text are positioned correctly", { From 859f61823a397ecbb6d8b4e4c87488c7a049d8de Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 5 Dec 2024 10:27:11 +0100 Subject: [PATCH 182/264] delete test-data.R (#6214) --- tests/testthat/test-data.R | 25 ------------------------- 1 file changed, 25 deletions(-) delete mode 100644 tests/testthat/test-data.R diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R deleted file mode 100644 index 57acb22544..0000000000 --- a/tests/testthat/test-data.R +++ /dev/null @@ -1,25 +0,0 @@ -test_that("stringsAsFactors doesn't affect results", { - skip_if(as.integer(R.Version()$major) >= 4L, "stringsAsFactors only affects R <4.0") - - old <- getOption("stringsAsFactors") - on.exit(options(stringsAsFactors = old), add = TRUE) - - dat.character <- data_frame(x = letters[5:1], y = 1:5) - dat.factor <- data_frame(x = letters[5:1], y = 1:5) - - base <- ggplot(mapping = aes(x, y)) + geom_point() - xlabels <- function(x) x$layout$panel_params[[1]]$x$get_labels() - - options(stringsAsFactors = TRUE) - char_true <- ggplot_build(base %+% dat.character) - factor_true <- ggplot_build(base %+% dat.factor) - - options(stringsAsFactors = FALSE) - char_false <- ggplot_build(base %+% dat.character) - factor_false <- ggplot_build(base %+% dat.factor) - - expect_equal(xlabels(char_true), letters[1:5]) - expect_equal(xlabels(char_false), letters[1:5]) - expect_equal(xlabels(factor_true), letters[1:5]) - expect_equal(xlabels(factor_false), letters[1:5]) -}) From 679ff96bcd04444e4738df5f2717d462d73934be Mon Sep 17 00:00:00 2001 From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com> Date: Thu, 5 Dec 2024 23:27:46 +0100 Subject: [PATCH 183/264] 6122 fix exposed roxygen2 (#6219) * Remove exposed #' roxygen tag in example * devtools::document() * Remove exposed roxygen `#'` tag * devtools::document() --- R/coord-polar.R | 2 +- R/guide-axis-stack.R | 2 +- man/coord_polar.Rd | 2 +- man/guide_axis_stack.Rd | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/coord-polar.R b/R/coord-polar.R index aa5e7c538b..de9453ddb9 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -20,7 +20,7 @@ #' # to demonstrate how these common plots can be described in the #' # grammar. Use with EXTREME caution. #' -#' #' # A pie chart = stacked bar chart + polar coordinates +#' # A pie chart = stacked bar chart + polar coordinates #' pie <- ggplot(mtcars, aes(x = factor(1), fill = factor(cyl))) + #' geom_bar(width = 1) #' pie + coord_polar(theta = "y") diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R index 74fe2b2b3a..a58a4344cc 100644 --- a/R/guide-axis-stack.R +++ b/R/guide-axis-stack.R @@ -22,7 +22,7 @@ NULL #' @export #' #' @examples -#' #' # A standard plot +#' # A standard plot #' p <- ggplot(mpg, aes(displ, hwy)) + #' geom_point() + #' theme(axis.line = element_line()) diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index 12957c2fd9..d2e03956bd 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -86,7 +86,7 @@ sensible when \code{inner.radius > 0}. # to demonstrate how these common plots can be described in the # grammar. Use with EXTREME caution. -#' # A pie chart = stacked bar chart + polar coordinates +# A pie chart = stacked bar chart + polar coordinates pie <- ggplot(mtcars, aes(x = factor(1), fill = factor(cyl))) + geom_bar(width = 1) pie + coord_polar(theta = "y") diff --git a/man/guide_axis_stack.Rd b/man/guide_axis_stack.Rd index a001a35ac2..4a18fc3fdb 100644 --- a/man/guide_axis_stack.Rd +++ b/man/guide_axis_stack.Rd @@ -53,7 +53,7 @@ The \code{first} guide will be placed closest to the panel and any subsequent guides provided through \code{...} will follow in the given order. } \examples{ -#' # A standard plot +# A standard plot p <- ggplot(mpg, aes(displ, hwy)) + geom_point() + theme(axis.line = element_line()) From 4dedb82e46b0eca3a2e0642216e5c57f7b5926de Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 10 Dec 2024 11:10:31 +0100 Subject: [PATCH 184/264] Tweaks to `map_data()`/fortify.map()` (#6218) * link maps as strings * inline `fortify.map` into `map_data()` * deprecate `fortify.map` * add deprecation badges * document * throw error instead --- R/fortify-map.R | 36 ++++++++++++++++++++++++++----- R/fortify-spatial.R | 3 +++ man/fortify.map.Rd | 2 ++ man/fortify.sp.Rd | 2 ++ man/map_data.Rd | 8 +++---- tests/testthat/_snaps/geom-map.md | 9 ++++++++ tests/testthat/test-geom-map.R | 5 +++++ 7 files changed, 56 insertions(+), 9 deletions(-) diff --git a/R/fortify-map.R b/R/fortify-map.R index d0dc76b716..e124e57e54 100644 --- a/R/fortify-map.R +++ b/R/fortify-map.R @@ -1,5 +1,8 @@ #' Fortify method for map objects #' +#' @description +#' `r lifecycle::badge("deprecated")` +#' #' This function turns a map into a data frame that can more easily be #' plotted with ggplot2. #' @@ -24,6 +27,9 @@ #' geom_polygon(aes(group = group), colour = "white") #' } fortify.map <- function(model, data, ...) { + lifecycle::deprecate_warn( + "3.6.0", I("`fortify()`"), "map_data()" + ) df <- data_frame0( long = model$x, lat = model$y, @@ -46,10 +52,10 @@ fortify.map <- function(model, data, ...) { #' for plotting with ggplot2. #' #' @param map name of map provided by the \pkg{maps} package. These -#' include [maps::county()], [maps::france()], -#' [maps::italy()], [maps::nz()], -#' [maps::state()], [maps::usa()], -#' [maps::world()], [maps::world2()]. +#' include [`"county"`][maps::county], [`"france"`][maps::france], +#' [`"italy"`][maps::italy], [`"nz"`][maps::nz], +#' [`"state"`][maps::state], [`"usa"`][maps::usa], +#' [`"world"`][maps::world], or [`"world2"`][maps::world2]. #' @param region name(s) of subregion(s) to include. Defaults to `.` which #' includes all subregions. See documentation for [maps::map()] #' for more details. @@ -80,7 +86,27 @@ fortify.map <- function(model, data, ...) { map_data <- function(map, region = ".", exact = FALSE, ...) { check_installed("maps", reason = "for `map_data()`.") map_obj <- maps::map(map, region, exact = exact, plot = FALSE, fill = TRUE, ...) - fortify(map_obj) + + if (!inherits(map_obj, "map")) { + cli::cli_abort(c( + "{.fn maps::map} must return an object of type {.cls map}, not \\ + {obj_type_friendly(map_obj)}.", + i = "Did you pass the right arguments?" + )) + } + + df <- data_frame0( + long = map_obj$x, + lat = map_obj$y, + group = cumsum(is.na(map_obj$x) & is.na(map_obj$y)) + 1, + order = seq_along(map_obj$x), + .size = length(map_obj$x) + ) + + names <- lapply(strsplit(map_obj$names, "[:,]"), "[", 1:2) + names <- vec_rbind(!!!names, .name_repair = ~ c("region", "subregion")) + df[names(names)] <- vec_slice(names, df$group) + vec_slice(df, stats::complete.cases(df$lat, df$long)) } #' Create a layer of map borders diff --git a/R/fortify-spatial.R b/R/fortify-spatial.R index 0e9f37d046..2bdcf06557 100644 --- a/R/fortify-spatial.R +++ b/R/fortify-spatial.R @@ -1,5 +1,8 @@ #' Fortify method for classes from the sp package. #' +#' @description +#' `r lifecycle::badge("deprecated")` +#' #' To figure out the correct variable name for region, inspect #' `as.data.frame(model)`. #' diff --git a/man/fortify.map.Rd b/man/fortify.map.Rd index 6ed4d9cd1b..ba1c5fbc63 100644 --- a/man/fortify.map.Rd +++ b/man/fortify.map.Rd @@ -14,6 +14,8 @@ \item{...}{not used by this method} } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} + This function turns a map into a data frame that can more easily be plotted with ggplot2. } diff --git a/man/fortify.sp.Rd b/man/fortify.sp.Rd index af1a587f5d..0603c1ee05 100644 --- a/man/fortify.sp.Rd +++ b/man/fortify.sp.Rd @@ -35,6 +35,8 @@ \item{...}{not used by this method} } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} + To figure out the correct variable name for region, inspect \code{as.data.frame(model)}. } diff --git a/man/map_data.Rd b/man/map_data.Rd index 5f8d2d2078..37832d29ca 100644 --- a/man/map_data.Rd +++ b/man/map_data.Rd @@ -8,10 +8,10 @@ map_data(map, region = ".", exact = FALSE, ...) } \arguments{ \item{map}{name of map provided by the \pkg{maps} package. These -include \code{\link[maps:county]{maps::county()}}, \code{\link[maps:france]{maps::france()}}, -\code{\link[maps:italy]{maps::italy()}}, \code{\link[maps:nz]{maps::nz()}}, -\code{\link[maps:state]{maps::state()}}, \code{\link[maps:usa]{maps::usa()}}, -\code{\link[maps:world]{maps::world()}}, \code{\link[maps:world2]{maps::world2()}}.} +include \code{\link[maps:county]{"county"}}, \code{\link[maps:france]{"france"}}, +\code{\link[maps:italy]{"italy"}}, \code{\link[maps:nz]{"nz"}}, +\code{\link[maps:state]{"state"}}, \code{\link[maps:usa]{"usa"}}, +\code{\link[maps:world]{"world"}}, or \code{\link[maps:world2]{"world2"}}.} \item{region}{name(s) of subregion(s) to include. Defaults to \code{.} which includes all subregions. See documentation for \code{\link[maps:map]{maps::map()}} diff --git a/tests/testthat/_snaps/geom-map.md b/tests/testthat/_snaps/geom-map.md index 03bef91fa5..4228af232e 100644 --- a/tests/testthat/_snaps/geom-map.md +++ b/tests/testthat/_snaps/geom-map.md @@ -6,3 +6,12 @@ `map` must have the columns `x`, `y`, and `id`. +# map_data() checks it input + + Code + map_data("world", namesonly = TRUE) + Condition + Error in `map_data()`: + ! `maps::map()` must return an object of type , not a character vector. + i Did you pass the right arguments? + diff --git a/tests/testthat/test-geom-map.R b/tests/testthat/test-geom-map.R index 7e02599209..6bbfb065e4 100644 --- a/tests/testthat/test-geom-map.R +++ b/tests/testthat/test-geom-map.R @@ -2,3 +2,8 @@ test_that("geom_map() checks its input", { expect_snapshot_error(geom_map(map = letters)) expect_snapshot_error(geom_map(map = mtcars)) }) + +test_that("map_data() checks it input", { + skip_if_not_installed("maps") + expect_snapshot(map_data("world", namesonly = TRUE), error = TRUE) +}) From 4c84e8a22a7b5ff85675632b8b453a0ededf0945 Mon Sep 17 00:00:00 2001 From: Salim B Date: Thu, 12 Dec 2024 09:15:35 +0100 Subject: [PATCH 185/264] docs: fix typo and internal links (#6233) * docs: fix typo and internal links * document --- R/coord-radial.R | 4 ++-- man/coord_polar.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/coord-radial.R b/R/coord-radial.R index de3bac2d00..1b4da20a23 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -27,10 +27,10 @@ #' @param r_axis_inside,rotate_angle `r lifecycle::badge("deprecated")` #' #' @note -#' In `coord_radial()`, position guides are can be defined by using +#' In `coord_radial()`, position guides can be defined by using #' `guides(r = ..., theta = ..., r.sec = ..., theta.sec = ...)`. Note that #' these guides require `r` and `theta` as available aesthetics. The classic -#' `guide_axis()` can be used for the `r` positions and `guide_axis_theta()` can +#' [guide_axis()] can be used for the `r` positions and [guide_axis_theta()] can #' be used for the `theta` positions. Using the `theta.sec` position is only #' sensible when `inner.radius > 0`. #' diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index d2e03956bd..57be882bea 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -73,10 +73,10 @@ are a stacked bar chart in polar coordinates. \code{coord_radial()} has extended options. } \note{ -In \code{coord_radial()}, position guides are can be defined by using +In \code{coord_radial()}, position guides can be defined by using \code{guides(r = ..., theta = ..., r.sec = ..., theta.sec = ...)}. Note that these guides require \code{r} and \code{theta} as available aesthetics. The classic -\code{guide_axis()} can be used for the \code{r} positions and \code{guide_axis_theta()} can +\code{\link[=guide_axis]{guide_axis()}} can be used for the \code{r} positions and \code{\link[=guide_axis_theta]{guide_axis_theta()}} can be used for the \code{theta} positions. Using the \code{theta.sec} position is only sensible when \code{inner.radius > 0}. } From ebecea5559a069e999a9a58b9d35e2155d88a135 Mon Sep 17 00:00:00 2001 From: Yunuuuu Date: Thu, 12 Dec 2024 16:58:54 +0800 Subject: [PATCH 186/264] add padding cell in final gtable for NULL `plot.margin` (#6235) --- R/plot-build.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/plot-build.R b/R/plot-build.R index b55c599198..f855dddd78 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -286,7 +286,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot_table <- table_add_tag(plot_table, plot$labels$tag, theme) # Margins - plot_margin <- calc_element("plot.margin", theme) + plot_margin <- calc_element("plot.margin", theme) %||% margin() plot_table <- gtable_add_padding(plot_table, plot_margin) if (is.theme_element(theme$plot.background)) { From b35cf638a932cbd234188e07fd0a768bd34084e8 Mon Sep 17 00:00:00 2001 From: Carl Suster Date: Fri, 13 Dec 2024 19:02:28 +1100 Subject: [PATCH 187/264] Explain how to fix fill guide for points with filled shapes (#6229) * Explain how to fix fill guide for points with filled shapes * Refine filled point example in docs --- R/geom-point.R | 7 +++++++ man/geom_point.Rd | 7 +++++++ vignettes/ggplot2-specs.Rmd | 2 ++ 3 files changed, 16 insertions(+) diff --git a/R/geom-point.R b/R/geom-point.R index 3efa394c31..bf73cf8749 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -85,6 +85,13 @@ #' ggplot(mtcars, aes(wt, mpg)) + #' geom_point(shape = 21, colour = "black", fill = "white", size = 5, stroke = 5) #' +#' # The default shape in legends is not filled, but you can override the shape +#' # in the guide to reflect the fill in the legend +#' ggplot(mtcars, aes(wt, mpg, fill = factor(carb), shape = factor(cyl))) + +#' geom_point(size = 5, stroke = 1) + +#' scale_shape_manual(values = 21:25) + +#' scale_fill_ordinal(guide = guide_legend(override.aes = list(shape = 21))) +#' #' \donttest{ #' # You can create interesting shapes by layering multiple points of #' # different sizes diff --git a/man/geom_point.Rd b/man/geom_point.Rd index 56264c0a36..ccf615e007 100644 --- a/man/geom_point.Rd +++ b/man/geom_point.Rd @@ -182,6 +182,13 @@ d + geom_point(alpha = 1/100) ggplot(mtcars, aes(wt, mpg)) + geom_point(shape = 21, colour = "black", fill = "white", size = 5, stroke = 5) +# The default shape in legends is not filled, but you can override the shape +# in the guide to reflect the fill in the legend +ggplot(mtcars, aes(wt, mpg, fill = factor(carb), shape = factor(cyl))) + + geom_point(size = 5, stroke = 1) + + scale_shape_manual(values = 21:25) + + scale_fill_ordinal(guide = guide_legend(override.aes = list(shape = 21))) + \donttest{ # You can create interesting shapes by layering multiple points of # different sizes diff --git a/vignettes/ggplot2-specs.Rmd b/vignettes/ggplot2-specs.Rmd index 79c6f29d01..21d90e12af 100644 --- a/vignettes/ggplot2-specs.Rmd +++ b/vignettes/ggplot2-specs.Rmd @@ -251,6 +251,8 @@ ggplot(sizes, aes(size, stroke, size = size, stroke = stroke)) + scale_size_identity() ``` +Because points are not typically filled, you may need to change some default settings when using these shapes and mapping `fill`. In particular, discrete `fill` guides will be drawn with an unfilled shape unless overridden (refer to `geom_point()` for an example of this). + ## Text ### Font family From 4efa5cbaaef8871db996e704c2c30123cfe68e26 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 17 Dec 2024 11:57:25 +0100 Subject: [PATCH 188/264] tweak docs (#6245) --- R/limits.R | 4 +++- man/lims.Rd | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/R/limits.R b/R/limits.R index bca92392a9..57f2465018 100644 --- a/R/limits.R +++ b/R/limits.R @@ -4,7 +4,9 @@ #' scales. By default, any values outside the limits specified are replaced with #' `NA`. Be warned that this will remove data outside the limits and this can #' produce unintended results. For changing x or y axis limits \strong{without} -#' dropping data observations, see [coord_cartesian()]. +#' dropping data observations, see +#' [`coord_cartesian(xlim, ylim)`][coord_cartesian], or use a full scale with +#' [`oob = scales::oob_keep`][scales::oob_keep]. #' #' @param ... For `xlim()` and `ylim()`: Two numeric values, specifying the left/lower #' limit and the right/upper limit of the scale. If the larger value is given first, diff --git a/man/lims.Rd b/man/lims.Rd index b6d6559f65..c0a137058e 100644 --- a/man/lims.Rd +++ b/man/lims.Rd @@ -31,7 +31,9 @@ This is a shortcut for supplying the \code{limits} argument to the individual scales. By default, any values outside the limits specified are replaced with \code{NA}. Be warned that this will remove data outside the limits and this can produce unintended results. For changing x or y axis limits \strong{without} -dropping data observations, see \code{\link[=coord_cartesian]{coord_cartesian()}}. +dropping data observations, see +\code{\link[=coord_cartesian]{coord_cartesian(xlim, ylim)}}, or use a full scale with +\code{\link[scales:oob]{oob = scales::oob_keep}}. } \examples{ # Zoom into a specified area From efc53cc000e7d86e3db22e1f43089d366fe24f2e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 17 Dec 2024 11:59:59 +0100 Subject: [PATCH 189/264] Fix `geom_ribbon(na.rm)` (#6244) * custom `GeomRibbon$handle_na` method * modify test * add news bullet --- NEWS.md | 2 ++ R/geom-ribbon.R | 27 +++++++++++++++++++++++++-- tests/testthat/_snaps/geom-ribbon.md | 4 ++++ tests/testthat/test-geom-ribbon.R | 8 +++++++- 4 files changed, 38 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index dd574ac1aa..e19471d2e2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `geom_ribbon()` now appropriately warns about, and removes, missing values + (@teunbrand, #6243). * `guide_*()` can now accept two inside legend theme elements: `legend.position.inside` and `legend.justification.inside`, allowing inside legends to be placed at different positions. Only inside legends with the same diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index a8f6b1be42..f1d339a2eb 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -126,7 +126,31 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, draw_key = draw_key_polygon, - handle_na = function(data, params) { + handle_na = function(self, data, params) { + + vars <- vapply( + strsplit(self$required_aes, "|", fixed = TRUE), + `[[`, i = 1, character(1) + ) + if (params$flipped_aes || any(data$flipped_aes) %||% FALSE) { + vars <- switch_orientation(vars) + } + vars <- c(vars, self$non_missing_aes) + + missing <- detect_missing(data, vars, finite = FALSE) + if (!any(missing)) { + return(data) + } + # We're rearranging groups to account for missing values + data$group <- vec_identify_runs(data_frame0(missing, data$group)) + data <- vec_slice(data, !missing) + + if (!params$na.rm) { + cli::cli_warn( + "Removed {sum(missing)} row{?s} containing missing values or values \\ + outside the scale range ({.fn {snake_class(self)}})." + ) + } data }, @@ -135,7 +159,6 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, flipped_aes = FALSE, outline.type = "both") { data <- check_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) - if (na.rm) data <- data[stats::complete.cases(data[c("x", "ymin", "ymax")]), ] data <- data[order(data$group), ] # Check that aesthetics are constant diff --git a/tests/testthat/_snaps/geom-ribbon.md b/tests/testthat/_snaps/geom-ribbon.md index a2db3d427d..4c1fbb5ecc 100644 --- a/tests/testthat/_snaps/geom-ribbon.md +++ b/tests/testthat/_snaps/geom-ribbon.md @@ -23,3 +23,7 @@ `outline.type` must be one of "both", "upper", "lower", or "full", not "test". +# NAs are dropped from the data + + Removed 1 row containing missing values or values outside the scale range (`geom_ribbon()`). + diff --git a/tests/testthat/test-geom-ribbon.R b/tests/testthat/test-geom-ribbon.R index c923942dde..6bd08875f1 100644 --- a/tests/testthat/test-geom-ribbon.R +++ b/tests/testthat/test-geom-ribbon.R @@ -13,13 +13,19 @@ test_that("geom_ribbon() checks the aesthetics", { expect_snapshot_error(geom_ribbon(aes(year, ymin = level - 5, ymax = level + 5), outline.type = "test")) }) -test_that("NAs are not dropped from the data", { +test_that("NAs are dropped from the data", { df <- data_frame(x = 1:5, y = c(1, 1, NA, 1, 1)) p <- ggplot(df, aes(x))+ geom_ribbon(aes(ymin = y - 1, ymax = y + 1)) + p <- ggplot_build(p) expect_equal(get_layer_data(p)$ymin, c(0, 0, NA, 0, 0)) + expect_snapshot_warning( + grob <- get_layer_grob(p)[[1]] + ) + # We expect the ribbon to be broken up into 2 parts + expect_length(grob$children, 2) }) test_that("geom_ribbon works in both directions", { From 50b7d30447dd69f032b61df75c77a0848864ba6e Mon Sep 17 00:00:00 2001 From: Luke Hannan Date: Thu, 9 Jan 2025 14:55:08 +0200 Subject: [PATCH 190/264] Fix typo in coord_radial documentation (#6277) --- R/coord-radial.R | 2 +- man/coord_polar.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/coord-radial.R b/R/coord-radial.R index 1b4da20a23..d02f88fd11 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -4,7 +4,7 @@ #' @param end Position from 12 o'clock in radians where plot ends, to allow #' for partial polar coordinates. The default, `NULL`, is set to #' `start + 2 * pi`. -#' @param expand If `TRUE`, the default, adds a small expansion factor the +#' @param expand If `TRUE`, the default, adds a small expansion factor to #' the limits to prevent overlap between data and axes. If `FALSE`, limits #' are taken directly from the scale. #' @param r.axis.inside One of the following: diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index 57be882bea..35d9083bfd 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -38,7 +38,7 @@ means no. For details, please see \code{\link[=coord_cartesian]{coord_cartesian( for partial polar coordinates. The default, \code{NULL}, is set to \code{start + 2 * pi}.} -\item{expand}{If \code{TRUE}, the default, adds a small expansion factor the +\item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to prevent overlap between data and axes. If \code{FALSE}, limits are taken directly from the scale.} From 3d1102cc1c2a2d6ab06382476849fb15205ef0a5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 21 Jan 2025 11:31:42 +0100 Subject: [PATCH 191/264] Restore old guides in `guides()` (#6167) * Early exit earlier * fix `is.guide()` -> `inherits()` * explicitly test `guides()` adds old S3 guides properly --- R/guides-.R | 14 ++++++-------- tests/testthat/test-guides.R | 6 +++++- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/R/guides-.R b/R/guides-.R index debb99237e..0e7ca26882 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -68,11 +68,14 @@ NULL #' } guides <- function(...) { args <- list2(...) - if (length(args) > 0) { - if (is.list(args[[1]]) && !is.guide(args[[1]])) args <- args[[1]] - args <- rename_aes(args) + # If there are no guides do nothing + if (length(args) == 0) { + return(NULL) } + if (is.list(args[[1]]) && !inherits(args[[1]], "guide")) args <- args[[1]] + args <- rename_aes(args) + idx_false <- vapply(args, isFALSE, FUN.VALUE = logical(1L)) if (isTRUE(any(idx_false))) { deprecate_warn0("3.3.4", "guides(`` = 'cannot be `FALSE`. Use \"none\" instead')") @@ -84,11 +87,6 @@ guides <- function(...) { return(guides_list(guides = args)) } - # If there are no guides, do nothing - if (length(args) == 0) { - return(NULL) - } - # Raise warning about unnamed guides nms <- names(args) if (is.null(nms)) { diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 31ce6c8b98..5718e4f2ad 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -577,12 +577,16 @@ test_that("old S3 guides can be implemented", { withr::local_environment(my_env) + my_guides <- guides(x = guide_circle()) + expect_length(my_guides$guides, 1) + expect_s3_class(my_guides$guides[[1]], "guide") + expect_snapshot_warning( expect_doppelganger( "old S3 guide drawing a circle", ggplot(mtcars, aes(disp, mpg)) + geom_point() + - guides(x = "circle") + my_guides ) ) }) From 97edd6260a44c71a8ce7954ae4ad6be29224bda3 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 21 Jan 2025 13:48:23 +0100 Subject: [PATCH 192/264] Continuous limits for discrete scales (#6273) * simplify expansion * add `continuous.limits` as scale argument * allow `scale$continuous_limits` to overrule expansion limits * document * confine and improve * add news bullet * add tests * fix wrong description * Better parity with continuous limits --- NEWS.md | 2 ++ R/scale-discrete-.R | 16 ++++++++++++++-- R/scale-expansion.R | 22 +++++++++++++++++----- man/scale_discrete.Rd | 15 +++++++++++++-- tests/testthat/test-scale-expansion.R | 21 +++++++++++++++++++++ 5 files changed, 67 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index e19471d2e2..539dee258c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `scale_{x/y}_discrete(continuous.limits)` is a new argument to control the + display range of discrete scales (@teunbrand, #4174, #6259). * `geom_ribbon()` now appropriately warns about, and removes, missing values (@teunbrand, #6243). * `guide_*()` can now accept two inside legend theme elements: diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index f6fc512f9c..a5ff3289a4 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -16,6 +16,12 @@ #' argument (the number of levels in the scale) returns the numerical values #' that they should take. #' @param sec.axis [dup_axis()] is used to specify a secondary axis. +#' @param continuous.limits One of: +#' * `NULL` to use the default scale range +#' * A numeric vector of length two providing a display range for the scale. +#' Use `NA` to refer to the existing minimum or maximum. +#' * A function that accepts the limits and returns a numeric vector of +#' length two. #' @rdname scale_discrete #' @family position scales #' @seealso @@ -69,7 +75,8 @@ #' } scale_x_discrete <- function(name = waiver(), ..., palette = seq_len, expand = waiver(), guide = waiver(), - position = "bottom", sec.axis = waiver()) { + position = "bottom", sec.axis = waiver(), + continuous.limits = NULL) { sc <- discrete_scale( aesthetics = ggplot_global$x_aes, name = name, palette = palette, ..., @@ -78,13 +85,15 @@ scale_x_discrete <- function(name = waiver(), ..., palette = seq_len, ) sc$range_c <- ContinuousRange$new() + sc$continuous_limits <- continuous.limits set_sec_axis(sec.axis, sc) } #' @rdname scale_discrete #' @export scale_y_discrete <- function(name = waiver(), ..., palette = seq_len, expand = waiver(), guide = waiver(), - position = "left", sec.axis = waiver()) { + position = "left", sec.axis = waiver(), + continuous.limits = NULL) { sc <- discrete_scale( aesthetics = ggplot_global$y_aes, name = name, palette = palette, ..., @@ -93,6 +102,7 @@ scale_y_discrete <- function(name = waiver(), ..., palette = seq_len, ) sc$range_c <- ContinuousRange$new() + sc$continuous_limits <- continuous.limits set_sec_axis(sec.axis, sc) } @@ -106,6 +116,8 @@ scale_y_discrete <- function(name = waiver(), ..., palette = seq_len, #' @usage NULL #' @export ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, + continuous_limits = NULL, + train = function(self, x) { if (is.discrete(x)) { self$range$train(x, drop = self$drop, na.rm = !self$na.translate) diff --git a/R/scale-expansion.R b/R/scale-expansion.R index a132f5cd22..9c682eeaa6 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -81,9 +81,7 @@ expand_range4 <- function(limits, expand) { # Calculate separate range expansion for the lower and # upper range limits, and then combine them into one vector - lower <- expand_range(limits, expand[1], expand[2])[1] - upper <- expand_range(limits, expand[3], expand[4])[2] - c(lower, upper) + expand_range(limits, expand[c(1, 3)], expand[c(2, 4)]) } #' Calculate the default expansion for a scale @@ -153,7 +151,8 @@ expand_limits_scale <- function(scale, expand = expansion(0, 0), limits = waiver scale$map(limits), expand, coord_limits, - range_continuous = scale$range_c$range + range_continuous = scale$range_c$range, + continuous_limits = scale$continuous_limits ) } else { # using the inverse transform to resolve the NA value is needed for date/datetime/time @@ -170,7 +169,20 @@ expand_limits_continuous <- function(limits, expand = expansion(0, 0), coord_lim } expand_limits_discrete <- function(limits, expand = expansion(0, 0), coord_limits = c(NA, NA), - range_continuous = NULL) { + range_continuous = NULL, continuous_limits = NULL) { + if (is.function(continuous_limits)) { + continuous_limits <- continuous_limits(limits) + } + if (!is.null(continuous_limits)) { + if (!anyNA(continuous_limits)) { + continuous_limits <- range(continuous_limits) + } + check_numeric(continuous_limits, arg = "continuous.limits") + check_length(continuous_limits, 2L, arg = "continuous.limits") + missing <- is.na(continuous_limits) + limits <- ifelse(missing, range(limits), continuous_limits) + } + limit_info <- expand_limits_discrete_trans( limits, expand, diff --git a/man/scale_discrete.Rd b/man/scale_discrete.Rd index 0bab3ad985..19e1df99fb 100644 --- a/man/scale_discrete.Rd +++ b/man/scale_discrete.Rd @@ -12,7 +12,8 @@ scale_x_discrete( expand = waiver(), guide = waiver(), position = "bottom", - sec.axis = waiver() + sec.axis = waiver(), + continuous.limits = NULL ) scale_y_discrete( @@ -22,7 +23,8 @@ scale_y_discrete( expand = waiver(), guide = waiver(), position = "left", - sec.axis = waiver() + sec.axis = waiver(), + continuous.limits = NULL ) } \arguments{ @@ -107,6 +109,15 @@ expand the scale by 5\% on each side for continuous variables, and by \code{left} or \code{right} for y axes, \code{top} or \code{bottom} for x axes.} \item{sec.axis}{\code{\link[=dup_axis]{dup_axis()}} is used to specify a secondary axis.} + +\item{continuous.limits}{One of: +\itemize{ +\item \code{NULL} to use the default scale range +\item A numeric vector of length two providing a display range for the scale. +Use \code{NA} to refer to the existing minimum or maximum. +\item A function that accepts the limits and returns a numeric vector of +length two. +}} } \description{ \code{scale_x_discrete()} and \code{scale_y_discrete()} are used to set the values for diff --git a/tests/testthat/test-scale-expansion.R b/tests/testthat/test-scale-expansion.R index 41bd9430e7..331c6a651d 100644 --- a/tests/testthat/test-scale-expansion.R +++ b/tests/testthat/test-scale-expansion.R @@ -96,6 +96,27 @@ test_that("expand_limits_discrete() can override limits with a both discrete and expand_limits_discrete(c("one", "two"), coord_limits = c(0, NA), range_continuous = c(1, 2)), c(0, 2) ) + expect_identical( + expand_limits_discrete(1:2, range_continuous = c(1, 2), continuous_limits = c(0, 3)), + c(0, 3) + ) + expect_identical( + expand_limits_discrete(1:2, range_continuous = c(1, 2), continuous_limits = c(NA, 4)), + c(1, 4) + ) + expect_identical( + expand_limits_discrete(1:2, range_continuous = c(1, 2), continuous_limits = c(0, NA)), + c(0, 2) + ) + expect_identical( + expand_limits_discrete(1:2, range_continuous = c(1, 2), continuous_limits = c(NA_real_, NA_real_)), + c(1, 2) + ) + expect_identical( + expand_limits_discrete(1:2, range_continuous = 1:2, + continuous_limits = function(x) x + c(-1, 1)), + c(0, 3) + ) }) test_that("expand_limits_continuous_trans() works with inverted transformations", { From 180355242b82dd38f60853599f5ad862e3051e25 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 11:55:23 +0100 Subject: [PATCH 193/264] Subtheme functions (#5430) * Draft subtheme * warn when elements are unknown * Document * add tests * Add news bullet * Tweak test * Add topic to pkgdown index * rename prefix to `theme_sub_*()` * cleanup merge debris --- DESCRIPTION | 1 + NAMESPACE | 11 +++ NEWS.md | 5 ++ R/theme-sub.R | 144 +++++++++++++++++++++++++++++ _pkgdown.yml | 1 + man/subtheme.Rd | 159 +++++++++++++++++++++++++++++++++ tests/testthat/_snaps/theme.md | 4 + tests/testthat/test-theme.R | 26 ++++++ 8 files changed, 351 insertions(+) create mode 100644 R/theme-sub.R create mode 100644 man/subtheme.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 978cbf725c..777d755861 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -274,6 +274,7 @@ Collate: 'theme.R' 'theme-defaults.R' 'theme-current.R' + 'theme-sub.R' 'utilities-break.R' 'utilities-grid.R' 'utilities-help.R' diff --git a/NAMESPACE b/NAMESPACE index 391f435b30..690b9fb0ed 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -725,6 +725,17 @@ export(theme_linedraw) export(theme_minimal) export(theme_replace) export(theme_set) +export(theme_sub_axis) +export(theme_sub_axis_bottom) +export(theme_sub_axis_left) +export(theme_sub_axis_right) +export(theme_sub_axis_top) +export(theme_sub_axis_x) +export(theme_sub_axis_y) +export(theme_sub_legend) +export(theme_sub_panel) +export(theme_sub_plot) +export(theme_sub_strip) export(theme_test) export(theme_transparent) export(theme_update) diff --git a/NEWS.md b/NEWS.md index 539dee258c..62a18cfd4d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,10 @@ # ggplot2 (development version) +* New function family for setting parts of a theme. For example, you can now use + `theme_sub_axis(line, text, ticks, ticks.length, line)` as a substitute for + `theme(axis.line, axis.text, axis.ticks, axis.ticks.length, axis.line)`. This + should allow slightly terser and more organised theme declarations + (@teunbrand, #5301). * `scale_{x/y}_discrete(continuous.limits)` is a new argument to control the display range of discrete scales (@teunbrand, #4174, #6259). * `geom_ribbon()` now appropriately warns about, and removes, missing values diff --git a/R/theme-sub.R b/R/theme-sub.R new file mode 100644 index 0000000000..abfb178c44 --- /dev/null +++ b/R/theme-sub.R @@ -0,0 +1,144 @@ +#' Shortcuts for theme settings +#' +#' This collection of functions serves as a shortcut for [`theme()`][theme] with +#' shorter argument names. Besides the shorter arguments, it also helps in +#' keeping theme declarations more organised. +#' +#' @eval subtheme_param_doc() +#' +#' @return A `theme`-class object that can be added to a plot. +#' @name subtheme +#' +#' @examples +#' # A standard plot +#' p <- ggplot(mtcars, aes(disp, mpg, colour = drat)) + +#' geom_point() +#' +#' red_text <- element_text(colour = "red") +#' red_line <- element_line(colour = "red") +#' +#' # The theme settings below: +#' p + theme( +#' axis.title.x.bottom = red_text, +#' axis.text.x.bottom = red_text, +#' axis.line.x.bottom = red_line, +#' axis.ticks.x.bottom = red_line +#' ) +#' +#' # Are equivalent to these less verbose theme settings +#' p + theme_sub_axis_bottom( +#' title = red_text, +#' text = red_text, +#' line = red_line, +#' ticks = red_line +#' ) +NULL + +subtheme <- function(elements, prefix = "", suffix = "", call = caller_env()) { + if (length(elements) < 1) { + return(theme()) + } + names(elements) <- paste0(prefix, names(elements), suffix) + + extra <- setdiff(names(elements), names(get_element_tree())) + if (length(extra) > 0) { + cli::cli_warn( + "Ignoring unknown {.fn theme} element{?s}: {.and {.field {extra}}}.", + call = call + ) + elements <- elements[setdiff(names(elements), extra)] + } + + exec(theme, !!!elements) +} + +#' @export +#' @describeIn subtheme Theme specification for all axes. +theme_sub_axis <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.") +} + +#' @export +#' @describeIn subtheme Theme specification for both x axes. +theme_sub_axis_x <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".x") +} + +#' @export +#' @describeIn subtheme Theme specification for both y axes. +theme_sub_axis_y <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".y") +} + +#' @export +#' @describeIn subtheme Theme specification for the bottom x axis. +theme_sub_axis_bottom <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".x.bottom") +} + +#' @export +#' @describeIn subtheme Theme specification for the top x axis. +theme_sub_axis_top <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".x.top") +} + +#' @export +#' @describeIn subtheme Theme specification for the left y axis. +theme_sub_axis_left <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".y.left") +} + +#' @export +#' @describeIn subtheme Theme specification for the right y axis. +theme_sub_axis_right <- function(title, text, ticks, ticks.length, line) { + subtheme(find_args(), "axis.", ".y.right") +} + +#' @export +#' @describeIn subtheme Theme specification for the legend. +theme_sub_legend <- function(background, margin, spacing, spacing.x, spacing.y, + key, key.size, key.height, key.width, text, title, + position, direction, justification, box, box.just, + box.margin, box.background, box.spacing) { + subtheme(find_args(), "legend.") +} + +#' @export +#' @describeIn subtheme Theme specification for the panels. +theme_sub_panel <- function(background, border, spacing, spacing.x, spacing.y, + grid, grid.major, grid.minor, grid.major.x, + grid.major.y, grid.minor.x, grid.minor.y, ontop) { + subtheme(find_args(), "panel.") +} + +#' @export +#' @describeIn subtheme Theme specification for the whole plot. +theme_sub_plot <- function(background, title, title.position, subtitle, caption, + caption.position, tag, tag.position, tag.location, + margin) { + subtheme(find_args(), "plot.") +} + +#' @export +#' @describeIn subtheme Theme specification for facet strips. +theme_sub_strip <- function(background, background.x, background.y, clip, + placement, text, text.x, text.x.bottom, text.x.top, + text.y, text.y.left, text.y.right, + switch.pad.grid, switch.pad.wrap) { + subtheme(find_args(), "strip.") +} + +subtheme_param_doc <- function() { + funs <- list( + theme_sub_axis, theme_sub_axis_x, theme_sub_axis_y, theme_sub_axis_bottom, + theme_sub_axis_top, theme_sub_axis_left, theme_sub_axis_right, theme_sub_legend, + theme_sub_panel, theme_sub_plot, theme_sub_strip + ) + args <- sort(unique(unlist(lapply(funs, fn_fmls_names), use.names = FALSE))) + paste0( + "@param ", + paste0(args, collapse = ","), + " Arguments that are renamed and passed on to ", + "\\code{\\link[=theme]{theme()}}." + ) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index 593f015590..0259312234 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -186,6 +186,7 @@ reference: - theme - theme_bw - theme_update + - subtheme - element_line - margin diff --git a/man/subtheme.Rd b/man/subtheme.Rd new file mode 100644 index 0000000000..a05a98a54c --- /dev/null +++ b/man/subtheme.Rd @@ -0,0 +1,159 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/theme-sub.R +\name{subtheme} +\alias{subtheme} +\alias{theme_sub_axis} +\alias{theme_sub_axis_x} +\alias{theme_sub_axis_y} +\alias{theme_sub_axis_bottom} +\alias{theme_sub_axis_top} +\alias{theme_sub_axis_left} +\alias{theme_sub_axis_right} +\alias{theme_sub_legend} +\alias{theme_sub_panel} +\alias{theme_sub_plot} +\alias{theme_sub_strip} +\title{Shortcuts for theme settings} +\usage{ +theme_sub_axis(title, text, ticks, ticks.length, line) + +theme_sub_axis_x(title, text, ticks, ticks.length, line) + +theme_sub_axis_y(title, text, ticks, ticks.length, line) + +theme_sub_axis_bottom(title, text, ticks, ticks.length, line) + +theme_sub_axis_top(title, text, ticks, ticks.length, line) + +theme_sub_axis_left(title, text, ticks, ticks.length, line) + +theme_sub_axis_right(title, text, ticks, ticks.length, line) + +theme_sub_legend( + background, + margin, + spacing, + spacing.x, + spacing.y, + key, + key.size, + key.height, + key.width, + text, + title, + position, + direction, + justification, + box, + box.just, + box.margin, + box.background, + box.spacing +) + +theme_sub_panel( + background, + border, + spacing, + spacing.x, + spacing.y, + grid, + grid.major, + grid.minor, + grid.major.x, + grid.major.y, + grid.minor.x, + grid.minor.y, + ontop +) + +theme_sub_plot( + background, + title, + title.position, + subtitle, + caption, + caption.position, + tag, + tag.position, + tag.location, + margin +) + +theme_sub_strip( + background, + background.x, + background.y, + clip, + placement, + text, + text.x, + text.x.bottom, + text.x.top, + text.y, + text.y.left, + text.y.right, + switch.pad.grid, + switch.pad.wrap +) +} +\arguments{ +\item{background, background.x, background.y, border, box, box.background, box.just, box.margin, box.spacing, caption, caption.position, clip, direction, grid, grid.major, grid.major.x, grid.major.y, grid.minor, grid.minor.x, grid.minor.y, justification, key, key.height, key.size, key.width, line, margin, ontop, placement, position, spacing, spacing.x, spacing.y, subtitle, switch.pad.grid, switch.pad.wrap, tag, tag.location, tag.position, text, text.x, text.x.bottom, text.x.top, text.y, text.y.left, text.y.right, ticks, ticks.length, title, title.position}{Arguments that are renamed and passed on to \code{\link[=theme]{theme()}}.} +} +\value{ +A \code{theme}-class object that can be added to a plot. +} +\description{ +This collection of functions serves as a shortcut for \code{\link[=theme]{theme()}} with +shorter argument names. Besides the shorter arguments, it also helps in +keeping theme declarations more organised. +} +\section{Functions}{ +\itemize{ +\item \code{theme_sub_axis()}: Theme specification for all axes. + +\item \code{theme_sub_axis_x()}: Theme specification for both x axes. + +\item \code{theme_sub_axis_y()}: Theme specification for both y axes. + +\item \code{theme_sub_axis_bottom()}: Theme specification for the bottom x axis. + +\item \code{theme_sub_axis_top()}: Theme specification for the top x axis. + +\item \code{theme_sub_axis_left()}: Theme specification for the left y axis. + +\item \code{theme_sub_axis_right()}: Theme specification for the right y axis. + +\item \code{theme_sub_legend()}: Theme specification for the legend. + +\item \code{theme_sub_panel()}: Theme specification for the panels. + +\item \code{theme_sub_plot()}: Theme specification for the whole plot. + +\item \code{theme_sub_strip()}: Theme specification for facet strips. + +}} +\examples{ +# A standard plot +p <- ggplot(mtcars, aes(disp, mpg, colour = drat)) + + geom_point() + +red_text <- element_text(colour = "red") +red_line <- element_line(colour = "red") + +# The theme settings below: +p + theme( + axis.title.x.bottom = red_text, + axis.text.x.bottom = red_text, + axis.line.x.bottom = red_line, + axis.ticks.x.bottom = red_line +) + +# Are equivalent to these less verbose theme settings +p + theme_sub_axis_bottom( + title = red_text, + text = red_text, + line = red_line, + ticks = red_line +) +} diff --git a/tests/testthat/_snaps/theme.md b/tests/testthat/_snaps/theme.md index fa7237d37d..322cce92b7 100644 --- a/tests/testthat/_snaps/theme.md +++ b/tests/testthat/_snaps/theme.md @@ -77,6 +77,10 @@ `plot.tag.position` must be one of "topleft", "top", "topright", "left", "right", "bottomleft", "bottom", or "bottomright", not "test". i Did you mean "left"? +# subtheme functions rename arguments as intended + + Ignoring unknown `theme()` elements: foo and bar. + # Theme validation behaves as expected The `aspect.ratio` theme element must be a object. diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index ef358b10b6..b6248acaa3 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -514,6 +514,32 @@ test_that("Theme elements are checked during build", { expect_snapshot_error(ggplotGrob(p)) }) +test_that("subtheme functions rename arguments as intended", { + + line <- element_line(colour = "red") + rect <- element_rect(colour = "red") + + expect_equal(theme_sub_axis(ticks = line), theme(axis.ticks = line)) + expect_equal(theme_sub_axis_x(ticks = line), theme(axis.ticks.x = line)) + expect_equal(theme_sub_axis_y(ticks = line), theme(axis.ticks.y = line)) + expect_equal(theme_sub_axis_top(ticks = line), theme(axis.ticks.x.top = line)) + expect_equal(theme_sub_axis_bottom(ticks = line), theme(axis.ticks.x.bottom = line)) + expect_equal(theme_sub_axis_left(ticks = line), theme(axis.ticks.y.left = line)) + expect_equal(theme_sub_axis_right(ticks = line), theme(axis.ticks.y.right = line)) + expect_equal(theme_sub_legend(key = rect), theme(legend.key = rect)) + expect_equal(theme_sub_panel(border = rect), theme(panel.border = rect)) + expect_equal(theme_sub_plot(background = rect), theme(plot.background = rect)) + expect_equal(theme_sub_strip(background = rect), theme(strip.background = rect)) + + # Test rejection of unknown theme elements + expect_snapshot_warning( + expect_equal( + subtheme(list(foo = 1, bar = 2, axis.line = line)), + theme(axis.line = line) + ) + ) +}) + test_that("Theme validation behaves as expected", { tree <- get_element_tree() expect_silent(validate_element(1, "aspect.ratio", tree)) From 628d7ab5ee286ae86e816b14879406289c23a7b0 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 12:02:30 +0100 Subject: [PATCH 194/264] Standardise `width` calculation (#6065) * helper for computing size * use helper * add news bullet --- NEWS.md | 2 ++ R/geom-bar.R | 13 ++++++------- R/geom-boxplot.R | 17 +++++++++-------- R/geom-dotplot.R | 12 ++++++++---- R/geom-errorbar.R | 12 ++++++++---- R/geom-tile.R | 21 ++++++++++++++------- R/geom-violin.R | 11 +++++++---- R/utilities.R | 29 +++++++++++++++++++++++++++++ 8 files changed, 83 insertions(+), 34 deletions(-) diff --git a/NEWS.md b/NEWS.md index 62a18cfd4d..140d7dd25b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -252,6 +252,8 @@ * `geom_abline()` clips to the panel range in the vertical direction too (@teunbrand, #6086). * Added `panel.widths` and `panel.heights` to `theme()` (#5338, @teunbrand). +* Standardised the calculation of `width`, which are now implemented as + aesthetics (@teunbrand, #2800). # ggplot2 3.5.1 diff --git a/R/geom-bar.R b/R/geom-bar.R index de7490bfc4..19c86dfbb1 100644 --- a/R/geom-bar.R +++ b/R/geom-bar.R @@ -130,7 +130,7 @@ GeomBar <- ggproto("GeomBar", GeomRect, # limits, not just those for which x and y are outside the limits non_missing_aes = c("xmin", "xmax", "ymin", "ymax"), - default_aes = aes(!!!GeomRect$default_aes, width = NULL), + default_aes = aes(!!!GeomRect$default_aes, width = 0.9), setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params) @@ -139,14 +139,13 @@ GeomBar <- ggproto("GeomBar", GeomRect, extra_params = c("just", "na.rm", "orientation"), - setup_data = function(data, params) { + setup_data = function(self, data, params) { data$flipped_aes <- params$flipped_aes data <- flip_data(data, params$flipped_aes) - data$width <- data$width %||% - params$width %||% (min(vapply( - split(data$x, data$PANEL, drop = TRUE), - resolution, numeric(1), zero = FALSE - )) * 0.9) + data <- compute_data_size( + data, size = params$width, + default = self$default_aes$width, zero = FALSE + ) data$just <- params$just %||% 0.5 data <- transform(data, ymin = pmin(y, 0), ymax = pmax(y, 0), diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index efb6dd14bd..eaa950dced 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -236,21 +236,21 @@ geom_boxplot <- function(mapping = NULL, data = NULL, #' @export GeomBoxplot <- ggproto("GeomBoxplot", Geom, - # need to declare `width` here in case this geom is used with a stat that - # doesn't have a `width` parameter (e.g., `stat_identity`). - extra_params = c("na.rm", "width", "orientation", "outliers"), + extra_params = c("na.rm", "orientation", "outliers"), setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params) params }, - setup_data = function(data, params) { + setup_data = function(self, data, params) { data$flipped_aes <- params$flipped_aes data <- flip_data(data, params$flipped_aes) - data$width <- data$width %||% - params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9) - + data <- compute_data_size( + data, params$width, + default = self$default_aes$width, + zero = FALSE, discrete = TRUE + ) if (isFALSE(params$outliers)) { data$outliers <- NULL } @@ -389,7 +389,8 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, weight = 1, colour = from_theme(col_mix(ink, paper, 0.2)), fill = from_theme(paper), size = from_theme(pointsize), alpha = NA, shape = from_theme(pointshape), linetype = from_theme(bordertype), - linewidth = from_theme(borderwidth) + linewidth = from_theme(borderwidth), + width = 0.9 ), required_aes = c("x|y", "lower|xlower", "upper|xupper", "middle|xmiddle", "ymin|xmin", "ymax|xmax"), diff --git a/R/geom-dotplot.R b/R/geom-dotplot.R index 54b7ce1f57..09ebeb793e 100644 --- a/R/geom-dotplot.R +++ b/R/geom-dotplot.R @@ -194,12 +194,16 @@ GeomDotplot <- ggproto("GeomDotplot", Geom, alpha = NA, stroke = from_theme(borderwidth * 2), linetype = from_theme(linetype), - weight = 1 + weight = 1, + width = 0.9 ), - setup_data = function(data, params) { - data$width <- data$width %||% - params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9) + setup_data = function(self, data, params) { + data <- compute_data_size( + data, params$width, + default = self$default_aes$width, + zero = FALSE, discrete = TRUE + ) # Set up the stacking function and range if (is.null(params$stackdir) || params$stackdir == "up") { diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R index 7551f0be59..b75d81cd9d 100644 --- a/R/geom-errorbar.R +++ b/R/geom-errorbar.R @@ -62,7 +62,7 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom, colour = from_theme(ink), linewidth = from_theme(linewidth), linetype = from_theme(linetype), - width = 0.5, + width = 0.9, alpha = NA ), @@ -76,17 +76,21 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom, extra_params = c("na.rm", "orientation"), - setup_data = function(data, params) { + setup_data = function(self, data, params) { data$flipped_aes <- params$flipped_aes data <- flip_data(data, params$flipped_aes) - data$width <- data$width %||% - params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9) + data <- compute_data_size( + data, params$width, + default = self$default_aes$width, + zero = FALSE, discrete = TRUE + ) data <- transform(data, xmin = x - width / 2, xmax = x + width / 2, width = NULL ) flip_data(data, params$flipped_aes) }, + # Note: `width` is vestigial draw_panel = function(self, data, panel_params, coord, lineend = "butt", width = NULL, flipped_aes = FALSE) { data <- check_linewidth(data, snake_class(self)) diff --git a/R/geom-tile.R b/R/geom-tile.R index e7bb6bc9e3..04ff0b71c2 100644 --- a/R/geom-tile.R +++ b/R/geom-tile.R @@ -109,13 +109,20 @@ geom_tile <- function(mapping = NULL, data = NULL, GeomTile <- ggproto("GeomTile", GeomRect, extra_params = c("na.rm"), - setup_data = function(data, params) { - - data$width <- data$width %||% params$width %||% - stats::ave(data$x, data$PANEL, FUN = function(x) resolution(x, FALSE, TRUE)) - data$height <- data$height %||% params$height %||% - stats::ave(data$y, data$PANEL, FUN = function(y) resolution(y, FALSE, TRUE)) + setup_data = function(self, data, params) { + data <- compute_data_size( + data, params$width, + default = self$default_aes$width, + panels = "by", target = "width", + zero = FALSE, discrete = TRUE + ) + data <- compute_data_size( + data, params$height, + default = self$default_aes$height, + panels = "by", target = "height", + zero = FALSE, discrete = TRUE + ) transform(data, xmin = x - width / 2, xmax = x + width / 2, width = NULL, ymin = y - height / 2, ymax = y + height / 2, height = NULL @@ -127,7 +134,7 @@ GeomTile <- ggproto("GeomTile", GeomRect, colour = NA, linewidth = from_theme(0.4 * borderwidth), linetype = from_theme(bordertype), - alpha = NA, width = NA, height = NA + alpha = NA, width = 1, height = 1 ), required_aes = c("x", "y"), diff --git a/R/geom-violin.R b/R/geom-violin.R index 9976e5b8a4..e53c29396f 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -131,11 +131,13 @@ GeomViolin <- ggproto("GeomViolin", Geom, extra_params = c("na.rm", "orientation", "lineend", "linejoin", "linemitre"), - setup_data = function(data, params) { + setup_data = function(self, data, params) { data$flipped_aes <- params$flipped_aes data <- flip_data(data, params$flipped_aes) - data$width <- data$width %||% - params$width %||% (resolution(data$x, FALSE, TRUE) * 0.9) + data <- compute_data_size( + data, params$width, + default = self$default_aes$width + ) # ymin, ymax, xmin, and xmax define the bounding rectangle for each group data <- dapply(data, "group", transform, xmin = x - width / 2, @@ -203,7 +205,8 @@ GeomViolin <- ggproto("GeomViolin", Geom, fill = from_theme(paper), linewidth = from_theme(borderwidth), linetype = from_theme(bordertype), - alpha = NA + alpha = NA, + width = 0.9 ), required_aes = c("x", "y"), diff --git a/R/utilities.R b/R/utilities.R index 54087eba68..adb2475047 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -909,3 +909,32 @@ prompt_install <- function(pkg, reason = NULL) { utils::install.packages(pkg) is_installed(pkg) } + +compute_data_size <- function(data, size, default = 0.9, + target = "width", + panels = c("across", "by", "ignore"), + ...) { + + data[[target]] <- data[[target]] %||% size + if (!is.null(data[[target]])) { + return(data) + } + + var <- if (target == "height") "y" else "x" + panels <- arg_match0(panels, c("across", "by", "ignore")) + + if (panels == "across") { + res <- split(data[[var]], data$PANEL, drop = FALSE) + res <- vapply(res, resolution, FUN.VALUE = numeric(1), ...) + res <- min(res, na.rm = TRUE) + } else if (panels == "by") { + res <- ave(data[[var]], data$PANEL, FUN = function(x) resolution(x, ...)) + } else { + res <- resolution(data[[var]], ...) + } + if (is_quosure(default)) { + default <- eval_tidy(default, data = data) + } + data[[target]] <- res * (default %||% 0.9) + data +} From 9eeeafed53bf57b23212efc7ce2689faa6f61230 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 12:24:00 +0100 Subject: [PATCH 195/264] Improve consistency of naming internal functions (#6072) * rename `validate_facets()` to `check_facets()` * write prevalidation/postvalidation as checks * more responsibility for `check_nondata_cols()` * `check_subclass()` is actually validator * path checker is validator * plot_dev is a validator * `check_breaks_labels()` has no return value * make `check_scale_type()` consistent * `validate_theme/element()` is a check * update labeller deprecation message * `check_labeller()` performs an update * `check_linewidth()` performs an update * `check_polar_guide()` is validator * `update_labeller()` -> `fix_labeller()` * `update_linewidth()` -> `fix_linewidth()` * `check_facet_class()` --> `check_vars()` --- R/coord-radial.R | 4 +- R/facet-.R | 6 +- R/facet-grid-.R | 2 +- R/facet-wrap.R | 2 +- R/fortify.R | 46 ++++++++++------ R/geom-.R | 18 ++---- R/geom-boxplot.R | 2 +- R/geom-crossbar.R | 3 +- R/geom-defaults.R | 4 +- R/geom-errorbar.R | 2 +- R/geom-hex.R | 2 +- R/geom-path.R | 2 +- R/geom-polygon.R | 2 +- R/geom-rect.R | 2 +- R/geom-ribbon.R | 2 +- R/geom-rug.R | 2 +- R/geom-segment.R | 2 +- R/guide-.R | 4 +- R/labeller.R | 14 ++--- R/layer.R | 64 ++++++++-------------- R/save.R | 10 ++-- R/scale-.R | 9 +-- R/scale-colour.R | 9 ++- R/scales-.R | 1 + R/theme-elements.R | 2 +- R/theme.R | 8 +-- R/utilities-help.R | 4 +- R/utilities.R | 34 ++++++++---- tests/testthat/_snaps/facet-.md | 6 +- tests/testthat/_snaps/facet-labels.md | 4 +- tests/testthat/_snaps/fortify.md | 24 ++++---- tests/testthat/_snaps/geom-.md | 8 +-- tests/testthat/_snaps/ggsave.md | 4 +- tests/testthat/_snaps/layer.md | 26 ++++----- tests/testthat/test-facet-.R | 6 +- tests/testthat/test-ggsave.R | 12 ++-- tests/testthat/test-layer.R | 4 +- tests/testthat/test-scales-breaks-labels.R | 4 +- tests/testthat/test-theme.R | 8 +-- 39 files changed, 183 insertions(+), 185 deletions(-) diff --git a/R/coord-radial.R b/R/coord-radial.R index d02f88fd11..1fea09dcde 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -191,7 +191,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, # Validate appropriateness of guides drop_guides <- character(0) for (type in aesthetics) { - drop_guides <- check_polar_guide(drop_guides, guides, type) + drop_guides <- validate_polar_guide(drop_guides, guides, type) } guide_params <- guides$get_params(aesthetics) @@ -603,7 +603,7 @@ theta_grid <- function(theta, element, inner_radius = c(0, 0.4), ) } -check_polar_guide <- function(drop_list, guides, type = "theta") { +validate_polar_guide <- function(drop_list, guides, type = "theta") { guide <- guides$get_guide(type) primary <- gsub("\\.sec$", "", type) if (inherits(guide, "GuideNone") || primary %in% guide$available_aes) { diff --git a/R/facet-.R b/R/facet-.R index b124b54872..0c120beba3 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -443,7 +443,7 @@ df.grid <- function(a, b) { # facetting variables. as_facets_list <- function(x) { - x <- validate_facets(x) + check_vars(x) if (is_quosures(x)) { x <- quos_auto_name(x) return(list(x)) @@ -487,7 +487,7 @@ as_facets_list <- function(x) { x } -validate_facets <- function(x) { +check_vars <- function(x) { if (is.mapping(x)) { cli::cli_abort("Please use {.fn vars} to supply facet variables.") } @@ -499,7 +499,7 @@ validate_facets <- function(x) { "i" = "Did you use {.code %>%} or {.code |>} instead of {.code +}?" )) } - x + invisible() } # Flatten a list of quosures objects to a quosures object, and compact it diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 784e394885..be11524541 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -177,7 +177,7 @@ facet_grid <- function(rows = NULL, cols = NULL, scales = "fixed", facets_list <- grid_as_facets_list(rows, cols) # Check for deprecated labellers - labeller <- check_labeller(labeller) + labeller <- fix_labeller(labeller) ggproto(NULL, FacetGrid, shrink = shrink, diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 114b3332d9..6bc72f8af4 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -174,7 +174,7 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", ) # Check for deprecated labellers - labeller <- check_labeller(labeller) + labeller <- fix_labeller(labeller) # Flatten all facets dimensions into a single one facets <- compact_facets(facets) diff --git a/R/fortify.R b/R/fortify.R index da4bcf7892..17d6e37b12 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -44,34 +44,46 @@ fortify.grouped_df <- function(model, data, ...) { # There are a lot of ways that dim(), colnames(), or as.data.frame() could # do non-sensical things (they are not even guaranteed to work!) hence the # paranoid mode. -.prevalidate_data_frame_like_object <- function(data) { +check_data_frame_like <- function(data) { orig_dims <- dim(data) - if (!vec_is(orig_dims, integer(), size=2)) - cli::cli_abort(paste0("{.code dim(data)} must return ", - "an {.cls integer} of length 2.")) - if (anyNA(orig_dims) || any(orig_dims < 0)) # extra-paranoid mode - cli::cli_abort(paste0("{.code dim(data)} can't have {.code NA}s ", - "or negative values.")) + if (!vec_is(orig_dims, integer(), size = 2)) { + cli::cli_abort( + "{.code dim(data)} must return an {.cls integer} of length 2." + ) + } + if (anyNA(orig_dims) || any(orig_dims < 0)) { # extra-paranoid mode + cli::cli_abort( + "{.code dim(data)} can't have {.code NA}s or negative values." + ) + } orig_colnames <- colnames(data) - if (!vec_is(orig_colnames, character(), size = ncol(data))) - cli::cli_abort(paste0("{.code colnames(data)} must return a ", - "{.cls character} of length {.code ncol(data)}.")) + if (!vec_is(orig_colnames, character(), size = ncol(data))) { + cli::cli_abort( + "{.code colnames(data)} must return a {.cls character} of length {.code ncol(data)}." + ) + } + invisible() } -.postvalidate_data_frame_like_object <- function(df, data) { +check_data_frame_conversion <- function(new, old) { msg0 <- "{.code as.data.frame(data)} must " - if (!is.data.frame(df)) + if (!is.data.frame(new)) { cli::cli_abort(paste0(msg0, "return a {.cls data.frame}.")) - if (!identical(dim(df), dim(data))) + } + if (!identical(dim(new), dim(old))) { cli::cli_abort(paste0(msg0, "preserve dimensions.")) - if (!identical(colnames(df), colnames(data))) + } + if (!identical(colnames(new), colnames(old))) { cli::cli_abort(paste0(msg0, "preserve column names.")) + } + invisible() } validate_as_data_frame <- function(data) { - if (is.data.frame(data)) + if (is.data.frame(data)) { return(data) - .prevalidate_data_frame_like_object(data) + } + check_data_frame_like(data) df <- as.data.frame(data) - .postvalidate_data_frame_like_object(df, data) + check_data_frame_conversion(df, data) df } diff --git a/R/geom-.R b/R/geom-.R index 50bdeb66a6..f8b5027438 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -170,17 +170,11 @@ Geom <- ggproto("Geom", ) # Check that all output are valid data - nondata_modified <- check_nondata_cols(modified_aes) - if (length(nondata_modified) > 0) { - issues <- paste0("{.code ", nondata_modified, " = ", as_label(modifiers[[nondata_modified]]), "}") - names(issues) <- rep("x", length(issues)) - cli::cli_abort(c( - "Aesthetic modifiers returned invalid values", - "x" = "The following mappings are invalid", - issues, - "i" = "Did you map the modifier in the wrong layer?" - )) - } + check_nondata_cols( + modified_aes, modifiers, + problem = "Aesthetic modifiers returned invalid values.", + hint = "Did you map the modifier in the wrong layer?" + ) modified_aes <- cleanup_mismatched_data(modified_aes, nrow(data), "after_scale") @@ -283,7 +277,7 @@ check_aesthetics <- function(x, n) { )) } -check_linewidth <- function(data, name) { +fix_linewidth <- function(data, name) { if (is.null(data$linewidth) && !is.null(data$size)) { deprecate_soft0("3.4.0", I(paste0("Using the `size` aesthetic with ", name)), I("the `linewidth` aesthetic")) data$linewidth <- data$size diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index eaa950dced..edd6117538 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -286,7 +286,7 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, whisker_gp = NULL, staple_gp = NULL, median_gp = NULL, box_gp = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, flipped_aes = FALSE) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) # this may occur when using geom_boxplot(stat = "identity") if (nrow(data) != 1) { diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index be7ce1f658..7316033de6 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -84,8 +84,7 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom, draw_panel = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre", fatten = 2.5, width = NULL, flipped_aes = FALSE, middle_gp = NULL, box_gp = NULL) { - - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) middle <- transform(data, x = xmin, xend = xmax, yend = y, linewidth = linewidth * fatten, alpha = NA) diff --git a/R/geom-defaults.R b/R/geom-defaults.R index 732f5ddb32..c1bc8a782f 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -106,7 +106,7 @@ get_geom_defaults <- function(geom, theme = theme_get()) { return(data) } if (is.character(geom)) { - geom <- check_subclass(geom, "Geom") + geom <- validate_subclass(geom, "Geom") } if (is.geom(geom)) { out <- geom$use_defaults(data = NULL, theme = theme) @@ -126,7 +126,7 @@ reset_stat_defaults <- function() reset_defaults("stat") cache_defaults <- new_environment() update_defaults <- function(name, subclass, new, env = parent.frame()) { - obj <- check_subclass(name, subclass, env = env) + obj <- validate_subclass(name, subclass, env = env) index <- snake_class(obj) if (is.null(new)) { # Reset from cache diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R index b75d81cd9d..3e50c59877 100644 --- a/R/geom-errorbar.R +++ b/R/geom-errorbar.R @@ -93,7 +93,7 @@ GeomErrorbar <- ggproto("GeomErrorbar", Geom, # Note: `width` is vestigial draw_panel = function(self, data, panel_params, coord, lineend = "butt", width = NULL, flipped_aes = FALSE) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) x <- vec_interleave(data$xmin, data$xmax, NA, data$x, data$x, NA, data$xmin, data$xmax) y <- vec_interleave(data$ymax, data$ymax, NA, data$ymax, data$ymin, NA, data$ymin, data$ymin) diff --git a/R/geom-hex.R b/R/geom-hex.R index 152227a40b..5add9250c8 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -58,7 +58,7 @@ geom_hex <- function(mapping = NULL, data = NULL, GeomHex <- ggproto("GeomHex", Geom, draw_group = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre", linemitre = 10) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) if (empty(data)) { return(zeroGrob()) } diff --git a/R/geom-path.R b/R/geom-path.R index 72c4f7154e..fe930363a6 100644 --- a/R/geom-path.R +++ b/R/geom-path.R @@ -165,7 +165,7 @@ GeomPath <- ggproto("GeomPath", Geom, draw_panel = function(self, data, panel_params, coord, arrow = NULL, arrow.fill = NULL, lineend = "butt", linejoin = "round", linemitre = 10, na.rm = FALSE) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) if (!anyDuplicated(data$group)) { cli::cli_inform(c( "{.fn {snake_class(self)}}: Each group consists of only one observation.", diff --git a/R/geom-polygon.R b/R/geom-polygon.R index a271ef5011..a97d3c2194 100644 --- a/R/geom-polygon.R +++ b/R/geom-polygon.R @@ -109,7 +109,7 @@ geom_polygon <- function(mapping = NULL, data = NULL, GeomPolygon <- ggproto("GeomPolygon", Geom, draw_panel = function(self, data, panel_params, coord, rule = "evenodd", lineend = "butt", linejoin = "round", linemitre = 10) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) n <- nrow(data) if (n == 1) return(zeroGrob()) diff --git a/R/geom-rect.R b/R/geom-rect.R index 8473474525..1765a2506a 100644 --- a/R/geom-rect.R +++ b/R/geom-rect.R @@ -69,7 +69,7 @@ GeomRect <- ggproto("GeomRect", Geom, }, draw_panel = function(self, data, panel_params, coord, lineend = "butt", linejoin = "mitre") { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) if (!coord$is_linear()) { aesthetics <- setdiff( names(data), c("x", "y", "xmin", "xmax", "ymin", "ymax") diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index f1d339a2eb..4365c122d5 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -157,7 +157,7 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, draw_group = function(self, data, panel_params, coord, lineend = "butt", linejoin = "round", linemitre = 10, na.rm = FALSE, flipped_aes = FALSE, outline.type = "both") { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) data <- flip_data(data, flipped_aes) data <- data[order(data$group), ] diff --git a/R/geom-rug.R b/R/geom-rug.R index ffc761b91c..8992f1069d 100644 --- a/R/geom-rug.R +++ b/R/geom-rug.R @@ -90,7 +90,7 @@ GeomRug <- ggproto("GeomRug", Geom, draw_panel = function(self, data, panel_params, coord, lineend = "butt", sides = "bl", outside = FALSE, length = unit(0.03, "npc")) { - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) check_inherits(length, "unit") rugs <- list() data <- coord$transform(data, panel_params) diff --git a/R/geom-segment.R b/R/geom-segment.R index 00d9eff87a..51de135b53 100644 --- a/R/geom-segment.R +++ b/R/geom-segment.R @@ -116,7 +116,7 @@ GeomSegment <- ggproto("GeomSegment", Geom, lineend = "butt", linejoin = "round", na.rm = FALSE) { data$xend <- data$xend %||% data$x data$yend <- data$yend %||% data$y - data <- check_linewidth(data, snake_class(self)) + data <- fix_linewidth(data, snake_class(self)) data <- remove_missing(data, na.rm = na.rm, c("x", "y", "xend", "yend", "linetype", "linewidth"), name = "geom_segment" diff --git a/R/guide-.R b/R/guide-.R index c700329cb3..54cae7c873 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -19,7 +19,7 @@ NULL new_guide <- function(..., available_aes = "any", super) { pf <- parent.frame() - super <- check_subclass(super, "Guide", env = pf) + super <- validate_subclass(super, "Guide", env = pf) args <- list2(...) @@ -51,7 +51,7 @@ new_guide <- function(..., available_aes = "any", super) { # Validate theme settings if (!is.null(params$theme)) { check_object(params$theme, is.theme, what = "a {.cls theme} object") - validate_theme(params$theme, call = caller_env()) + check_theme(params$theme, call = caller_env()) params$direction <- params$direction %||% params$theme$legend.direction } diff --git a/R/labeller.R b/R/labeller.R index 4ca220c2b4..a9ba883a79 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -577,21 +577,21 @@ assemble_strips <- function(grobs, theme, horizontal = TRUE, clip) { }) } -# Check for old school labeller -check_labeller <- function(labeller) { +# Repair old school labeller +fix_labeller <- function(labeller) { labeller <- match.fun(labeller) is_deprecated <- all(c("variable", "value") %in% names(formals(labeller))) if (is_deprecated) { + deprecate_warn0( + "2.0.0", what = "facet_(labeller)", + details = + "Modern labellers do not take `variable` and `value` arguments anymore." + ) old_labeller <- labeller labeller <- function(labels) { Map(old_labeller, names(labels), labels) } - # TODO Update to lifecycle after next lifecycle release - cli::cli_warn(c( - "The {.arg labeller} API has been updated. Labellers taking {.arg variable} and {.arg value} arguments are now deprecated.", - "i" = "See labellers documentation." - )) } labeller diff --git a/R/layer.R b/R/layer.R index d2355a46ba..a915763e3c 100644 --- a/R/layer.R +++ b/R/layer.R @@ -101,12 +101,6 @@ layer <- function(geom = NULL, stat = NULL, show.legend = NA, key_glyph = NULL, layer_class = Layer) { call_env <- caller_env() user_env <- caller_env(2) - if (is.null(geom)) - cli::cli_abort("Can't create layer without a geom.", call = call_env) - if (is.null(stat)) - cli::cli_abort("Can't create layer without a stat.", call = call_env) - if (is.null(position)) - cli::cli_abort("Can't create layer without a position.", call = call_env) # Handle show_guide/show.legend if (!is.null(params$show_guide)) { @@ -125,9 +119,9 @@ layer <- function(geom = NULL, stat = NULL, data <- fortify(data) - geom <- check_subclass(geom, "Geom", env = parent.frame(), call = call_env) - stat <- check_subclass(stat, "Stat", env = parent.frame(), call = call_env) - position <- check_subclass(position, "Position", env = parent.frame(), call = call_env) + geom <- validate_subclass(geom, "Geom", env = parent.frame(), call = call_env) + stat <- validate_subclass(stat, "Stat", env = parent.frame(), call = call_env) + position <- validate_subclass(position, "Position", env = parent.frame(), call = call_env) # Special case for na.rm parameter needed by all layers params$na.rm <- params$na.rm %||% FALSE @@ -314,17 +308,11 @@ Layer <- ggproto("Layer", NULL, warn_for_aes_extract_usage(aesthetics, data[setdiff(names(data), "PANEL")]) # Check aesthetic values - nondata_cols <- check_nondata_cols(evaled) - if (length(nondata_cols) > 0) { - issues <- paste0("{.code ", nondata_cols, " = ", as_label(aesthetics[[nondata_cols]]), "}") - names(issues) <- rep("x", length(issues)) - cli::cli_abort(c( - "Aesthetics are not valid data columns.", - "x" = "The following aesthetics are invalid:", - issues, - "i" = "Did you mistype the name of a data column or forget to add {.fn after_stat}?" - )) - } + check_nondata_cols( + evaled, aesthetics, + problem = "Aesthetics are not valid data columns.", + hint = "Did you mistype the name of a data column or forget to add {.fn after_stat}?" + ) n <- nrow(data) aes_n <- list_sizes(evaled) @@ -392,17 +380,11 @@ Layer <- ggproto("Layer", NULL, mask = list(stage = stage_calculated) ) # Check that all columns in aesthetic stats are valid data - nondata_stat_cols <- check_nondata_cols(stat_data) - if (length(nondata_stat_cols) > 0) { - issues <- paste0("{.code ", nondata_stat_cols, " = ", as_label(aesthetics[[nondata_stat_cols]]), "}") - names(issues) <- rep("x", length(issues)) - cli::cli_abort(c( - "Aesthetics must be valid computed stats.", - "x" = "The following aesthetics are invalid:", - issues, - "i" = "Did you map your stat in the wrong layer?" - )) - } + check_nondata_cols( + stat_data, aesthetics, + problem = "Aesthetics must be valid computed stats.", + hint = "Did you map your stat in the wrong layer?" + ) stat_data <- data_frame0(!!!stat_data) @@ -464,24 +446,26 @@ Layer <- ggproto("Layer", NULL, } ) -check_subclass <- function(x, subclass, - argname = to_lower_ascii(subclass), - env = parent.frame(), - call = caller_env()) { +validate_subclass <- function(x, subclass, + argname = to_lower_ascii(subclass), + x_arg = caller_arg(x), + env = parent.frame(), + call = caller_env()) { + if (inherits(x, subclass)) { - x + return(x) } else if (is_scalar_character(x)) { name <- paste0(subclass, camelize(x, first = TRUE)) obj <- find_global(name, env = env) if (is.null(obj) || !inherits(obj, subclass)) { cli::cli_abort("Can't find {argname} called {.val {x}}.", call = call) - } else { - obj } - } else { - stop_input_type(x, as_cli("either a string or a {.cls {subclass}} object")) + return(obj) + } else if (is.null(x)) { + cli::cli_abort("The {.arg {x_arg}} argument cannot be empty.", call = call) } + stop_input_type(x, as_cli("either a string or a {.cls {subclass}} object")) } # helper function to adjust the draw_key slot of a geom diff --git a/R/save.R b/R/save.R index b06c567b2e..5e1ef5983a 100644 --- a/R/save.R +++ b/R/save.R @@ -95,10 +95,10 @@ ggsave <- function(filename, plot = get_last_plot(), dpi = 300, limitsize = TRUE, bg = NULL, create.dir = FALSE, ...) { - filename <- check_path(path, filename, create.dir) + filename <- validate_path(path, filename, create.dir) dpi <- parse_dpi(dpi) - dev <- plot_dev(device, filename, dpi = dpi) + dev <- validate_device(device, filename, dpi = dpi) dim <- plot_dim(c(width, height), scale = scale, units = units, limitsize = limitsize, dpi = dpi) @@ -116,8 +116,8 @@ ggsave <- function(filename, plot = get_last_plot(), invisible(filename) } -check_path <- function(path, filename, create.dir, - call = caller_env()) { +validate_path <- function(path, filename, create.dir, + call = caller_env()) { if (length(filename) > 1 && is.character(filename)) { cli::cli_warn(c( @@ -235,7 +235,7 @@ plot_dim <- function(dim = c(NA, NA), scale = 1, units = "in", dim } -plot_dev <- function(device, filename = NULL, dpi = 300, call = caller_env()) { +validate_device <- function(device, filename = NULL, dpi = 300, call = caller_env()) { force(filename) force(dpi) diff --git a/R/scale-.R b/R/scale-.R index 4bf54328b3..b2f9ef346a 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -622,11 +622,8 @@ Scale <- ggproto("Scale", NULL, ) check_breaks_labels <- function(breaks, labels, call = NULL) { - if (is.null(breaks)) { - return(TRUE) - } - if (is.null(labels)) { - return(TRUE) + if (is.null(breaks) || is.null(labels)) { + return(invisible()) } bad_labels <- is.atomic(breaks) && is.atomic(labels) && @@ -638,7 +635,7 @@ check_breaks_labels <- function(breaks, labels, call = NULL) { ) } - TRUE + invisible() } default_transform <- function(self, x) { diff --git a/R/scale-colour.R b/R/scale-colour.R index a17d872dbe..592aa288e1 100644 --- a/R/scale-colour.R +++ b/R/scale-colour.R @@ -81,7 +81,6 @@ scale_colour_continuous <- function(..., aesthetics = "colour", guide = "colourbar", na.value = "grey50", type = getOption("ggplot2.continuous.colour")) { - if (!is.null(type)) { scale <- scale_backward_compatibility( ..., guide = guide, na.value = na.value, scale = type, @@ -179,8 +178,7 @@ check_scale_type <- function(scale, name, aesthetic, scale_is_discrete = FALSE, "x" = "The provided scale is {scale_types[2]}." ), call = call) } - - scale + invisible() } # helper function for backwards compatibility through setting defaults @@ -241,8 +239,9 @@ scale_backward_compatibility <- function(..., scale, aesthetic, type) { if (!"..." %in% fn_fmls_names(scale)) { args <- args[intersect(names(args), fn_fmls_names(scale))] } - scale <- check_scale_type( - exec(scale, !!!args), + scale <- exec(scale, !!!args) + check_scale_type( + scale, paste("scale", aesthetic, type, sep = "_"), aesthetic, scale_is_discrete = type == "discrete" diff --git a/R/scales-.R b/R/scales-.R index 769613a2d8..87c5f6f586 100644 --- a/R/scales-.R +++ b/R/scales-.R @@ -154,6 +154,7 @@ ScalesList <- ggproto("ScalesList", NULL, return() } + for (aes in new_aesthetics) { self$add(find_scale(aes, data[[aes]], env)) } diff --git a/R/theme-elements.R b/R/theme-elements.R index 947e4e0af3..5a6b1a43cf 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -698,7 +698,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { # @param el an element # @param elname the name of the element # @param element_tree the element tree to validate against -validate_element <- function(el, elname, element_tree, call = caller_env()) { +check_element <- function(el, elname, element_tree, call = caller_env()) { eldef <- element_tree[[elname]] if (is.null(eldef)) { diff --git a/R/theme.R b/R/theme.R index 2ebd892f62..cb7859dfe2 100644 --- a/R/theme.R +++ b/R/theme.R @@ -208,7 +208,7 @@ #' differently when added to a ggplot object. Also, when setting #' `complete = TRUE` all elements will be set to inherit from blank #' elements. -#' @param validate `TRUE` to run `validate_element()`, `FALSE` to bypass checks. +#' @param validate `TRUE` to run `check_element()`, `FALSE` to bypass checks. #' @export #' @seealso #' [+.gg()] and [%+replace%], @@ -561,12 +561,12 @@ is_theme_validate <- function(x) { isTRUE(validate %||% TRUE) } -validate_theme <- function(theme, tree = get_element_tree(), call = caller_env()) { +check_theme <- function(theme, tree = get_element_tree(), call = caller_env()) { if (!is_theme_validate(theme)) { return() } mapply( - validate_element, theme, names(theme), + check_element, theme, names(theme), MoreArgs = list(element_tree = tree, call = call) ) } @@ -627,7 +627,7 @@ plot_theme <- function(x, default = get_theme()) { theme[missing] <- ggplot_global$theme_default[missing] # Check that all elements have the correct class (element_text, unit, etc) - validate_theme(theme) + check_theme(theme) # Remove elements that are not registered theme[setdiff(names(theme), names(get_element_tree()))] <- NULL diff --git a/R/utilities-help.R b/R/utilities-help.R index 87f5419612..22bddc7dcd 100644 --- a/R/utilities-help.R +++ b/R/utilities-help.R @@ -2,8 +2,8 @@ # Geoms and there's some difference among their aesthetics). rd_aesthetics <- function(type, name, extra_note = NULL) { obj <- switch(type, - geom = check_subclass(name, "Geom", env = globalenv()), - stat = check_subclass(name, "Stat", env = globalenv()) + geom = validate_subclass(name, "Geom", env = globalenv()), + stat = validate_subclass(name, "Stat", env = globalenv()) ) aes <- rd_aesthetics_item(obj) diff --git a/R/utilities.R b/R/utilities.R index adb2475047..3b0e9ec806 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -277,17 +277,29 @@ is.discrete <- function(x) { is.factor(x) || is.character(x) || is.logical(x) } -# This function checks that all columns of a dataframe `x` are data and returns -# the names of any columns that are not. -# We define "data" as atomic types or lists, not functions or otherwise. -# The `inherits(x, "Vector")` check is for checking S4 classes from Bioconductor -# and whether they can be expected to follow behavior typical of vectors. See -# also #3835 -check_nondata_cols <- function(x) { - idx <- (vapply(x, function(x) { - is.null(x) || rlang::is_vector(x) || inherits(x, "Vector") - }, logical(1))) - names(x)[which(!idx)] +check_nondata_cols <- function(data, mapping, problem = NULL, hint = NULL) { + # We define "data" as atomic types or lists, not functions or otherwise. + # The `inherits(x, "Vector")` check is for checking S4 classes from Bioconductor + # and whether they can be expected to follow behaviour typical of vectors. See + # also #3835 + invalid <- which(!vapply( + data, FUN.VALUE = logical(1), + function(x) is.null(x) || rlang::is_vector(x) || inherits(x, "Vector") + )) + invalid <- names(data)[invalid] + + if (length(invalid) < 1) { + return(invisible()) + } + + mapping <- vapply(mapping[invalid], as_label, character(1)) + issues <- paste0("{.code ", invalid, " = ", mapping, "}") + names(issues) <- rep("*", length(issues)) + issues <- c(x = "The following aesthetics are invalid:", issues) + + # Using 'call = NULL' here because `by_layer()` does a good job of indicating + # the origin of the error + cli::cli_abort(c(problem, issues, i = hint), call = NULL) } compact <- function(x) { diff --git a/tests/testthat/_snaps/facet-.md b/tests/testthat/_snaps/facet-.md index 17d76b1f86..154499e38a 100644 --- a/tests/testthat/_snaps/facet-.md +++ b/tests/testthat/_snaps/facet-.md @@ -3,7 +3,7 @@ Code facet_wrap(aes(foo)) Condition - Error in `validate_facets()`: + Error in `check_vars()`: ! Please use `vars()` to supply facet variables. --- @@ -11,7 +11,7 @@ Code facet_grid(aes(foo)) Condition - Error in `validate_facets()`: + Error in `check_vars()`: ! Please use `vars()` to supply facet variables. # facet_grid() fails if passed both a formula and a vars() @@ -73,7 +73,7 @@ Error: ! object 'no_such_variable' not found -# validate_facets() provide meaningful errors +# check_vars() provide meaningful errors Please use `vars()` to supply facet variables. diff --git a/tests/testthat/_snaps/facet-labels.md b/tests/testthat/_snaps/facet-labels.md index 6cdd9c1ad0..525e0dd0b7 100644 --- a/tests/testthat/_snaps/facet-labels.md +++ b/tests/testthat/_snaps/facet-labels.md @@ -16,6 +16,6 @@ # old school labellers still work - The `labeller` API has been updated. Labellers taking `variable` and `value` arguments are now deprecated. - i See labellers documentation. + The `labeller` argument of `facet_()` is deprecated as of ggplot2 2.0.0. + i Modern labellers do not take `variable` and `value` arguments anymore. diff --git a/tests/testthat/_snaps/fortify.md b/tests/testthat/_snaps/fortify.md index 2034f092fb..605829d9d8 100644 --- a/tests/testthat/_snaps/fortify.md +++ b/tests/testthat/_snaps/fortify.md @@ -10,7 +10,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` must return an of length 2. --- @@ -20,7 +20,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` must return an of length 2. --- @@ -30,7 +30,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `colnames(data)` must return a of length `ncol(data)`. --- @@ -50,7 +50,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` must return an of length 2. --- @@ -60,7 +60,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` must return an of length 2. --- @@ -70,7 +70,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` can't have `NA`s or negative values. --- @@ -80,7 +80,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `dim(data)` can't have `NA`s or negative values. --- @@ -100,7 +100,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `colnames(data)` must return a of length `ncol(data)`. --- @@ -110,7 +110,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.prevalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_like()`: ! `colnames(data)` must return a of length `ncol(data)`. --- @@ -130,7 +130,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.postvalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_conversion()`: ! `as.data.frame(data)` must return a . --- @@ -140,7 +140,7 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.postvalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_conversion()`: ! `as.data.frame(data)` must preserve dimensions. --- @@ -150,6 +150,6 @@ Condition Error in `fortify()`: ! `data` must be a , or an object coercible by `fortify()`, or a valid -like object coercible by `as.data.frame()`. - Caused by error in `.postvalidate_data_frame_like_object()`: + Caused by error in `check_data_frame_conversion()`: ! `as.data.frame(data)` must preserve column names. diff --git a/tests/testthat/_snaps/geom-.md b/tests/testthat/_snaps/geom-.md index 0eae2d74ba..b0ca0c7e85 100644 --- a/tests/testthat/_snaps/geom-.md +++ b/tests/testthat/_snaps/geom-.md @@ -2,10 +2,10 @@ Problem while setting up geom aesthetics. i Error occurred in the 1st layer. - Caused by error in `use_defaults()`: - ! Aesthetic modifiers returned invalid values - x The following mappings are invalid - x `colour = after_scale(data)` + Caused by error: + ! Aesthetic modifiers returned invalid values. + x The following aesthetics are invalid: + * `colour = after_scale(data)` i Did you map the modifier in the wrong layer? --- diff --git a/tests/testthat/_snaps/ggsave.md b/tests/testthat/_snaps/ggsave.md index 372d324b95..03440c5eba 100644 --- a/tests/testthat/_snaps/ggsave.md +++ b/tests/testthat/_snaps/ggsave.md @@ -58,7 +58,7 @@ --- Code - plot_dev("xyz") + validate_device("xyz") Condition Error: ! Unknown graphics device "xyz" @@ -66,7 +66,7 @@ --- Code - plot_dev(NULL, "test.xyz") + validate_device(NULL, "test.xyz") Condition Error: ! Unknown graphics device "xyz" diff --git a/tests/testthat/_snaps/layer.md b/tests/testthat/_snaps/layer.md index 70573a3d7c..79b561b17d 100644 --- a/tests/testthat/_snaps/layer.md +++ b/tests/testthat/_snaps/layer.md @@ -1,14 +1,14 @@ # layer() checks its input - Can't create layer without a geom. + The `geom` argument cannot be empty. --- - Can't create layer without a stat. + The `stat` argument cannot be empty. --- - Can't create layer without a position. + The `position` argument cannot be empty. --- @@ -43,20 +43,20 @@ Problem while computing aesthetics. i Error occurred in the 1st layer. - Caused by error in `compute_aesthetics()`: + Caused by error: ! Aesthetics are not valid data columns. x The following aesthetics are invalid: - x `fill = data` + * `fill = data` i Did you mistype the name of a data column or forget to add `after_stat()`? --- Problem while mapping stat to aesthetics. i Error occurred in the 1st layer. - Caused by error in `map_statistic()`: + Caused by error: ! Aesthetics must be valid computed stats. x The following aesthetics are invalid: - x `fill = after_stat(data)` + * `fill = after_stat(data)` i Did you map your stat in the wrong layer? # missing aesthetics trigger informative error @@ -85,22 +85,22 @@ Problem while computing aesthetics. i Error occurred in the 1st layer. - Caused by error in `compute_aesthetics()`: + Caused by error: ! Aesthetics are not valid data columns. x The following aesthetics are invalid: - x `colour = NULL` - x `fill = NULL` + * `colour = density` + * `fill = density` i Did you mistype the name of a data column or forget to add `after_stat()`? # computed stats are in appropriate layer Problem while mapping stat to aesthetics. i Error occurred in the 1st layer. - Caused by error in `map_statistic()`: + Caused by error: ! Aesthetics must be valid computed stats. x The following aesthetics are invalid: - x `colour = NULL` - x `fill = NULL` + * `colour = after_stat(density)` + * `fill = after_stat(density)` i Did you map your stat in the wrong layer? # layer reports the error with correct index etc diff --git a/tests/testthat/test-facet-.R b/tests/testthat/test-facet-.R index 11e86247ca..a24a5e4ca5 100644 --- a/tests/testthat/test-facet-.R +++ b/tests/testthat/test-facet-.R @@ -469,9 +469,9 @@ test_that("eval_facet() is tolerant for missing columns (#2963)", { ) }) -test_that("validate_facets() provide meaningful errors", { - expect_snapshot_error(validate_facets(aes(var))) - expect_snapshot_error(validate_facets(ggplot())) +test_that("check_vars() provide meaningful errors", { + expect_snapshot_error(check_vars(aes(var))) + expect_snapshot_error(check_vars(ggplot())) }) test_that("check_layout() throws meaningful errors", { diff --git a/tests/testthat/test-ggsave.R b/tests/testthat/test-ggsave.R index 4180eadc98..158dae2594 100644 --- a/tests/testthat/test-ggsave.R +++ b/tests/testthat/test-ggsave.R @@ -125,19 +125,19 @@ test_that("scale multiplies height & width", { # plot_dev --------------------------------------------------------------------- test_that("unknown device triggers error", { - expect_snapshot_error(plot_dev(1)) - expect_snapshot(plot_dev("xyz"), error = TRUE) - expect_snapshot(plot_dev(NULL, "test.xyz"), error = TRUE) + expect_snapshot_error(validate_device(1)) + expect_snapshot(validate_device("xyz"), error = TRUE) + expect_snapshot(validate_device(NULL, "test.xyz"), error = TRUE) }) test_that("text converted to function", { - expect_identical(body(plot_dev("png"))[[1]], quote(png_dev)) - expect_identical(body(plot_dev("pdf"))[[1]], quote(grDevices::pdf)) + expect_identical(body(validate_device("png"))[[1]], quote(png_dev)) + expect_identical(body(validate_device("pdf"))[[1]], quote(grDevices::pdf)) }) test_that("if device is NULL, guess from extension", { - expect_identical(body(plot_dev(NULL, "test.png"))[[1]], quote(png_dev)) + expect_identical(body(validate_device(NULL, "test.png"))[[1]], quote(png_dev)) }) # parse_dpi --------------------------------------------------------------- diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 225cedd947..59970c7db5 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -8,8 +8,8 @@ test_that("layer() checks its input", { expect_snapshot_error(layer("point", "identity", mapping = 1:4, position = "identity")) expect_snapshot_error(layer("point", "identity", mapping = ggplot(), position = "identity")) - expect_snapshot_error(check_subclass("test", "geom")) - expect_snapshot_error(check_subclass(environment(), "geom")) + expect_snapshot_error(validate_subclass("test", "geom")) + expect_snapshot_error(validate_subclass(environment(), "geom")) }) test_that("aesthetics go in aes_params", { diff --git a/tests/testthat/test-scales-breaks-labels.R b/tests/testthat/test-scales-breaks-labels.R index 42e3d67bb3..e0b8474a40 100644 --- a/tests/testthat/test-scales-breaks-labels.R +++ b/tests/testthat/test-scales-breaks-labels.R @@ -12,8 +12,8 @@ test_that("labels match breaks", { }) test_that("labels don't have to match null breaks", { - expect_true(check_breaks_labels(breaks = 1:3, labels = NULL)) - expect_true(check_breaks_labels(breaks = NULL, labels = 1:2)) + expect_silent(check_breaks_labels(breaks = 1:3, labels = NULL)) + expect_silent(check_breaks_labels(breaks = NULL, labels = 1:2)) }) test_that("labels don't have extra spaces", { diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index b6248acaa3..7477e41317 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -250,7 +250,7 @@ test_that("complete and non-complete themes interact correctly with ggplot objec expect_equal(p$plot$theme$text$face, "italic") }) -test_that("theme(validate=FALSE) means do not validate_element", { +test_that("theme(validate=FALSE) means do not check_element", { p <- ggplot(data.frame(x = 1:3), aes(x, x)) + geom_point() bw <- p + theme_bw() red.text <- theme(text = element_text(colour = "red")) @@ -542,9 +542,9 @@ test_that("subtheme functions rename arguments as intended", { test_that("Theme validation behaves as expected", { tree <- get_element_tree() - expect_silent(validate_element(1, "aspect.ratio", tree)) - expect_silent(validate_element(1L, "aspect.ratio", tree)) - expect_snapshot_error(validate_element("A", "aspect.ratio", tree)) + expect_silent(check_element(1, "aspect.ratio", tree)) + expect_silent(check_element(1L, "aspect.ratio", tree)) + expect_snapshot_error(check_element("A", "aspect.ratio", tree)) }) test_that("Element subclasses are inherited", { From 123b26e581032dd91442aaa17a4a4809cce713a6 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:19:32 +0100 Subject: [PATCH 196/264] Violin quantiles are based on observations (#5912) * plumbing for `draw_quantiles` in `stat_ydensity()` * stat computes quantiles * geom draws quantiles, not compute them * migrate docs * add test * accept snapshot changes * add news bullet * stat param is named `quantiles` * quantile drawing is controlled by graphical params * adapt tests * document * add news bullets * dedup news bullets * Deprecation of the `draw_quantiles` parameter coming from `geom_violin()` parity --- NEWS.md | 7 ++ R/geom-violin.R | 93 ++++++++++++------- R/stat-ydensity.R | 51 +++++++++- man/geom_violin.Rd | 21 ++++- tests/testthat/_snaps/geom-violin.md | 14 ++- tests/testthat/_snaps/geom-violin/basic.svg | 6 +- ...is-many-groups-center-should-be-at-2-0.svg | 2 +- ...s-single-group-center-should-be-at-1-0.svg | 2 +- .../_snaps/geom-violin/coord-flip.svg | 6 +- .../_snaps/geom-violin/coord-polar.svg | 6 +- .../geom-violin/dodging-and-coord-flip.svg | 6 +- tests/testthat/_snaps/geom-violin/dodging.svg | 6 +- ...grouping-on-x-and-fill-dodge-width-0-5.svg | 12 +-- .../geom-violin/grouping-on-x-and-fill.svg | 12 +-- .../_snaps/geom-violin/narrower-width-5.svg | 6 +- .../testthat/_snaps/geom-violin/quantiles.svg | 69 -------------- ...scale-area-to-sample-size-c-is-smaller.svg | 6 +- .../_snaps/geom-violin/styled-quantiles.svg | 69 ++++++++++++++ .../with-smaller-bandwidth-and-points.svg | 6 +- .../geom-violin/with-tails-and-points.svg | 6 +- tests/testthat/test-geom-violin.R | 18 ++-- tests/testthat/test-stat-ydensity.R | 12 +++ 22 files changed, 272 insertions(+), 164 deletions(-) delete mode 100644 tests/testthat/_snaps/geom-violin/quantiles.svg create mode 100644 tests/testthat/_snaps/geom-violin/styled-quantiles.svg diff --git a/NEWS.md b/NEWS.md index 140d7dd25b..3d9a9f7f99 100644 --- a/NEWS.md +++ b/NEWS.md @@ -51,6 +51,13 @@ (@teunbrand, #4320) * `geom_boxplot()` gains additional arguments to style the colour, linetype and linewidths of the box, whiskers, median line and staples (@teunbrand, #5126) +* `geom_violin()` gains additional arguments to style the colour, linetype and + linewidths of the quantiles, which replace the now-deprecated `draw_quantiles` + argument (#5912). +* (breaking) `geom_violin(quantiles)` now has actual quantiles based on + the data, rather than inferred quantiles based on the computed density. The + `quantiles` parameter that replaces `draw_quantiles` now belongs to + `stat_ydensity()` instead of `geom_violin()` (@teunbrand, #4120). * (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now evaluated in the context of data (@teunbrand, #6135) * Fixed bug where binned scales wouldn't simultaneously accept transformations diff --git a/R/geom-violin.R b/R/geom-violin.R index e53c29396f..8c3d23ad71 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -10,8 +10,6 @@ #' @eval rd_aesthetics("geom", "violin") #' @inheritParams layer #' @inheritParams geom_bar -#' @param draw_quantiles If `not(NULL)` (default), draw horizontal lines -#' at the given quantiles of the density estimate. #' @param trim If `TRUE` (default), trim the tails of the violins #' to the range of the data. If `FALSE`, don't trim the tails. #' @param geom,stat Use to override the default connection between @@ -23,6 +21,12 @@ #' finite, boundary effect of default density estimation will be corrected by #' reflecting tails outside `bounds` around their closest edge. Data points #' outside of bounds are removed with a warning. +#' @param quantile.colour,quantile.color,quantile.linewidth,quantile.linetype +#' Default aesthetics for the quantile lines. Set to `NULL` to inherit from +#' the data's aesthetics. By default, quantile lines are hidden and can be +#' turned on by changing `quantile.linetype`. +#' @param draw_quantiles `r lifecycle::badge("deprecated")` Previous +#' specification of drawing quantiles. #' @export #' @references Hintze, J. L., Nelson, R. D. (1998) Violin Plots: A Box #' Plot-Density Trace Synergism. The American Statistician 52, 181-184. @@ -91,14 +95,46 @@ geom_violin <- function(mapping = NULL, data = NULL, stat = "ydensity", position = "dodge", ..., - draw_quantiles = NULL, trim = TRUE, bounds = c(-Inf, Inf), + quantile.colour = NULL, + quantile.color = NULL, + quantile.linetype = 0L, + quantile.linewidth = NULL, + draw_quantiles = deprecated(), scale = "area", na.rm = FALSE, orientation = NA, show.legend = NA, inherit.aes = TRUE) { + + extra <- list() + if (lifecycle::is_present(draw_quantiles)) { + deprecate_soft0( + "3.6.0", + what = "geom_violin(draw_quantiles)", + with = "geom_violin(quantiles.linetype)" + ) + check_numeric(draw_quantiles) + + # Pass on to stat when stat accepts 'quantiles' + stat <- check_subclass(stat, "Stat", current_call(), caller_env()) + if ("quantiles" %in% stat$parameters()) { + extra$quantiles <- draw_quantiles + } + + # Turn on quantile lines + if (!is.null(quantile.linetype)) { + quantile.linetype <- max(quantile.linetype, 1) + } + } + + quantile_gp <- list( + colour = quantile.color %||% quantile.colour, + linetype = quantile.linetype, + linewidth = quantile.linewidth + ) + layer( data = data, mapping = mapping, @@ -110,10 +146,11 @@ geom_violin <- function(mapping = NULL, data = NULL, params = list2( trim = trim, scale = scale, - draw_quantiles = draw_quantiles, na.rm = na.rm, orientation = orientation, bounds = bounds, + quantile_gp = quantile_gp, + !!!extra, ... ) ) @@ -146,7 +183,7 @@ GeomViolin <- ggproto("GeomViolin", Geom, flip_data(data, params$flipped_aes) }, - draw_group = function(self, data, ..., draw_quantiles = NULL, flipped_aes = FALSE) { + draw_group = function(self, data, ..., quantile_gp = list(linetype = 0), flipped_aes = FALSE) { data <- flip_data(data, flipped_aes) # Find the points for the line to go all the way around data <- transform(data, @@ -165,36 +202,28 @@ GeomViolin <- ggproto("GeomViolin", Geom, newdata <- vec_rbind0(newdata, newdata[1,]) newdata <- flip_data(newdata, flipped_aes) + violin_grob <- GeomPolygon$draw_panel(newdata, ...) + + if (!"quantile" %in% names(newdata) || + all(quantile_gp$linetype == 0) || + all(quantile_gp$linetype == "blank")) { + return(ggname("geom_violin", violin_grob)) + } + # Draw quantiles if requested, so long as there is non-zero y range - if (length(draw_quantiles) > 0 & !scales::zero_range(range(data$y))) { - if (!(all(draw_quantiles >= 0) && all(draw_quantiles <= 1))) { - cli::cli_abort("{.arg draw_quantiles} must be between 0 and 1.") - } - - # Compute the quantile segments and combine with existing aesthetics - quantiles <- create_quantile_segment_frame(data, draw_quantiles) - aesthetics <- data[ - rep(1, nrow(quantiles)), - setdiff(names(data), c("x", "y", "group")), - drop = FALSE - ] - aesthetics$alpha <- rep(1, nrow(quantiles)) - both <- vec_cbind(quantiles, aesthetics) - both <- both[!is.na(both$group), , drop = FALSE] - both <- flip_data(both, flipped_aes) - quantile_grob <- if (nrow(both) == 0) { - zeroGrob() - } else { - GeomPath$draw_panel(both, ...) - } - - ggname("geom_violin", grobTree( - GeomPolygon$draw_panel(newdata, ...), - quantile_grob) - ) + quantiles <- newdata[!is.na(newdata$quantile),] + quantiles$group <- match(quantiles$quantile, unique(quantiles$quantile)) + quantiles$linetype <- quantile_gp$linetype %||% quantiles$linetype + quantiles$linewidth <- quantile_gp$linewidth %||% quantiles$linewidth + quantiles$colour <- quantile_gp$colour %||% quantiles$colour + + quantile_grob <- if (nrow(quantiles) == 0) { + zeroGrob() } else { - ggname("geom_violin", GeomPolygon$draw_panel(newdata, ...)) + GeomPath$draw_panel(quantiles, ...) } + + ggname("geom_violin", grobTree(violin_grob, quantile_grob)) }, draw_key = draw_key_polygon, diff --git a/R/stat-ydensity.R b/R/stat-ydensity.R index 4eadd8ca58..6b0e4f0ff8 100644 --- a/R/stat-ydensity.R +++ b/R/stat-ydensity.R @@ -7,6 +7,8 @@ #' @param drop Whether to discard groups with less than 2 observations #' (`TRUE`, default) or keep such groups for position adjustment purposes #' (`FALSE`). +#' @param quantiles If not `NULL` (default), compute the `quantile` variable +#' and draw horizontal lines at the given quantiles in `geom_violin()`. #' #' @eval rd_computed_vars( #' density = "Density estimate.", @@ -16,7 +18,8 @@ #' violinwidth = "Density scaled for the violin plot, according to area, #' counts or to a constant maximum width.", #' n = "Number of points.", -#' width = "Width of violin bounding box." +#' width = "Width of violin bounding box.", +#' quantile = "Whether the row is part of the `quantiles` computation." #' ) #' #' @seealso [geom_violin()] for examples, and [stat_density()] @@ -26,6 +29,7 @@ stat_ydensity <- function(mapping = NULL, data = NULL, geom = "violin", position = "dodge", ..., + quantiles = c(0.25, 0.50, 0.75), bw = "nrd0", adjust = 1, kernel = "gaussian", @@ -56,6 +60,7 @@ stat_ydensity <- function(mapping = NULL, data = NULL, drop = drop, na.rm = na.rm, bounds = bounds, + quantiles = quantiles, ... ) ) @@ -73,14 +78,26 @@ StatYdensity <- ggproto("StatYdensity", Stat, setup_params = function(data, params) { params$flipped_aes <- has_flipped_aes(data, params, main_is_orthogonal = TRUE, group_has_equal = TRUE) + if (!is.null(params$draw_quantiles)) { + deprecate_soft0( + "3.6.0", + what = "stat_ydensity(draw_quantiles)", + with = "stat_ydensity(quantiles)" + ) + params$quantiles <- params$draw_quantiles + check_numeric(params$quantiles, arg = "quantiles") + } + params }, - extra_params = c("na.rm", "orientation"), + # `draw_quantiles` is here for deprecation repair reasons + extra_params = c("na.rm", "orientation", "draw_quantiles"), compute_group = function(self, data, scales, width = NULL, bw = "nrd0", adjust = 1, kernel = "gaussian", trim = TRUE, na.rm = FALSE, - drop = TRUE, flipped_aes = FALSE, bounds = c(-Inf, Inf)) { + drop = TRUE, flipped_aes = FALSE, bounds = c(-Inf, Inf), + quantiles = c(0.25, 0.50, 0.75)) { if (nrow(data) < 2) { if (isTRUE(drop)) { cli::cli_warn(c( @@ -115,17 +132,43 @@ StatYdensity <- ggproto("StatYdensity", Stat, } dens$width <- width + if (!is.null(quantiles)) { + if (!(all(quantiles >= 0) && all(quantiles <= 1))) { + cli::cli_abort("{.arg quantiles} must be between 0 and 1.") + } + if (!is.null(data[["weight"]]) || !all(data[["weight"]] == 1)) { + cli::cli_warn( + "{.arg quantiles} for weighted data is not implemented." + ) + } + quants <- quantile(data$y, probs = quantiles) + quants <- data_frame0( + y = unname(quants), + quantile = quantiles + ) + + # Interpolate other metrics + for (var in setdiff(names(dens), names(quants))) { + quants[[var]] <- + approx(dens$y, dens[[var]], xout = quants$y, ties = "ordered")$y + } + + dens <- vec_slice(dens, !dens$y %in% quants$y) + dens <- vec_c(dens, quants) + } + dens }, compute_panel = function(self, data, scales, width = NULL, bw = "nrd0", adjust = 1, kernel = "gaussian", trim = TRUE, na.rm = FALSE, scale = "area", flipped_aes = FALSE, drop = TRUE, - bounds = c(-Inf, Inf)) { + bounds = c(-Inf, Inf), quantiles = c(0.25, 0.50, 0.75)) { data <- flip_data(data, flipped_aes) data <- ggproto_parent(Stat, self)$compute_panel( data, scales, width = width, bw = bw, adjust = adjust, kernel = kernel, trim = trim, na.rm = na.rm, drop = drop, bounds = bounds, + quantiles = quantiles ) if (!drop && any(data$n < 2)) { cli::cli_warn( diff --git a/man/geom_violin.Rd b/man/geom_violin.Rd index 974d1c5bdc..244a7ac7ea 100644 --- a/man/geom_violin.Rd +++ b/man/geom_violin.Rd @@ -11,9 +11,13 @@ geom_violin( stat = "ydensity", position = "dodge", ..., - draw_quantiles = NULL, trim = TRUE, bounds = c(-Inf, Inf), + quantile.colour = NULL, + quantile.color = NULL, + quantile.linetype = 0L, + quantile.linewidth = NULL, + draw_quantiles = deprecated(), scale = "area", na.rm = FALSE, orientation = NA, @@ -27,6 +31,7 @@ stat_ydensity( geom = "violin", position = "dodge", ..., + quantiles = c(0.25, 0.5, 0.75), bw = "nrd0", adjust = 1, kernel = "gaussian", @@ -102,9 +107,6 @@ lists which parameters it can accept. \link[=draw_key]{key glyphs}, to change the display of the layer in the legend. }} -\item{draw_quantiles}{If \code{not(NULL)} (default), draw horizontal lines -at the given quantiles of the density estimate.} - \item{trim}{If \code{TRUE} (default), trim the tails of the violins to the range of the data. If \code{FALSE}, don't trim the tails.} @@ -114,6 +116,13 @@ finite, boundary effect of default density estimation will be corrected by reflecting tails outside \code{bounds} around their closest edge. Data points outside of bounds are removed with a warning.} +\item{quantile.colour, quantile.color, quantile.linewidth, quantile.linetype}{Default aesthetics for the quantile lines. Set to \code{NULL} to inherit from +the data's aesthetics. By default, quantile lines are hidden and can be +turned on by changing \code{quantile.linetype}.} + +\item{draw_quantiles}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Previous +specification of drawing quantiles.} + \item{scale}{if "area" (default), all violins have the same area (before trimming the tails). If "count", areas are scaled proportionally to the number of observations. If "width", all violins have the same maximum width.} @@ -144,6 +153,9 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} overriding these connections, see how the \link[=layer_stats]{stat} and \link[=layer_geoms]{geom} arguments work.} +\item{quantiles}{If not \code{NULL} (default), compute the \code{quantile} variable +and draw horizontal lines at the given quantiles in \code{geom_violin()}.} + \item{bw}{The smoothing bandwidth to be used. If numeric, the standard deviation of the smoothing kernel. If character, a rule to choose the bandwidth, as listed in @@ -198,6 +210,7 @@ These are calculated by the 'stat' part of layers and can be accessed with \link \item \code{after_stat(violinwidth)}\cr Density scaled for the violin plot, according to area, counts or to a constant maximum width. \item \code{after_stat(n)}\cr Number of points. \item \code{after_stat(width)}\cr Width of violin bounding box. +\item \code{after_stat(quantile)}\cr Whether the row is part of the \code{quantiles} computation. } } diff --git a/tests/testthat/_snaps/geom-violin.md b/tests/testthat/_snaps/geom-violin.md index 80da5aad02..68cc4c1c5a 100644 --- a/tests/testthat/_snaps/geom-violin.md +++ b/tests/testthat/_snaps/geom-violin.md @@ -1,14 +1,12 @@ # quantiles fails outside 0-1 bound - Problem while converting geom to grob. - i Error occurred in the 1st layer. - Caused by error in `draw_group()`: - ! `draw_quantiles` must be between 0 and 1. + Computation failed in `stat_ydensity()`. + Caused by error in `compute_group()`: + ! `quantiles` must be between 0 and 1. --- - Problem while converting geom to grob. - i Error occurred in the 1st layer. - Caused by error in `draw_group()`: - ! `draw_quantiles` must be between 0 and 1. + Computation failed in `stat_ydensity()`. + Caused by error in `compute_group()`: + ! `quantiles` must be between 0 and 1. diff --git a/tests/testthat/_snaps/geom-violin/basic.svg b/tests/testthat/_snaps/geom-violin/basic.svg index 206a6b4626..16e7518c21 100644 --- a/tests/testthat/_snaps/geom-violin/basic.svg +++ b/tests/testthat/_snaps/geom-violin/basic.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/continuous-x-axis-many-groups-center-should-be-at-2-0.svg b/tests/testthat/_snaps/geom-violin/continuous-x-axis-many-groups-center-should-be-at-2-0.svg index f737690144..611f73f969 100644 --- a/tests/testthat/_snaps/geom-violin/continuous-x-axis-many-groups-center-should-be-at-2-0.svg +++ b/tests/testthat/_snaps/geom-violin/continuous-x-axis-many-groups-center-should-be-at-2-0.svg @@ -27,7 +27,7 @@ - + diff --git a/tests/testthat/_snaps/geom-violin/continuous-x-axis-single-group-center-should-be-at-1-0.svg b/tests/testthat/_snaps/geom-violin/continuous-x-axis-single-group-center-should-be-at-1-0.svg index f11a934abb..74fc5ed64e 100644 --- a/tests/testthat/_snaps/geom-violin/continuous-x-axis-single-group-center-should-be-at-1-0.svg +++ b/tests/testthat/_snaps/geom-violin/continuous-x-axis-single-group-center-should-be-at-1-0.svg @@ -27,7 +27,7 @@ - + diff --git a/tests/testthat/_snaps/geom-violin/coord-flip.svg b/tests/testthat/_snaps/geom-violin/coord-flip.svg index 434afe96c8..59f095248a 100644 --- a/tests/testthat/_snaps/geom-violin/coord-flip.svg +++ b/tests/testthat/_snaps/geom-violin/coord-flip.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/coord-polar.svg b/tests/testthat/_snaps/geom-violin/coord-polar.svg index e70e3b11f3..02ae1107df 100644 --- a/tests/testthat/_snaps/geom-violin/coord-polar.svg +++ b/tests/testthat/_snaps/geom-violin/coord-polar.svg @@ -36,9 +36,9 @@ - - - + + + A B C diff --git a/tests/testthat/_snaps/geom-violin/dodging-and-coord-flip.svg b/tests/testthat/_snaps/geom-violin/dodging-and-coord-flip.svg index 86a328e5b5..6af10a6faa 100644 --- a/tests/testthat/_snaps/geom-violin/dodging-and-coord-flip.svg +++ b/tests/testthat/_snaps/geom-violin/dodging-and-coord-flip.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/dodging.svg b/tests/testthat/_snaps/geom-violin/dodging.svg index c1ccf480ce..d1d537e3b2 100644 --- a/tests/testthat/_snaps/geom-violin/dodging.svg +++ b/tests/testthat/_snaps/geom-violin/dodging.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill-dodge-width-0-5.svg b/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill-dodge-width-0-5.svg index 17142781de..fcf5700ada 100644 --- a/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill-dodge-width-0-5.svg +++ b/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill-dodge-width-0-5.svg @@ -27,12 +27,12 @@ - - - - - - + + + + + + diff --git a/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill.svg b/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill.svg index 56049d8ef6..477f9a02c5 100644 --- a/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill.svg +++ b/tests/testthat/_snaps/geom-violin/grouping-on-x-and-fill.svg @@ -27,12 +27,12 @@ - - - - - - + + + + + + diff --git a/tests/testthat/_snaps/geom-violin/narrower-width-5.svg b/tests/testthat/_snaps/geom-violin/narrower-width-5.svg index d7a23e057b..d233183697 100644 --- a/tests/testthat/_snaps/geom-violin/narrower-width-5.svg +++ b/tests/testthat/_snaps/geom-violin/narrower-width-5.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/quantiles.svg b/tests/testthat/_snaps/geom-violin/quantiles.svg deleted file mode 100644 index 8bec1ac1a6..0000000000 --- a/tests/testthat/_snaps/geom-violin/quantiles.svg +++ /dev/null @@ -1,69 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --3 --2 --1 -0 -1 -2 -3 - - - - - - - - - - -A -B -C -x -y -quantiles - - diff --git a/tests/testthat/_snaps/geom-violin/scale-area-to-sample-size-c-is-smaller.svg b/tests/testthat/_snaps/geom-violin/scale-area-to-sample-size-c-is-smaller.svg index 1c0bf845b4..ca9f1bf889 100644 --- a/tests/testthat/_snaps/geom-violin/scale-area-to-sample-size-c-is-smaller.svg +++ b/tests/testthat/_snaps/geom-violin/scale-area-to-sample-size-c-is-smaller.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/styled-quantiles.svg b/tests/testthat/_snaps/geom-violin/styled-quantiles.svg new file mode 100644 index 0000000000..0b8d55329f --- /dev/null +++ b/tests/testthat/_snaps/geom-violin/styled-quantiles.svg @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-3 +-2 +-1 +0 +1 +2 +3 + + + + + + + + + + +A +B +C +x +y +styled quantiles + + diff --git a/tests/testthat/_snaps/geom-violin/with-smaller-bandwidth-and-points.svg b/tests/testthat/_snaps/geom-violin/with-smaller-bandwidth-and-points.svg index 1494c6bd08..3dc573d465 100644 --- a/tests/testthat/_snaps/geom-violin/with-smaller-bandwidth-and-points.svg +++ b/tests/testthat/_snaps/geom-violin/with-smaller-bandwidth-and-points.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/_snaps/geom-violin/with-tails-and-points.svg b/tests/testthat/_snaps/geom-violin/with-tails-and-points.svg index 1db22dd441..d109c20fbc 100644 --- a/tests/testthat/_snaps/geom-violin/with-tails-and-points.svg +++ b/tests/testthat/_snaps/geom-violin/with-tails-and-points.svg @@ -27,9 +27,9 @@ - - - + + + diff --git a/tests/testthat/test-geom-violin.R b/tests/testthat/test-geom-violin.R index a93a534b40..ff3cae8de8 100644 --- a/tests/testthat/test-geom-violin.R +++ b/tests/testthat/test-geom-violin.R @@ -40,7 +40,8 @@ test_that("create_quantile_segment_frame functions for 3 quantiles", { test_that("quantiles do not fail on zero-range data", { zero.range.data <- data_frame(y = rep(1,3)) - p <- ggplot(zero.range.data) + geom_violin(aes(1, y), draw_quantiles = 0.5) + p <- ggplot(zero.range.data) + + geom_violin(aes(1, y), quantiles = 0.5, quantile.linetype = NULL) # This should return without error and have length one expect_length(get_layer_grob(p), 1) @@ -48,10 +49,10 @@ test_that("quantiles do not fail on zero-range data", { test_that("quantiles fails outside 0-1 bound", { p <- ggplot(mtcars) + - geom_violin(aes(as.factor(gear), mpg), draw_quantiles = c(-1, 0.5)) + geom_violin(aes(as.factor(gear), mpg), quantiles = c(-1, 0.5)) expect_snapshot_error(ggplotGrob(p)) p <- ggplot(mtcars) + - geom_violin(aes(as.factor(gear), mpg), draw_quantiles = c(0.5, 2)) + geom_violin(aes(as.factor(gear), mpg), quantiles = c(0.5, 2)) expect_snapshot_error(ggplotGrob(p)) }) @@ -70,7 +71,7 @@ test_that("quantiles do not issue warning", { data <- data_frame(x = 1, y = c(0, 0.25, 0.5, 0.75, 5)) p <- ggplot(data, aes(x = x, y = y)) + - geom_violin(draw_quantiles = 0.5) + geom_violin(quantiles = 0.5, quantile.linetype = NULL) expect_silent(plot(p)) }) @@ -116,8 +117,13 @@ test_that("geom_violin draws correctly", { expect_doppelganger("continuous x axis, single group (center should be at 1.0)", ggplot(dat, aes(x = as.numeric(1), y = y)) + geom_violin() ) - expect_doppelganger("quantiles", - ggplot(dat, aes(x=x, y=y)) + geom_violin(draw_quantiles=c(0.25,0.5,0.75)) + expect_doppelganger("styled quantiles", + ggplot(dat, aes(x=x, y=y)) + + geom_violin( + quantile.colour = "red", + quantile.linetype = "dotted", + quantile.linewidth = 2 + ) ) dat2 <- data_frame(x = rep(factor(LETTERS[1:3]), 30), y = rnorm(90), g = rep(factor(letters[5:6]), 45)) diff --git a/tests/testthat/test-stat-ydensity.R b/tests/testthat/test-stat-ydensity.R index d43fbcc0e3..fb5d39c036 100644 --- a/tests/testthat/test-stat-ydensity.R +++ b/tests/testthat/test-stat-ydensity.R @@ -39,3 +39,15 @@ test_that("mapped_discrete class is preserved", { expect_s3_class(ld$x, "mapped_discrete") expect_equal(unique(ld$x), c(1, 3)) }) + +test_that("quantiles are based on actual data (#4120)", { + + df <- data.frame(y = 0:10) + q <- seq(0.1, 0.9, by = 0.1) + + p <- ggplot(df, aes("X", y)) + + stat_ydensity(quantiles = q) + ld <- get_layer_data(p) + + expect_equal(ld$y[!is.na(ld$quantile)], 1:9) +}) From ccda105a4c8fc1051746550dcb21ad8691504083 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:21:52 +0100 Subject: [PATCH 197/264] add note (#6170) --- R/aes.R | 7 +++++++ man/aes.Rd | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/R/aes.R b/R/aes.R index 0829f64daf..045d388d8a 100644 --- a/R/aes.R +++ b/R/aes.R @@ -38,6 +38,13 @@ NULL #' #' [Delayed evaluation][aes_eval] for working with computed variables. #' +#' @note +#' Using `I()` to create objects of class 'AsIs' causes scales to ignore the +#' variable and assumes the wrapped variable is direct input for the grid +#' package. Please be aware that variables are sometimes combined, like in +#' some stats or position adjustments, that may yield unexpected results with +#' 'AsIs' variables. +#' #' @family aesthetics documentation #' @return A list with class `uneval`. Components of the list are either #' quosures or constants. diff --git a/man/aes.Rd b/man/aes.Rd index c49fbefada..ed77c5d39e 100644 --- a/man/aes.Rd +++ b/man/aes.Rd @@ -30,6 +30,13 @@ This function also standardises aesthetic names by converting \code{color} to \c (also in substrings, e.g., \code{point_color} to \code{point_colour}) and translating old style R names to ggplot names (e.g., \code{pch} to \code{shape} and \code{cex} to \code{size}). } +\note{ +Using \code{I()} to create objects of class 'AsIs' causes scales to ignore the +variable and assumes the wrapped variable is direct input for the grid +package. Please be aware that variables are sometimes combined, like in +some stats or position adjustments, that may yield unexpected results with +'AsIs' variables. +} \section{Quasiquotation}{ From 8efc700377c6bfb0583909846f7dc235b0122c34 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 13:22:25 +0100 Subject: [PATCH 198/264] Use snapshot expectations for breaks (#6171) --- tests/testthat/_snaps/scales.md | 119 ++++++++++++++++++++++++++++++++ tests/testthat/test-scales.R | 69 +++++------------- 2 files changed, 136 insertions(+), 52 deletions(-) diff --git a/tests/testthat/_snaps/scales.md b/tests/testthat/_snaps/scales.md index 549769419c..33b36a3cd8 100644 --- a/tests/testthat/_snaps/scales.md +++ b/tests/testthat/_snaps/scales.md @@ -72,11 +72,130 @@ # numeric scale transforms can produce breaks + Code + test_breaks("asn", limits = c(0, 1)) + Output + [1] 0.00 0.25 0.50 0.75 1.00 + +--- + + Code + test_breaks("sqrt", limits = c(0, 10)) + Output + [1] 0.0 2.5 5.0 7.5 10.0 + +--- + + Code + test_breaks("atanh", limits = c(-0.9, 0.9)) + Output + [1] NA -0.5 0.0 0.5 NA + +--- + + Code + test_breaks(transform_boxcox(0), limits = c(1, 10)) + Output + [1] NA 2.5 5.0 7.5 10.0 + +--- + + Code + test_breaks(transform_modulus(0), c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + + Code + test_breaks(transform_yj(0), c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + + Code + test_breaks("exp", c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + + Code + test_breaks("identity", limits = c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + Code test_breaks("log", limits = c(0.1, 1000)) Output [1] NA 1.00000 20.08554 403.42879 +--- + + Code + test_breaks("log10", limits = c(0.1, 1000)) + Output + [1] 1e-01 1e+00 1e+01 1e+02 1e+03 + +--- + + Code + test_breaks("log2", limits = c(0.5, 32)) + Output + [1] 0.5 2.0 8.0 32.0 + +--- + + Code + test_breaks("log1p", limits = c(0, 10)) + Output + [1] 0.0 2.5 5.0 7.5 10.0 + +--- + + Code + test_breaks("pseudo_log", limits = c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + + Code + test_breaks("logit", limits = c(0.001, 0.999)) + Output + [1] NA 0.25 0.50 0.75 NA + +--- + + Code + test_breaks("probit", limits = c(0.001, 0.999)) + Output + [1] NA 0.25 0.50 0.75 NA + +--- + + Code + test_breaks("reciprocal", limits = c(1, 10)) + Output + [1] NA 2.5 5.0 7.5 10.0 + +--- + + Code + test_breaks("reverse", limits = c(-10, 10)) + Output + [1] -10 -5 0 5 10 + +--- + + Code + test_breaks("sqrt", limits = c(0, 10)) + Output + [1] 0.0 2.5 5.0 7.5 10.0 + # training incorrectly appropriately communicates the offenders Continuous values supplied to discrete scale. diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 514cb392a3..6fb4e4e667 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -469,59 +469,24 @@ test_that("numeric scale transforms can produce breaks", { scale$get_transformation()$inverse(view$get_breaks()) } - expect_equal(test_breaks("asn", limits = c(0, 1)), - seq(0, 1, by = 0.25)) - - expect_equal(test_breaks("sqrt", limits = c(0, 10)), - seq(0, 10, by = 2.5)) - - expect_equal(test_breaks("atanh", limits = c(-0.9, 0.9)), - c(NA, -0.5, 0, 0.5, NA)) - - expect_equal(test_breaks(transform_boxcox(0), limits = c(1, 10)), - c(NA, 2.5, 5.0, 7.5, 10)) - - expect_equal(test_breaks(transform_modulus(0), c(-10, 10)), - seq(-10, 10, by = 5)) - - expect_equal(test_breaks(transform_yj(0), c(-10, 10)), - seq(-10, 10, by = 5)) - - expect_equal(test_breaks("exp", c(-10, 10)), - seq(-10, 10, by = 5)) - - expect_equal(test_breaks("identity", limits = c(-10, 10)), - seq(-10, 10, by = 5)) - - # irrational numbers, so snapshot values + expect_snapshot(test_breaks("asn", limits = c(0, 1))) + expect_snapshot(test_breaks("sqrt", limits = c(0, 10))) + expect_snapshot(test_breaks("atanh", limits = c(-0.9, 0.9))) + expect_snapshot(test_breaks(transform_boxcox(0), limits = c(1, 10))) + expect_snapshot(test_breaks(transform_modulus(0), c(-10, 10))) + expect_snapshot(test_breaks(transform_yj(0), c(-10, 10))) + expect_snapshot(test_breaks("exp", c(-10, 10))) + expect_snapshot(test_breaks("identity", limits = c(-10, 10))) expect_snapshot(test_breaks("log", limits = c(0.1, 1000))) - - expect_equal(test_breaks("log10", limits = c(0.1, 1000)), - 10 ^ seq(-1, 3)) - - expect_equal(test_breaks("log2", limits = c(0.5, 32)), - c(0.5, 2, 8, 32)) - - expect_equal(test_breaks("log1p", limits = c(0, 10)), - seq(0, 10, by = 2.5)) - - expect_equal(test_breaks("pseudo_log", limits = c(-10, 10)), - seq(-10, 10, by = 5)) - - expect_equal(test_breaks("logit", limits = c(0.001, 0.999)), - c(NA, 0.25, 0.5, 0.75, NA)) - - expect_equal(test_breaks("probit", limits = c(0.001, 0.999)), - c(NA, 0.25, 0.5, 0.75, NA)) - - expect_equal(test_breaks("reciprocal", limits = c(1, 10)), - c(NA, 2.5, 5, 7.5, 10)) - - expect_equal(test_breaks("reverse", limits = c(-10, 10)), - seq(-10, 10, by = 5)) - - expect_equal(test_breaks("sqrt", limits = c(0, 10)), - seq(0, 10, by = 2.5)) + expect_snapshot(test_breaks("log10", limits = c(0.1, 1000))) + expect_snapshot(test_breaks("log2", limits = c(0.5, 32))) + expect_snapshot(test_breaks("log1p", limits = c(0, 10))) + expect_snapshot(test_breaks("pseudo_log", limits = c(-10, 10))) + expect_snapshot(test_breaks("logit", limits = c(0.001, 0.999))) + expect_snapshot(test_breaks("probit", limits = c(0.001, 0.999))) + expect_snapshot(test_breaks("reciprocal", limits = c(1, 10))) + expect_snapshot(test_breaks("reverse", limits = c(-10, 10))) + expect_snapshot(test_breaks("sqrt", limits = c(0, 10))) }) test_that("scale functions accurately report their calls", { From a62895aef8909ddb4c86a65554ecff4cd89d5983 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:02:10 +0100 Subject: [PATCH 199/264] Fix regression in `guide_bins(reverse)` (#6185) * bump NA to back of key * add test * add news bullet * Fix interaction between #5912 and #6072 --- NEWS.md | 1 + R/geom-violin.R | 2 +- R/guide-bins.R | 5 +- .../_snaps/guides/reversed-guide-bins.svg | 97 +++++++++++++++++++ tests/testthat/test-guides.R | 16 +++ 5 files changed, 119 insertions(+), 2 deletions(-) create mode 100644 tests/testthat/_snaps/guides/reversed-guide-bins.svg diff --git a/NEWS.md b/NEWS.md index 3d9a9f7f99..4d67350673 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* Fixed regression in `guide_bins(reverse = TRUE)` (@teunbrand, #6183). * New function family for setting parts of a theme. For example, you can now use `theme_sub_axis(line, text, ticks, ticks.length, line)` as a substitute for `theme(axis.line, axis.text, axis.ticks, axis.ticks.length, axis.line)`. This diff --git a/R/geom-violin.R b/R/geom-violin.R index 8c3d23ad71..1ad8c2172a 100644 --- a/R/geom-violin.R +++ b/R/geom-violin.R @@ -118,7 +118,7 @@ geom_violin <- function(mapping = NULL, data = NULL, check_numeric(draw_quantiles) # Pass on to stat when stat accepts 'quantiles' - stat <- check_subclass(stat, "Stat", current_call(), caller_env()) + stat <- validate_subclass(stat, "Stat", current_call(), caller_env()) if ("quantiles" %in% stat$parameters()) { extra$quantiles <- draw_quantiles } diff --git a/R/guide-bins.R b/R/guide-bins.R index c0344bbbe0..c03d5179d6 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -211,7 +211,10 @@ GuideBins <- ggproto( params$show.limits <- show.limits if (params$reverse) { - key <- key[rev(seq_len(nrow(key))), , drop = FALSE] + ord <- seq_len(nrow(key)) + key <- vec_slice(key, rev(ord)) + # Put NA back in the trailing position + key[params$aesthetic] <- vec_slice(key[params$aesthetic], c(ord[-1], ord[1])) key$.value <- 1 - key$.value } diff --git a/tests/testthat/_snaps/guides/reversed-guide-bins.svg b/tests/testthat/_snaps/guides/reversed-guide-bins.svg new file mode 100644 index 0000000000..16e8f7efca --- /dev/null +++ b/tests/testthat/_snaps/guides/reversed-guide-bins.svg @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 + + + + + + + + + + +0 +25 +50 +75 +100 +x +x + +x + + + + + + + + + + + + + + +100 +75 +50 +25 +0 + +x + + + + + + + + + + + + +75 +50 +25 +reversed guide_bins + + diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index 5718e4f2ad..1a3a31143a 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -411,6 +411,22 @@ test_that("guides title and text are positioned correctly", { expect_doppelganger("legends with all title justifications", p) }) +test_that("bin guide can be reversed", { + + p <- ggplot(data.frame(x = c(0, 100)), aes(x, x, colour = x, fill = x)) + + geom_point() + + guides( + colour = guide_bins(reverse = TRUE, show.limits = TRUE, order = 1), + fill = guide_bins( + reverse = TRUE, show.limits = FALSE, order = 2, + override.aes = list(shape = 21) + ) + ) + + expect_doppelganger("reversed guide_bins", p) + +}) + test_that("bin guide can be styled correctly", { df <- data_frame(x = c(1, 2, 3), y = c(6, 5, 7)) From a4264bc48fb990fc7408fae4a04dc4a442b6ca8a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:02:47 +0100 Subject: [PATCH 200/264] Checks for `register_theme_element(element_tree)` (#6169) * error on circular parents * more elaborate checks on element tree * add test * add news bullet --- NEWS.md | 1 + R/theme-elements.R | 39 ++++++++++++++++++++++++++++++++++ tests/testthat/_snaps/theme.md | 13 ++++++++++++ tests/testthat/test-theme.R | 11 ++++++++++ 4 files changed, 64 insertions(+) diff --git a/NEWS.md b/NEWS.md index 4d67350673..0a392e2b24 100644 --- a/NEWS.md +++ b/NEWS.md @@ -262,6 +262,7 @@ * Added `panel.widths` and `panel.heights` to `theme()` (#5338, @teunbrand). * Standardised the calculation of `width`, which are now implemented as aesthetics (@teunbrand, #2800). +* Stricter check on `register_theme_elements(element_tree)` (@teunbrand, #6162) # ggplot2 3.5.1 diff --git a/R/theme-elements.R b/R/theme-elements.R index 5a6b1a43cf..b83822ed3a 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -415,6 +415,8 @@ register_theme_elements <- function(..., element_tree = NULL, complete = TRUE) { t <- theme(..., complete = complete) ggplot_global$theme_default <- ggplot_global$theme_default %+replace% t + check_element_tree(element_tree) + # Merge element trees ggplot_global$element_tree <- defaults(element_tree, ggplot_global$element_tree) @@ -460,6 +462,43 @@ get_element_tree <- function() { ggplot_global$element_tree } +check_element_tree <- function(x, arg = caller_arg(x), call = caller_env()) { + check_object(x, is_bare_list, "a bare {.cls list}", arg = arg, call = call) + if (length(x) < 1) { + return(invisible(NULL)) + } + + if (!is_named(x)) { + cli::cli_abort("{.arg {arg}} must have names.", call = call) + } + + # All elements should be constructed with `el_def()` + fields <- names(el_def()) + bad_fields <- !vapply(x, function(el) all(fields %in% names(el)), logical(1)) + if (any(bad_fields)) { + bad_fields <- names(x)[bad_fields] + cli::cli_abort( + c("{.arg {arg}} must have elements constructed with {.fn el_def}.", + i = "Invalid structure: {.and {.val {bad_fields}}}"), + call = call + ) + } + + # Check element tree, prevent elements from being their own parent (#6162) + bad_parent <- unlist(Map( + function(name, el) any(name %in% el$inherit), + name = names(x), el = x + )) + if (any(bad_parent)) { + bad_parent <- names(x)[bad_parent] + cli::cli_abort( + "Invalid parent in {.arg {arg}}: {.and {.val {bad_parent}}}.", + call = call + ) + } + invisible(NULL) +} + #' @rdname register_theme_elements #' @details #' The function `el_def()` is used to define new or modified element types and diff --git a/tests/testthat/_snaps/theme.md b/tests/testthat/_snaps/theme.md index 322cce92b7..005e1b2abd 100644 --- a/tests/testthat/_snaps/theme.md +++ b/tests/testthat/_snaps/theme.md @@ -56,6 +56,19 @@ The `blablabla` theme element must be a object. +--- + + `element_tree` must have names. + +--- + + `element_tree` must have elements constructed with `el_def()`. + i Invalid structure: "foo" + +--- + + Invalid parent in `element_tree`: "foo". + # elements can be merged Code diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index 7477e41317..eba47a0c75 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -312,6 +312,17 @@ test_that("element tree can be modified", { p1 <- ggplot() + theme(blablabla = element_line()) expect_snapshot_error(ggplotGrob(p1)) + # Expect errors for invalid element trees + expect_snapshot_error( + register_theme_elements(element_tree = list(el_def("rect"), el_def("line"))) + ) + expect_snapshot_error( + register_theme_elements(element_tree = list(foo = "bar")) + ) + expect_snapshot_error( + register_theme_elements(element_tree = list(foo = el_def(inherit = "foo"))) + ) + # inheritance and final calculation of novel element works final_theme <- ggplot2:::plot_theme(p, theme_gray()) e1 <- calc_element("blablabla", final_theme) From c9fbb28d89402aeb54f936279881d374464246ba Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:28:32 +0100 Subject: [PATCH 201/264] Make `ScaleDiscrete$map()` compatible with vctrs-palettes (#6118) * sprinkle vctrs over `ScaleDiscrete$map()` * add test * prevent guide from clogging up * add news bullet --- NEWS.md | 1 + R/scale-.R | 29 +++++++++++++++++++---------- tests/testthat/test-scales.R | 29 +++++++++++++++++++++++++++++ 3 files changed, 49 insertions(+), 10 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0a392e2b24..f4815f325d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +* More stability for vctrs-based palettes (@teunbrand, #6117). * Fixed regression in `guide_bins(reverse = TRUE)` (@teunbrand, #6183). * New function family for setting parts of a theme. For example, you can now use `theme_sub_axis(line, text, ticks, ticks.length, line)` as a substitute for diff --git a/R/scale-.R b/R/scale-.R index b2f9ef346a..5ae52f65ab 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -963,10 +963,10 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, transform = identity, map = function(self, x, limits = self$get_limits()) { - limits <- limits[!is.na(limits)] - n <- length(limits) + limits <- vec_slice(limits, !is.na(limits)) + n <- vec_size(limits) if (n < 1) { - return(rep(self$na.value, length(x))) + return(vec_rep(self$na.value, vec_size(x))) } if (!is.null(self$n.breaks.cache) && self$n.breaks.cache == n) { pal <- self$palette.cache @@ -982,21 +982,30 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, self$n.breaks.cache <- n } - na_value <- if (self$na.translate) self$na.value else NA - pal_names <- names(pal) + na_value <- NA + if (self$na.translate) { + na_value <- self$na.value + if (obj_is_list(pal) && !obj_is_list(na_value)) { + # We prevent a casting error that occurs when mapping grid patterns + na_value <- list(na_value) + } + } + + pal_names <- vec_names(pal) if (!is_null(pal_names)) { # if pal is named, limit the pal by the names first, # then limit the values by the pal - pal[is.na(match(pal_names, limits))] <- na_value - pal <- unname(pal) + vec_slice(pal, is.na(match(pal_names, limits))) <- na_value + pal <- vec_set_names(pal, NULL) limits <- pal_names } - pal <- c(pal, na_value) - pal_match <- pal[match(as.character(x), limits, nomatch = length(pal))] + pal <- vec_c(pal, na_value) + pal_match <- + vec_slice(pal, match(as.character(x), limits, nomatch = vec_size(pal))) if (!is.na(na_value)) { - pal_match[is.na(x)] <- na_value + vec_slice(pal_match, is.na(x)) <- na_value } pal_match }, diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R index 6fb4e4e667..0a750e4821 100644 --- a/tests/testthat/test-scales.R +++ b/tests/testthat/test-scales.R @@ -747,3 +747,32 @@ test_that("discrete scales work with NAs in arbitrary positions", { expect_equal(test, output) }) + +test_that("discrete scales can map to 2D structures", { + + p <- ggplot(mtcars, aes(disp, mpg, colour = factor(cyl))) + + geom_point() + + # Test it can map to a vctrs rcrd class + rcrd <- new_rcrd(list(a = LETTERS[1:3], b = 3:1)) + + ld <- layer_data(p + scale_colour_manual(values = rcrd, na.value = NA)) + expect_s3_class(ld$colour, "vctrs_rcrd") + expect_length(ld$colour, nrow(mtcars)) + + # Test it can map to data.frames + df <- data_frame0(a = LETTERS[1:3], b = 3:1) + my_pal <- function(n) vec_slice(df, seq_len(n)) + + ld <- layer_data(p + discrete_scale("colour", palette = my_pal)) + expect_s3_class(ld$colour, "data.frame") + expect_equal(dim(ld$colour), c(nrow(mtcars), ncol(df))) + + # Test it can map to matrices + mtx <- cbind(a = LETTERS[1:3], b = LETTERS[4:6]) + my_pal <- function(n) vec_slice(mtx, seq_len(n)) + + ld <- layer_data(p + discrete_scale("colour", palette = my_pal)) + expect_true(is.matrix(ld$colour)) + expect_equal(dim(ld$colour), c(nrow(mtcars), ncol(df))) +}) From 5964f7a30c24077d9263cceb543e532e1c106a2e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:33:23 +0100 Subject: [PATCH 202/264] Ensure boxplot key can be drawn without `params` (#6192) * fallback for `staplewidth` in boxplot key * add test * add comment * test for completeness too --- R/legend-draw.R | 2 +- .../_snaps/legend-draw/all-legend-keys.svg | 63 ++++++++++++++++++ tests/testthat/test-legend-draw.R | 66 +++++++++++++++++++ 3 files changed, 130 insertions(+), 1 deletion(-) create mode 100644 tests/testthat/_snaps/legend-draw/all-legend-keys.svg create mode 100644 tests/testthat/test-legend-draw.R diff --git a/R/legend-draw.R b/R/legend-draw.R index d08c6c6c93..eb33cc24d7 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -128,7 +128,7 @@ draw_key_boxplot <- function(data, params, size) { lwd = params$box_gp$linewidth ) - staple_size <- 0.5 + c(0.375, -0.375) * params$staplewidth + staple_size <- 0.5 + c(0.375, -0.375) * (params$staplewidth %||% 0) staple <- gg_par( col = params$staple_gp$colour, lty = params$staple_gp$linetype, diff --git a/tests/testthat/_snaps/legend-draw/all-legend-keys.svg b/tests/testthat/_snaps/legend-draw/all-legend-keys.svg new file mode 100644 index 0000000000..c1ea77a335 --- /dev/null +++ b/tests/testthat/_snaps/legend-draw/all-legend-keys.svg @@ -0,0 +1,63 @@ + + + + + + + + + + + + +point + +abline + +rect + +polygon + +blank +boxplot + + + + + + +crossbar + + +path + +vpath + +dotplot + +linerange + +pointrange + + +smooth + +text +a +label + +a +vline + +timeseries + + + diff --git a/tests/testthat/test-legend-draw.R b/tests/testthat/test-legend-draw.R new file mode 100644 index 0000000000..5f4cc01032 --- /dev/null +++ b/tests/testthat/test-legend-draw.R @@ -0,0 +1,66 @@ + +test_that("all keys can be drawn without 'params'", { + + params <- list() + size <- convertUnit(calc_element("legend.key.size", theme_gray()), "cm", valueOnly = TRUE) + size <- size * 10 # cm to mm + + # Render every key + # If we're to develop new legend keys, we can keep appending this pattern + # for new keys and layout should adjust automatically. + # This is also an implicit test whether the key can be constructed without errors + keys <- list( + point = draw_key_point(GeomPoint$use_defaults(NULL), params, size), + abline = draw_key_abline(GeomAbline$use_defaults(NULL), params, size), + rect = draw_key_rect(GeomRect$use_defaults(NULL), params, size), + polygon = draw_key_polygon(GeomPolygon$use_defaults(NULL), params, size), + blank = draw_key_blank(GeomBlank$use_defaults(NULL), params, size), + boxplot = draw_key_boxplot(GeomBoxplot$use_defaults(NULL), params, size), + crossbar = draw_key_crossbar(GeomCrossbar$use_defaults(NULL), params, size), + path = draw_key_path(GeomPath$use_defaults(NULL), params, size), + vpath = draw_key_vpath(GeomPath$use_defaults(NULL), params, size), + dotplot = draw_key_dotplot(GeomDotplot$use_defaults(NULL), params, size), + linerange = draw_key_linerange(GeomLinerange$use_defaults(NULL), params, size), + pointrange = draw_key_pointrange(GeomPointrange$use_defaults(NULL), params, size), + smooth = draw_key_smooth(GeomSmooth$use_defaults(NULL), params, size), + text = draw_key_text(GeomText$use_defaults(NULL), params, size), + label = draw_key_label(GeomLabel$use_defaults(NULL), params, size), + vline = draw_key_vline(GeomVline$use_defaults(NULL), params, size), + timeseries = draw_key_timeseries(GeomPath$use_defaults(NULL), params, size) + ) + + # Test that we've covered all exported keys above + nse <- getNamespaceExports(asNamespace("ggplot2")) + nse <- grep("^draw_key", nse, value = TRUE) + nse <- gsub("^draw_key_", "", nse) + expect_in(nse, names(keys)) + + # Add title to every key + template <- gtable(width = unit(size, "mm"), heights = unit(c(1, size), c("lines", "mm"))) + keys <- Map( + function(key, name) { + text <- textGrob(name, gp = gpar(fontsize = 8)) + gtable_add_grob(template, list(text, key), t = 1:2, l = 1, clip = "off") + }, + key = keys, name = names(keys) + ) + + # Set layout + n <- length(keys) + nrow <- ceiling(n / 5) + ncol <- ceiling(n / nrow) + mtx <- matrix(list(zeroGrob()), nrow = nrow, ncol = ncol) + mtx[seq_along(keys)] <- keys + + # Render as gtable + gt <- gtable_matrix( + name = "layout", grobs = mtx, + widths = unit(rep(size, ncol(mtx)), "mm"), + heights = unit(rep(size, nrow(mtx)), "mm") + unit(1, "lines"), + clip = "off" + ) + gt <- gtable_add_col_space(gt, unit(1, "cm")) + gt <- gtable_add_row_space(gt, unit(1, "cm")) + + expect_doppelganger("all legend keys", gt) +}) From ed1b80dd37b5a05350421d95a8c0ff654efe4072 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 14:51:19 +0100 Subject: [PATCH 203/264] Aesthetics for position adjustments (#6100) * positions have `default_aes` field * positions communicate their aesthetics * positions populate defaults * simplify `PositionNudge$compute_layer()` * `position_nudge()` accepts nudge aesthetics * remove nudge specific stuff from `geom_text()`/`geom_label()` * document * `order` aesthetic for `position_dodge()` * document aesthetic * add news bullet * add test * fix small note * document --- NEWS.md | 3 ++ R/geom-label.R | 14 +------- R/geom-sf.R | 30 ++--------------- R/geom-text.R | 28 +--------------- R/layer.R | 7 ++-- R/position-.R | 32 +++++++++++++++++++ R/position-dodge.R | 24 +++++++++++++- R/position-nudge.R | 29 ++++++++--------- R/utilities-help.R | 3 +- R/utilities.R | 2 +- man/geom_boxplot.Rd | 1 + man/geom_dotplot.Rd | 1 + man/geom_text.Rd | 16 +++------- man/geom_violin.Rd | 1 + man/ggsf.Rd | 12 ++----- man/position_dodge.Rd | 9 ++++++ man/position_nudge.Rd | 12 ++++++- man/theme.Rd | 2 +- tests/testthat/_snaps/geom-label.md | 3 +- tests/testthat/_snaps/geom-sf.md | 6 ++-- tests/testthat/_snaps/geom-text.md | 3 +- tests/testthat/_snaps/prohibited-functions.md | 10 ++---- tests/testthat/test-geom-label.R | 2 +- tests/testthat/test-geom-sf.R | 4 +-- tests/testthat/test-geom-text.R | 2 +- tests/testthat/test-position_dodge.R | 15 +++++++++ 26 files changed, 137 insertions(+), 134 deletions(-) diff --git a/NEWS.md b/NEWS.md index f4815f325d..643e11bc65 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* Position adjustments can now have auxiliary aesthetics (@teunbrand). + * `position_nudge()` gains `nudge_x` and `nudge_y` aesthetics (#3026, #5445). + * `position_dodge()` gains `order` aesthetic (#3022, #3345) * More stability for vctrs-based palettes (@teunbrand, #6117). * Fixed regression in `guide_bins(reverse = TRUE)` (@teunbrand, #6183). * New function family for setting parts of a theme. For example, you can now use diff --git a/R/geom-label.R b/R/geom-label.R index 6f21478da0..68f4549b6e 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -4,11 +4,9 @@ #' @param label.r Radius of rounded corners. Defaults to 0.15 lines. #' @param label.size Size of label border, in mm. geom_label <- function(mapping = NULL, data = NULL, - stat = "identity", position = "identity", + stat = "identity", position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), label.size = 0.25, @@ -16,16 +14,6 @@ geom_label <- function(mapping = NULL, data = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { - if (!missing(nudge_x) || !missing(nudge_y)) { - if (!missing(position)) { - cli::cli_abort(c( - "Both {.arg position} and {.arg nudge_x}/{.arg nudge_y} are supplied.", - "i" = "Choose one approach to alter the position." - )) - } - - position <- position_nudge(nudge_x, nudge_y) - } layer( data = data, diff --git a/R/geom-sf.R b/R/geom-sf.R index 1d53d67499..4b61300108 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -314,11 +314,9 @@ geom_sf <- function(mapping = aes(), data = NULL, stat = "sf", #' @inheritParams geom_label #' @inheritParams stat_sf_coordinates geom_sf_label <- function(mapping = aes(), data = NULL, - stat = "sf_coordinates", position = "identity", + stat = "sf_coordinates", position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), label.size = 0.25, @@ -327,17 +325,6 @@ geom_sf_label <- function(mapping = aes(), data = NULL, inherit.aes = TRUE, fun.geometry = NULL) { - if (!missing(nudge_x) || !missing(nudge_y)) { - if (!missing(position)) { - cli::cli_abort(c( - "Both {.arg position} and {.arg nudge_x}/{.arg nudge_y} are supplied.", - "i" = "Only use one approach to alter the position." - )) - } - - position <- position_nudge(nudge_x, nudge_y) - } - layer_sf( data = data, mapping = mapping, @@ -363,28 +350,15 @@ geom_sf_label <- function(mapping = aes(), data = NULL, #' @inheritParams geom_text #' @inheritParams stat_sf_coordinates geom_sf_text <- function(mapping = aes(), data = NULL, - stat = "sf_coordinates", position = "identity", + stat = "sf_coordinates", position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, check_overlap = FALSE, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, fun.geometry = NULL) { - if (!missing(nudge_x) || !missing(nudge_y)) { - if (!missing(position)) { - cli::cli_abort(c( - "Both {.arg position} and {.arg nudge_x}/{.arg nudge_y} are supplied.", - "i" = "Only use one approach to alter the position." - )) - } - - position <- position_nudge(nudge_x, nudge_y) - } - layer_sf( data = data, mapping = mapping, diff --git a/R/geom-text.R b/R/geom-text.R index 78e601f8f9..7e7a1b8f81 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -41,19 +41,6 @@ #' @inheritParams geom_point #' @param parse If `TRUE`, the labels will be parsed into expressions and #' displayed as described in `?plotmath`. -#' @param nudge_x,nudge_y Horizontal and vertical adjustment to nudge labels by. -#' Useful for offsetting text from points, particularly on discrete scales. -#' Cannot be jointly specified with `position`. -#' @param position A position adjustment to use on the data for this layer. -#' Cannot be jointy specified with `nudge_x` or `nudge_y`. This -#' can be used in various ways, including to prevent overplotting and -#' improving the display. The `position` argument accepts the following: -#' * The result of calling a position function, such as `position_jitter()`. -#' * A string naming the position adjustment. To give the position as a -#' string, strip the function name of the `position_` prefix. For example, -#' to use `position_jitter()`, give the position as `"jitter"`. -#' * For more information and other ways to specify the position, see the -#' [layer position][layer_positions] documentation. #' @param check_overlap If `TRUE`, text that overlaps previous text in the #' same layer will not be plotted. `check_overlap` happens at draw time and in #' the order of the data. Therefore data should be arranged by the label @@ -166,28 +153,15 @@ #' geom_text(aes(label = text), vjust = "inward", hjust = "inward") #' } geom_text <- function(mapping = NULL, data = NULL, - stat = "identity", position = "identity", + stat = "identity", position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, check_overlap = FALSE, size.unit = "mm", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { - if (!missing(nudge_x) || !missing(nudge_y)) { - if (!missing(position)) { - cli::cli_abort(c( - "Both {.arg position} and {.arg nudge_x}/{.arg nudge_y} are supplied.", - "i" = "Only use one approach to alter the position." - )) - } - - position <- position_nudge(nudge_x, nudge_y) - } - layer( data = data, mapping = mapping, diff --git a/R/layer.R b/R/layer.R index a915763e3c..6be74b5d72 100644 --- a/R/layer.R +++ b/R/layer.R @@ -128,12 +128,12 @@ layer <- function(geom = NULL, stat = NULL, # Split up params between aesthetics, geom, and stat params <- rename_aes(params) - aes_params <- params[intersect(names(params), geom$aesthetics())] + aes_params <- params[intersect(names(params), union(geom$aesthetics(), position$aesthetics()))] geom_params <- params[intersect(names(params), geom$parameters(TRUE))] stat_params <- params[intersect(names(params), stat$parameters(TRUE))] ignore <- c("key_glyph", "name") - all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics(), ignore) + all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics(), position$aesthetics(), ignore) # Take care of plain patterns provided as aesthetic pattern <- vapply(aes_params, is_pattern, logical(1)) @@ -164,7 +164,7 @@ layer <- function(geom = NULL, stat = NULL, extra_aes <- setdiff( mapped_aesthetics(mapping), - c(geom$aesthetics(), stat$aesthetics()) + c(geom$aesthetics(), stat$aesthetics(), position$aesthetics()) ) # Take care of size->linewidth aes renaming if (geom$rename_size && "size" %in% extra_aes && !"linewidth" %in% mapped_aesthetics(mapping)) { @@ -415,6 +415,7 @@ Layer <- ggproto("Layer", NULL, compute_position = function(self, data, layout) { if (empty(data)) return(data_frame0()) + data <- self$position$use_defaults(data, self$aes_params) params <- self$position$setup_params(data) data <- self$position$setup_data(data, params) diff --git a/R/position-.R b/R/position-.R index 88d6f914a9..c78ca0fc4c 100644 --- a/R/position-.R +++ b/R/position-.R @@ -46,6 +46,8 @@ Position <- ggproto("Position", required_aes = character(), + default_aes = aes(), + setup_params = function(self, data) { list() }, @@ -66,6 +68,36 @@ Position <- ggproto("Position", compute_panel = function(self, data, params, scales) { cli::cli_abort("Not implemented.") + }, + + aesthetics = function(self) { + required_aes <- self$required_aes + if (!is.null(required_aes)) { + required_aes <- unlist(strsplit(self$required_aes, "|", fixed = TRUE)) + } + c(union(required_aes, names(self$default_aes))) + }, + + use_defaults = function(self, data, params = list()) { + + aes <- self$aesthetics() + defaults <- self$default_aes + + params <- params[intersect(names(params), aes)] + params <- params[setdiff(names(params), names(data))] + defaults <- defaults[setdiff(names(defaults), c(names(params), names(data)))] + + if ((length(params) + length(defaults)) < 1) { + return(data) + } + + new <- compact(lapply(defaults, eval_tidy, data = data)) + new[names(params)] <- params + check_aesthetics(new, nrow(data)) + + data[names(new)] <- new + data + } ) diff --git a/R/position-dodge.R b/R/position-dodge.R index 78d4a9a45f..bd816eecc9 100644 --- a/R/position-dodge.R +++ b/R/position-dodge.R @@ -19,6 +19,8 @@ #' @param reverse If `TRUE`, will reverse the default stacking order. #' This is useful if you're rotating both the plot and legend. #' @family position adjustments +#' @eval rd_aesthetics("position", "dodge") +#' #' @export #' @examples #' ggplot(mtcars, aes(factor(cyl), fill = factor(vs))) + @@ -104,7 +106,10 @@ PositionDodge <- ggproto("PositionDodge", Position, preserve = "total", orientation = "x", reverse = NULL, + default_aes = aes(order = NULL), + setup_params = function(self, data) { + flipped_aes <- has_flipped_aes(data, default = self$orientation == "y") check_required_aesthetics( if (flipped_aes) "y|ymin" else "x|xmin", @@ -139,9 +144,22 @@ PositionDodge <- ggproto("PositionDodge", Position, setup_data = function(self, data, params) { data <- flip_data(data, params$flipped_aes) + if (!"x" %in% names(data) && all(c("xmin", "xmax") %in% names(data))) { data$x <- (data$xmin + data$xmax) / 2 } + + data$order <- xtfrm( # xtfrm makes anything 'sortable' + data$order %||% ave(data$group, data$x, data$PANEL, FUN = match_sorted) + ) + if (params$reverse) { + data$order <- -data$order + } + if (is.null(params$n)) { # preserve = "total" + data$order <- ave(data$order, data$x, data$PANEL, FUN = match_sorted) + } else { # preserve = "single" + data$order <- match_sorted(data$order) + } flip_data(data, params$flipped_aes) }, @@ -179,7 +197,7 @@ pos_dodge <- function(df, width, n = NULL) { # Have a new group index from 1 to number of groups. # This might be needed if the group numbers in this set don't include all of 1:n - groupidx <- match(df$group, unique0(df$group)) + groupidx <- df$order %||% match_sorted(df$group) # Find the center for each group, then use that to calculate xmin and xmax df$x <- df$x + width * ((groupidx - 0.5) / n - 0.5) @@ -188,3 +206,7 @@ pos_dodge <- function(df, width, n = NULL) { df } + +match_sorted <- function(x, y = x, ...) { + vec_match(x, vec_sort(unique0(y), ...)) +} diff --git a/R/position-nudge.R b/R/position-nudge.R index 56e4e8fe4d..6bf8a81f01 100644 --- a/R/position-nudge.R +++ b/R/position-nudge.R @@ -8,6 +8,7 @@ #' @family position adjustments #' @param x,y Amount of vertical and horizontal distance to move. #' @export +#' @eval rd_aesthetics("position", "nudge") #' @examples #' df <- data.frame( #' x = c(1,3,2,5), @@ -26,7 +27,7 @@ #' ggplot(df, aes(x, y)) + #' geom_point() + #' geom_text(aes(label = y), nudge_y = -0.1) -position_nudge <- function(x = 0, y = 0) { +position_nudge <- function(x = NULL, y = NULL) { ggproto(NULL, PositionNudge, x = x, y = y @@ -38,25 +39,21 @@ position_nudge <- function(x = 0, y = 0) { #' @usage NULL #' @export PositionNudge <- ggproto("PositionNudge", Position, - x = 0, - y = 0, + x = NULL, + y = NULL, + + default_aes = aes(nudge_x = 0, nudge_y = 0), setup_params = function(self, data) { - list(x = self$x, y = self$y) + list( + x = self$x %||% data$nudge_x, + y = self$y %||% data$nudge_y + ) }, compute_layer = function(self, data, params, layout) { - # transform only the dimensions for which non-zero nudging is requested - if (any(params$x != 0)) { - if (any(params$y != 0)) { - transform_position(data, function(x) x + params$x, function(y) y + params$y) - } else { - transform_position(data, function(x) x + params$x, NULL) - } - } else if (any(params$y != 0)) { - transform_position(data, NULL, function(y) y + params$y) - } else { - data # if both x and y are 0 we don't need to transform - } + trans_x <- if (any(params$x != 0)) function(x) x + params$x + trans_y <- if (any(params$y != 0)) function(y) y + params$y + transform_position(data, trans_x, trans_y) } ) diff --git a/R/utilities-help.R b/R/utilities-help.R index 22bddc7dcd..e97e7ad50e 100644 --- a/R/utilities-help.R +++ b/R/utilities-help.R @@ -3,7 +3,8 @@ rd_aesthetics <- function(type, name, extra_note = NULL) { obj <- switch(type, geom = validate_subclass(name, "Geom", env = globalenv()), - stat = validate_subclass(name, "Stat", env = globalenv()) + stat = validate_subclass(name, "Stat", env = globalenv()), + position = validate_subclass(name, "Position", env = globalenv()) ) aes <- rd_aesthetics_item(obj) diff --git a/R/utilities.R b/R/utilities.R index 3b0e9ec806..3bcdaacedc 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -940,7 +940,7 @@ compute_data_size <- function(data, size, default = 0.9, res <- vapply(res, resolution, FUN.VALUE = numeric(1), ...) res <- min(res, na.rm = TRUE) } else if (panels == "by") { - res <- ave(data[[var]], data$PANEL, FUN = function(x) resolution(x, ...)) + res <- stats::ave(data[[var]], data$PANEL, FUN = function(x) resolution(x, ...)) } else { res <- resolution(data[[var]], ...) } diff --git a/man/geom_boxplot.Rd b/man/geom_boxplot.Rd index d5026c013f..5760caa71a 100644 --- a/man/geom_boxplot.Rd +++ b/man/geom_boxplot.Rd @@ -240,6 +240,7 @@ See McGill et al. (1978) for more details. \item \code{\link[=aes_linetype_size_shape]{shape}} \item \code{\link[=aes_linetype_size_shape]{size}} \item \code{weight} +\item \code{width} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } diff --git a/man/geom_dotplot.Rd b/man/geom_dotplot.Rd index ff7f30a4fc..5dbf0614db 100644 --- a/man/geom_dotplot.Rd +++ b/man/geom_dotplot.Rd @@ -171,6 +171,7 @@ to match the number of dots. \item \code{\link[=aes_linetype_size_shape]{linetype}} \item \code{stroke} \item \code{weight} +\item \code{width} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } diff --git a/man/geom_text.Rd b/man/geom_text.Rd index e88e45a0e1..e92e3fe3d8 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -9,11 +9,9 @@ geom_label( mapping = NULL, data = NULL, stat = "identity", - position = "identity", + position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), label.size = 0.25, @@ -27,11 +25,9 @@ geom_text( mapping = NULL, data = NULL, stat = "identity", - position = "identity", + position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, check_overlap = FALSE, size.unit = "mm", na.rm = FALSE, @@ -73,12 +69,12 @@ give the stat as \code{"count"}. \link[=layer_stats]{layer stat} documentation. }} -\item{position}{A position adjustment to use on the data for this layer. -Cannot be jointy specified with \code{nudge_x} or \code{nudge_y}. This +\item{position}{A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The \code{position} argument accepts the following: \itemize{ \item The result of calling a position function, such as \code{position_jitter()}. +This method allows for passing extra arguments to the position. \item A string naming the position adjustment. To give the position as a string, strip the function name of the \code{position_} prefix. For example, to use \code{position_jitter()}, give the position as \code{"jitter"}. @@ -117,10 +113,6 @@ lists which parameters it can accept. \item{parse}{If \code{TRUE}, the labels will be parsed into expressions and displayed as described in \code{?plotmath}.} -\item{nudge_x, nudge_y}{Horizontal and vertical adjustment to nudge labels by. -Useful for offsetting text from points, particularly on discrete scales. -Cannot be jointly specified with \code{position}.} - \item{label.padding}{Amount of padding around label. Defaults to 0.25 lines.} \item{label.r}{Radius of rounded corners. Defaults to 0.15 lines.} diff --git a/man/geom_violin.Rd b/man/geom_violin.Rd index 244a7ac7ea..7b923b68ab 100644 --- a/man/geom_violin.Rd +++ b/man/geom_violin.Rd @@ -196,6 +196,7 @@ This geom treats each axis differently and, thus, can thus have two orientations \item \code{\link[=aes_linetype_size_shape]{linetype}} \item \code{\link[=aes_linetype_size_shape]{linewidth}} \item \code{weight} +\item \code{width} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } diff --git a/man/ggsf.Rd b/man/ggsf.Rd index 1fee9f59bb..1ab15f232a 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -44,11 +44,9 @@ geom_sf_label( mapping = aes(), data = NULL, stat = "sf_coordinates", - position = "identity", + position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), label.size = 0.25, @@ -62,11 +60,9 @@ geom_sf_text( mapping = aes(), data = NULL, stat = "sf_coordinates", - position = "identity", + position = "nudge", ..., parse = FALSE, - nudge_x = 0, - nudge_y = 0, check_overlap = FALSE, na.rm = FALSE, show.legend = NA, @@ -277,10 +273,6 @@ lists which parameters it can accept. \item{parse}{If \code{TRUE}, the labels will be parsed into expressions and displayed as described in \code{?plotmath}.} -\item{nudge_x, nudge_y}{Horizontal and vertical adjustment to nudge labels by. -Useful for offsetting text from points, particularly on discrete scales. -Cannot be jointly specified with \code{position}.} - \item{label.padding}{Amount of padding around label. Defaults to 0.25 lines.} \item{label.r}{Radius of rounded corners. Defaults to 0.15 lines.} diff --git a/man/position_dodge.Rd b/man/position_dodge.Rd index e4f9211110..5706e93e02 100644 --- a/man/position_dodge.Rd +++ b/man/position_dodge.Rd @@ -46,6 +46,15 @@ be specified in the global or \verb{geom_*} layer. Unlike \code{position_dodge() particularly useful for arranging box plots, which can have variable widths. } +\section{Aesthetics}{ + +\code{position_dodge()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \code{order} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. +} + \examples{ ggplot(mtcars, aes(factor(cyl), fill = factor(vs))) + geom_bar(position = "dodge2") diff --git a/man/position_nudge.Rd b/man/position_nudge.Rd index 3b2b2573cb..0db66c8035 100644 --- a/man/position_nudge.Rd +++ b/man/position_nudge.Rd @@ -4,7 +4,7 @@ \alias{position_nudge} \title{Nudge points a fixed distance} \usage{ -position_nudge(x = 0, y = 0) +position_nudge(x = NULL, y = NULL) } \arguments{ \item{x, y}{Amount of vertical and horizontal distance to move.} @@ -15,6 +15,16 @@ items on discrete scales by a small amount. Nudging is built in to \code{\link[=geom_text]{geom_text()}} because it's so useful for moving labels a small distance from what they're labelling. } +\section{Aesthetics}{ + +\code{position_nudge()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \code{nudge_x} +\item \code{nudge_y} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. +} + \examples{ df <- data.frame( x = c(1,3,2,5), diff --git a/man/theme.Rd b/man/theme.Rd index d28c10b149..51f92e1f96 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -384,7 +384,7 @@ differently when added to a ggplot object. Also, when setting \code{complete = TRUE} all elements will be set to inherit from blank elements.} -\item{validate}{\code{TRUE} to run \code{validate_element()}, \code{FALSE} to bypass checks.} +\item{validate}{\code{TRUE} to run \code{check_element()}, \code{FALSE} to bypass checks.} } \description{ Themes are a powerful way to customize the non-data components of your plots: diff --git a/tests/testthat/_snaps/geom-label.md b/tests/testthat/_snaps/geom-label.md index 2ea8c33c06..68ab4ebba4 100644 --- a/tests/testthat/_snaps/geom-label.md +++ b/tests/testthat/_snaps/geom-label.md @@ -1,7 +1,6 @@ # geom_label() throws meaningful errors - Both `position` and `nudge_x`/`nudge_y` are supplied. - i Choose one approach to alter the position. + Ignoring unknown parameters: `nudge_x` --- diff --git a/tests/testthat/_snaps/geom-sf.md b/tests/testthat/_snaps/geom-sf.md index 2d5217dd4f..74edd268e1 100644 --- a/tests/testthat/_snaps/geom-sf.md +++ b/tests/testthat/_snaps/geom-sf.md @@ -19,13 +19,11 @@ --- - Both `position` and `nudge_x`/`nudge_y` are supplied. - i Only use one approach to alter the position. + Ignoring unknown parameters: `nudge_x` --- - Both `position` and `nudge_x`/`nudge_y` are supplied. - i Only use one approach to alter the position. + Ignoring unknown parameters: `nudge_x` --- diff --git a/tests/testthat/_snaps/geom-text.md b/tests/testthat/_snaps/geom-text.md index e86cc9c905..917a4ca707 100644 --- a/tests/testthat/_snaps/geom-text.md +++ b/tests/testthat/_snaps/geom-text.md @@ -1,7 +1,6 @@ # geom_text() checks input - Both `position` and `nudge_x`/`nudge_y` are supplied. - i Only use one approach to alter the position. + Ignoring unknown parameters: `nudge_x` # geom_text() drops missing angles diff --git a/tests/testthat/_snaps/prohibited-functions.md b/tests/testthat/_snaps/prohibited-functions.md index 007e6521c4..4612a484bf 100644 --- a/tests/testthat/_snaps/prohibited-functions.md +++ b/tests/testthat/_snaps/prohibited-functions.md @@ -43,17 +43,11 @@ $geom_density_2d_filled [1] "contour_var" - $geom_label - [1] "nudge_x" "nudge_y" - - $geom_sf_label - [1] "nudge_x" "nudge_y" - $geom_sf_text - [1] "nudge_x" "nudge_y" "check_overlap" + [1] "check_overlap" $geom_text - [1] "nudge_x" "nudge_y" "check_overlap" + [1] "check_overlap" $geom_violin [1] "draw_quantiles" diff --git a/tests/testthat/test-geom-label.R b/tests/testthat/test-geom-label.R index 028c3c4980..c80be5e38b 100644 --- a/tests/testthat/test-geom-label.R +++ b/tests/testthat/test-geom-label.R @@ -1,5 +1,5 @@ test_that("geom_label() throws meaningful errors", { - expect_snapshot_error(geom_label(position = "jitter", nudge_x = 0.5)) + expect_snapshot_warning(geom_label(position = "jitter", nudge_x = 0.5)) expect_snapshot_error(labelGrob(label = 1:3)) }) diff --git a/tests/testthat/test-geom-sf.R b/tests/testthat/test-geom-sf.R index ed6914ba61..29f5da8323 100644 --- a/tests/testthat/test-geom-sf.R +++ b/tests/testthat/test-geom-sf.R @@ -137,8 +137,8 @@ test_that("errors are correctly triggered", { ) p <- ggplot(pts) + geom_sf() + coord_cartesian() expect_snapshot_error(ggplotGrob(p)) - expect_snapshot_error(geom_sf_label(position = "jitter", nudge_x = 0.5)) - expect_snapshot_error(geom_sf_text(position = "jitter", nudge_x = 0.5)) + expect_snapshot_warning(geom_sf_label(position = "jitter", nudge_x = 0.5)) + expect_snapshot_warning(geom_sf_text(position = "jitter", nudge_x = 0.5)) # #5204: missing linewidth should be dropped pts <- sf::st_sf( diff --git a/tests/testthat/test-geom-text.R b/tests/testthat/test-geom-text.R index a6fe3359d9..8fe509e724 100644 --- a/tests/testthat/test-geom-text.R +++ b/tests/testthat/test-geom-text.R @@ -1,5 +1,5 @@ test_that("geom_text() checks input", { - expect_snapshot_error(geom_text(position = "jitter", nudge_x = 0.5)) + expect_snapshot_warning(geom_text(position = "jitter", nudge_x = 0.5)) }) test_that("geom_text() drops missing angles", { diff --git a/tests/testthat/test-position_dodge.R b/tests/testthat/test-position_dodge.R index 14b79d3cad..878ee6d155 100644 --- a/tests/testthat/test-position_dodge.R +++ b/tests/testthat/test-position_dodge.R @@ -38,6 +38,21 @@ test_that("position_dodge() can reverse the dodge order", { expect_equal(ld$label[order(ld$x)], c("A", "A", "B", "B", "C")) }) +test_that("position_dodge() can use the order aesthetic", { + + major <- c(1,1,1,2,2,3,3,4,4,5,6,7) + minor <- c(1:3, 1:2, 1, 3, 2:3, 1:3) + df <- data_frame0( + x = LETTERS[major], + g = c("X", "Y", "Z")[minor] + ) + ld <- layer_data( + ggplot(df, aes(x, 1, colour = g, order = g)) + + geom_point(position = position_dodge(preserve = "single", width = 0.6)) + ) + expect_equal(ld$x, major + c(-0.2, 0, 0.2)[minor], ignore_attr = TRUE) +}) + test_that("position_dodge warns about missing required aesthetics", { # Bit of a contrived geom to not have a required 'x' aesthetic From aa6ee959602c415e5e5d1247c54857514704556e Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 15:21:50 +0100 Subject: [PATCH 204/264] Weighted ellipses (#6186) * add `weight` aesthetic * add news bullet * document aesthetics --- NEWS.md | 1 + R/stat-ellipse.R | 13 ++++++++++--- man/stat_ellipse.Rd | 12 ++++++++++++ 3 files changed, 23 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 643e11bc65..f325bec637 100644 --- a/NEWS.md +++ b/NEWS.md @@ -267,6 +267,7 @@ * Standardised the calculation of `width`, which are now implemented as aesthetics (@teunbrand, #2800). * Stricter check on `register_theme_elements(element_tree)` (@teunbrand, #6162) +* Added `weight` aesthetic for `stat_ellipse()` (@teunbrand, #5272) # ggplot2 3.5.1 diff --git a/R/stat-ellipse.R b/R/stat-ellipse.R index 5d1f41dd55..d462bf3575 100644 --- a/R/stat-ellipse.R +++ b/R/stat-ellipse.R @@ -20,6 +20,7 @@ #' @param segments The number of segments to be used in drawing the ellipse. #' @inheritParams layer #' @inheritParams geom_point +#' @eval rd_aesthetics("stat", "ellipse") #' @export #' @examples #' ggplot(faithful, aes(waiting, eruptions)) + @@ -76,6 +77,8 @@ stat_ellipse <- function(mapping = NULL, data = NULL, #' @export StatEllipse <- ggproto("StatEllipse", Stat, required_aes = c("x", "y"), + optional_aes = "weight", + dropped_aes = "weight", setup_params = function(data, params) { params$type <- params$type %||% "t" @@ -96,6 +99,9 @@ calculate_ellipse <- function(data, vars, type, level, segments){ dfn <- 2 dfd <- nrow(data) - 1 + weight <- data$weight %||% rep(1, nrow(data)) + weight <- weight / sum(weight) + if (!type %in% c("t", "norm", "euclid")) { cli::cli_inform("Unrecognized ellipse type") ellipse <- matrix(NA_real_, ncol = 2) @@ -104,11 +110,12 @@ calculate_ellipse <- function(data, vars, type, level, segments){ ellipse <- matrix(NA_real_, ncol = 2) } else { if (type == "t") { - v <- MASS::cov.trob(data[,vars]) + # Prone to convergence problems when `sum(weight) != nrow(data)` + v <- MASS::cov.trob(data[,vars], wt = weight * nrow(data)) } else if (type == "norm") { - v <- stats::cov.wt(data[,vars]) + v <- stats::cov.wt(data[,vars], wt = weight) } else if (type == "euclid") { - v <- stats::cov.wt(data[,vars]) + v <- stats::cov.wt(data[,vars], wt = weight) v$cov <- diag(rep(min(diag(v$cov)), 2)) } shape <- v$cov diff --git a/man/stat_ellipse.Rd b/man/stat_ellipse.Rd index 4bc30ef863..8ef16d92cc 100644 --- a/man/stat_ellipse.Rd +++ b/man/stat_ellipse.Rd @@ -125,6 +125,18 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} The method for calculating the ellipses has been modified from \code{car::dataEllipse} (Fox and Weisberg 2011, Friendly and Monette 2013) } +\section{Aesthetics}{ + +\code{stat_ellipse()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \strong{\code{\link[=aes_position]{x}}} +\item \strong{\code{\link[=aes_position]{y}}} +\item \code{\link[=aes_group_order]{group}} +\item \code{weight} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. +} + \examples{ ggplot(faithful, aes(waiting, eruptions)) + geom_point() + From e327a5e08f4dd6da14c769ad5020118095f70eff Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:07:29 +0100 Subject: [PATCH 205/264] Guide custom order (#6199) * apply order * add news bullet --- NEWS.md | 1 + R/guides-.R | 5 +++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index f325bec637..5b65a25614 100644 --- a/NEWS.md +++ b/NEWS.md @@ -268,6 +268,7 @@ aesthetics (@teunbrand, #2800). * Stricter check on `register_theme_elements(element_tree)` (@teunbrand, #6162) * Added `weight` aesthetic for `stat_ellipse()` (@teunbrand, #5272) +* Fixed a bug where the `guide_custom(order)` wasn't working (@teunbrand, #6195) # ggplot2 3.5.1 diff --git a/R/guides-.R b/R/guides-.R index 0e7ca26882..63a17cc430 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -306,8 +306,9 @@ Guides <- ggproto( return(no_guides) } - guides$guides <- c(guides$guides, custom$guides) - guides$params <- c(guides$params, custom$params) + ord <- order(c(names(guides$guides), names(custom$guides))) + guides$guides <- c(guides$guides, custom$guides)[ord] + guides$params <- c(guides$params, custom$params)[ord] guides }, From 0b6751674b14d5572a17267b95386547095e98b6 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:07:43 +0100 Subject: [PATCH 206/264] Clip qq line (#6220) * `geom/stat_qq_line()` use `stat = "abline"` * document new computed variables * add news bullet --- NEWS.md | 3 +++ R/stat-qq-line.R | 7 +++++-- R/stat-qq.R | 4 +++- man/geom_qq.Rd | 6 ++++-- 4 files changed, 15 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index 5b65a25614..70050e2ee2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # ggplot2 (development version) +* New default `geom_qq_line(geom = "abline")` for better clipping in the + vertical direction. In addition, `slope` and `intercept` are new computed + variables in `stat_qq_line()` (@teunbrand, #6087). * Position adjustments can now have auxiliary aesthetics (@teunbrand). * `position_nudge()` gains `nudge_x` and `nudge_y` aesthetics (#3026, #5445). * `position_dodge()` gains `order` aesthetic (#3022, #3345) diff --git a/R/stat-qq-line.R b/R/stat-qq-line.R index 8133216779..ab6c194cfe 100644 --- a/R/stat-qq-line.R +++ b/R/stat-qq-line.R @@ -6,7 +6,7 @@ #' the data geom_qq_line <- function(mapping = NULL, data = NULL, - geom = "path", + geom = "abline", position = "identity", ..., distribution = stats::qnorm, @@ -86,6 +86,9 @@ StatQqLine <- ggproto("StatQqLine", Stat, x <- range(theoretical) } - data_frame0(x = x, y = slope * x + intercept) + data_frame0( + x = x, y = slope * x + intercept, + slope = slope, intercept = intercept + ) } ) diff --git a/R/stat-qq.R b/R/stat-qq.R index 4ffab00320..71068bbd04 100644 --- a/R/stat-qq.R +++ b/R/stat-qq.R @@ -22,7 +22,9 @@ #' x = "x-coordinates of the endpoints of the line segment connecting the #' points at the chosen quantiles of the theoretical and the sample #' distributions.", -#' y = "y-coordinates of the endpoints." +#' y = "y-coordinates of the endpoints.", +#' slope = "Amount of change in `y` across 1 unit of `x`.", +#' intercept = "Value of `y` at `x == 0`." #' ) #' #' @export diff --git a/man/geom_qq.Rd b/man/geom_qq.Rd index d6bedf3427..88656bc53a 100644 --- a/man/geom_qq.Rd +++ b/man/geom_qq.Rd @@ -10,7 +10,7 @@ geom_qq_line( mapping = NULL, data = NULL, - geom = "path", + geom = "abline", position = "identity", ..., distribution = stats::qnorm, @@ -25,7 +25,7 @@ geom_qq_line( stat_qq_line( mapping = NULL, data = NULL, - geom = "path", + geom = "abline", position = "identity", ..., distribution = stats::qnorm, @@ -205,6 +205,8 @@ Variables computed by \code{stat_qq_line()}: \itemize{ \item \code{after_stat(x)}\cr x-coordinates of the endpoints of the line segment connecting the points at the chosen quantiles of the theoretical and the sample distributions. \item \code{after_stat(y)}\cr y-coordinates of the endpoints. +\item \code{after_stat(slope)}\cr Amount of change in \code{y} across 1 unit of \code{x}. +\item \code{after_stat(intercept)}\cr Value of \code{y} at \code{x == 0}. } } From 321b300bd9ef1b902ca84def2e0e69c88d16f54f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:10:54 +0100 Subject: [PATCH 207/264] missing contour parameter defaults to `TRUE` (#6222) --- R/stat-density-2d.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/stat-density-2d.R b/R/stat-density-2d.R index d8bbfed57b..af2b10b14d 100644 --- a/R/stat-density-2d.R +++ b/R/stat-density-2d.R @@ -143,7 +143,7 @@ StatDensity2d <- ggproto("StatDensity2d", Stat, data <- ggproto_parent(Stat, self)$compute_layer(data, params, layout) # if we're not contouring we're done - if (!isTRUE(params$contour)) return(data) + if (!isTRUE(params$contour %||% TRUE)) return(data) # set up data and parameters for contouring contour_var <- params$contour_var %||% "density" From 7eeb6365be8cfa559aabeda9b59828414515d785 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:52:01 +0100 Subject: [PATCH 208/264] Sanitise bin calculations (#6212) * capture bin argument fixup in function * capture binning logic in function * helper for cutting bins * consistency of `stat_bin2d()` * necromancy: resurrect `stat_bin(drop)` by sacrificing `stat_bin(keep.zeroes)` * fix `boundary = 0` * same treatment for `stat_summary2d()` * Implement `StatBin2d` as subclass of `StatSummary2d` * consistency for `stat_summary_bin()` * document * collect bin utilities in one place * remove vestigial `bin2d_breaks()` * discard superfluous `self` * bring `stat_bindot()` into the fold * centralise argument checking in `compute_bins()` * `stat_bin_2d(boundary)` internally defaults to 0 * add news bullets * allow lambda notation for breaks/binwidth/bins * improve docs --- DESCRIPTION | 2 +- NEWS.md | 6 +- R/bin.R | 109 ++++++++++++++++++++++++---- R/geom-bin2d.R | 2 +- R/stat-bin.R | 72 ++++++------------ R/stat-bin2d.R | 109 ++++++++-------------------- R/stat-bindot.R | 12 ++- R/stat-binhex.R | 7 ++ R/stat-summary-2d.R | 44 ++++++++--- R/stat-summary-bin.R | 17 +++-- man/geom_bin_2d.Rd | 47 ++++++++++-- man/geom_hex.Rd | 28 +++++-- man/geom_histogram.Rd | 7 +- man/ggplot2-ggproto.Rd | 10 +-- man/stat_summary_2d.Rd | 26 ++++++- tests/testthat/_snaps/stat-bin.md | 37 ++-------- tests/testthat/_snaps/stat-bin2d.md | 6 +- tests/testthat/test-stat-bin.R | 31 ++++---- tests/testthat/test-stat-bin2d.R | 2 +- 19 files changed, 327 insertions(+), 247 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 777d755861..753e7dd49a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -242,6 +242,7 @@ Collate: 'scales-.R' 'stat-align.R' 'stat-bin.R' + 'stat-summary-2d.R' 'stat-bin2d.R' 'stat-bindot.R' 'stat-binhex.R' @@ -263,7 +264,6 @@ Collate: 'stat-smooth-methods.R' 'stat-smooth.R' 'stat-sum.R' - 'stat-summary-2d.R' 'stat-summary-bin.R' 'stat-summary-hex.R' 'stat-summary.R' diff --git a/NEWS.md b/NEWS.md index 70050e2ee2..2eec9e3b33 100644 --- a/NEWS.md +++ b/NEWS.md @@ -254,7 +254,7 @@ * The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, `labs()` and several guides (@teunbrand, #3196). * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). -* Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449) +* Reintroduced `drop` argument to `stat_bin()` (@teunbrand, #3449) * (internal) removed barriers for using 2D structures as aesthetics (@teunbrand, #4189). * `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052) @@ -272,6 +272,10 @@ * Stricter check on `register_theme_elements(element_tree)` (@teunbrand, #6162) * Added `weight` aesthetic for `stat_ellipse()` (@teunbrand, #5272) * Fixed a bug where the `guide_custom(order)` wasn't working (@teunbrand, #6195) +* All binning stats now use the `boundary`/`center` parametrisation rather + than `origin`, following in `stat_bin()`'s footsteps (@teunbrand). +* `stat_summary_2d()` and `stat_bin_2d()` now deal with zero-range data + more elegantly (@teunbrand, #6207). # ggplot2 3.5.1 diff --git a/R/bin.R b/R/bin.R index 055721f0e4..f45fe90090 100644 --- a/R/bin.R +++ b/R/bin.R @@ -54,19 +54,12 @@ bin_breaks <- function(breaks, closed = c("right", "left")) { bin_breaks_width <- function(x_range, width = NULL, center = NULL, boundary = NULL, closed = c("right", "left")) { - check_length(x_range, 2L) - # binwidth seems to be the argument name supplied to width. (stat-bin and stat-bindot) - check_number_decimal(width, min = 0, allow_infinite = FALSE, arg = "binwidth") - - if (!is.null(boundary) && !is.null(center)) { - cli::cli_abort("Only one of {.arg boundary} and {.arg center} may be specified.") - } else if (is.null(boundary)) { + if (is.null(boundary)) { if (is.null(center)) { # If neither edge nor center given, compute both using tile layer's # algorithm. This puts min and max of data in outer half of their bins. boundary <- width / 2 - } else { # If center given but not boundary, compute boundary. boundary <- center - width / 2 @@ -75,9 +68,6 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL, # Find the left side of left-most bin: inputs could be Dates or POSIXct, so # coerce to numeric first. - x_range <- as.numeric(x_range) - width <- as.numeric(width) - boundary <- as.numeric(boundary) shift <- floor((x_range[1] - boundary) / width) origin <- boundary + shift * width @@ -104,9 +94,7 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL, bin_breaks_bins <- function(x_range, bins = 30, center = NULL, boundary = NULL, closed = c("right", "left")) { - check_length(x_range, 2L) - check_number_whole(bins, min = 1) if (zero_range(x_range)) { # 0.1 is the same width as the expansion `default_expansion()` gives for 0-width data width <- 0.1 @@ -128,6 +116,56 @@ bin_breaks_bins <- function(x_range, bins = 30, center = NULL, # Compute bins ------------------------------------------------------------ +compute_bins <- function(x, scale = NULL, breaks = NULL, binwidth = NULL, bins = NULL, + center = NULL, boundary = NULL, + closed = c("right", "left")) { + + range <- if (is.scale(scale)) scale$dimension() else range(x) + check_length(range, 2L) + + if (!is.null(breaks)) { + breaks <- allow_lambda(breaks) + if (is.function(breaks)) { + breaks <- breaks(x) + } + if (is.scale(scale) && !scale$is_discrete()) { + breaks <- scale$transform(breaks) + } + check_numeric(breaks) + bins <- bin_breaks(breaks, closed) + return(bins) + } + + check_number_decimal(boundary, allow_infinite = FALSE, allow_null = TRUE) + check_number_decimal(center, allow_infinite = FALSE, allow_null = TRUE) + if (!is.null(boundary) && !is.null(center)) { + cli::cli_abort("Only one of {.arg boundary} and {.arg center} may be specified.") + } + + if (!is.null(binwidth)) { + binwidth <- allow_lambda(binwidth) + if (is.function(binwidth)) { + binwidth <- binwidth(x) + } + check_number_decimal(binwidth, min = 0, allow_infinite = FALSE) + bins <- bin_breaks_width( + range, binwidth, + center = center, boundary = boundary, closed = closed + ) + return(bins) + } + + bins <- allow_lambda(bins) + if (is.function(bins)) { + bins <- bins(x) + } + check_number_whole(bins, min = 1, allow_infinite = FALSE) + bin_breaks_bins( + range, bins, + center = center, boundary = boundary, closed = closed + ) +} + bin_vector <- function(x, bins, weight = NULL, pad = FALSE) { check_object(bins, is_bins, "a {.cls ggplot2_bins} object") @@ -141,8 +179,7 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) { weight[is.na(weight)] <- 0 } - bin_idx <- cut(x, bins$fuzzy, right = bins$right_closed, - include.lowest = TRUE) + bin_idx <- bin_cut(x, bins) bin_count <- as.numeric(tapply(weight, bin_idx, sum, na.rm = TRUE)) bin_count[is.na(bin_count)] <- 0 @@ -170,6 +207,10 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) { bin_out(bin_count, bin_x, bin_widths) } +bin_cut <- function(x, bins) { + cut(x, bins$fuzzy, right = bins$right_closed, include.lowest = TRUE) +} + bin_out <- function(count = integer(0), x = numeric(0), width = numeric(0), xmin = x - width / 2, xmax = x + width / 2) { density <- count / width / sum(abs(count)) @@ -186,3 +227,41 @@ bin_out <- function(count = integer(0), x = numeric(0), width = numeric(0), .size = length(count) ) } + +bin_loc <- function(x, id) { + left <- x[-length(x)] + right <- x[-1] + + list( + left = left[id], + right = right[id], + mid = ((left + right) / 2)[id], + length = diff(x)[id] + ) +} + +fix_bin_params = function(params, fun, version) { + + if (!is.null(params$origin)) { + args <- paste0(fun, c("(origin)", "(boundary)")) + deprecate_warn0(version, args[1], args[2]) + params$boudnary <- params$origin + params$origin <- NULL + } + + if (!is.null(params$right)) { + args <- paste0(fun, c("(right)", "(closed)")) + deprecate_warn0(version, args[1], args[2]) + params$closed <- if (isTRUE(params$right)) "right" else "left" + params$right <- NULL + } + + if (is.null(params$breaks %||% params$binwidth %||% params$bins)) { + cli::cli_inform( + "{.fn {fun}} using {.code bins = 30}. Pick better value {.arg binwidth}." + ) + params$bins <- 30 + } + + params +} diff --git a/R/geom-bin2d.R b/R/geom-bin2d.R index 5a143df51d..e0c78ab5e4 100644 --- a/R/geom-bin2d.R +++ b/R/geom-bin2d.R @@ -25,7 +25,7 @@ NULL #' # You can control the size of the bins by specifying the number of #' # bins in each direction: #' d + geom_bin_2d(bins = 10) -#' d + geom_bin_2d(bins = 30) +#' d + geom_bin_2d(bins = list(x = 30, y = 10)) #' #' # Or by specifying the width of the bins #' d + geom_bin_2d(binwidth = c(0.1, 0.1)) diff --git a/R/stat-bin.R b/R/stat-bin.R index 9c571ae519..711b0c5ad7 100644 --- a/R/stat-bin.R +++ b/R/stat-bin.R @@ -26,10 +26,11 @@ #' or left edges of bins are included in the bin. #' @param pad If `TRUE`, adds empty bins at either end of x. This ensures #' frequency polygons touch 0. Defaults to `FALSE`. -#' @param keep.zeroes Treatment of zero count bins. If `"all"` (default), such +#' @param drop Treatment of zero count bins. If `"all"` (default), such #' bins are kept as-is. If `"none"`, all zero count bins are filtered out. #' If `"inner"` only zero count bins at the flanks are filtered out, but not -#' in the middle. +#' in the middle. `TRUE` is shorthand for `"all"` and `FALSE` is shorthand +#' for `"none"`. #' @eval rd_computed_vars( #' count = "number of points in bin.", #' density = "density of points in bin, scaled to integrate to 1.", @@ -59,7 +60,7 @@ stat_bin <- function(mapping = NULL, data = NULL, closed = c("right", "left"), pad = FALSE, na.rm = FALSE, - keep.zeroes = "all", + drop = "all", orientation = NA, show.legend = NA, inherit.aes = TRUE) { @@ -82,7 +83,7 @@ stat_bin <- function(mapping = NULL, data = NULL, pad = pad, na.rm = na.rm, orientation = orientation, - keep.zeroes = keep.zeroes, + drop = drop, ... ) ) @@ -95,9 +96,13 @@ stat_bin <- function(mapping = NULL, data = NULL, StatBin <- ggproto("StatBin", Stat, setup_params = function(self, data, params) { params$flipped_aes <- has_flipped_aes(data, params, main_is_orthogonal = FALSE) - params$keep.zeroes <- arg_match0( - params$keep.zeroes %||% "all", - c("all", "none", "inner"), arg_nm = "keep.zeroes" + + if (is.logical(params$drop)) { + params$drop <- if (isTRUE(params$drop)) "all" else "none" + } + params$drop <- arg_match0( + params$drop %||% "all", + c("all", "none", "inner"), arg_nm = "drop" ) has_x <- !(is.null(data$x) && is.null(params$x)) @@ -118,29 +123,7 @@ StatBin <- ggproto("StatBin", Stat, )) } - if (!is.null(params$drop)) { - deprecate_warn0("2.1.0", "stat_bin(drop)", "stat_bin(pad)") - params$drop <- NULL - } - if (!is.null(params$origin)) { - deprecate_warn0("2.1.0", "stat_bin(origin)", "stat_bin(boundary)") - params$boundary <- params$origin - params$origin <- NULL - } - if (!is.null(params$right)) { - deprecate_warn0("2.1.0", "stat_bin(right)", "stat_bin(closed)") - params$closed <- if (params$right) "right" else "left" - params$right <- NULL - } - if (!is.null(params$boundary) && !is.null(params$center)) { - cli::cli_abort("Only one of {.arg boundary} and {.arg center} may be specified in {.fn {snake_class(self)}}.") - } - - if (is.null(params$breaks) && is.null(params$binwidth) && is.null(params$bins)) { - cli::cli_inform("{.fn {snake_class(self)}} using {.code bins = 30}. Pick better value with {.arg binwidth}.") - params$bins <- 30 - } - + params <- fix_bin_params(params, fun = snake_class(self), version = "2.1.0") params }, @@ -149,33 +132,20 @@ StatBin <- ggproto("StatBin", Stat, compute_group = function(data, scales, binwidth = NULL, bins = NULL, center = NULL, boundary = NULL, closed = c("right", "left"), pad = FALSE, - breaks = NULL, flipped_aes = FALSE, keep.zeroes = "all", + breaks = NULL, flipped_aes = FALSE, drop = "all", # The following arguments are not used, but must # be listed so parameters are computed correctly - origin = NULL, right = NULL, drop = NULL) { + origin = NULL, right = NULL) { x <- flipped_names(flipped_aes)$x - if (!is.null(breaks)) { - if (is.function(breaks)) { - breaks <- breaks(data[[x]]) - } - if (!scales[[x]]$is_discrete()) { - breaks <- scales[[x]]$transform(breaks) - } - bins <- bin_breaks(breaks, closed) - } else if (!is.null(binwidth)) { - if (is.function(binwidth)) { - binwidth <- binwidth(data[[x]]) - } - bins <- bin_breaks_width(scales[[x]]$dimension(), binwidth, - center = center, boundary = boundary, closed = closed) - } else { - bins <- bin_breaks_bins(scales[[x]]$dimension(), bins, center = center, - boundary = boundary, closed = closed) - } + bins <- compute_bins( + data[[x]], scales[[x]], + breaks = breaks, binwidth = binwidth, bins = bins, + center = center, boundary = boundary, closed = closed + ) bins <- bin_vector(data[[x]], bins, weight = data$weight, pad = pad) keep <- switch( - keep.zeroes, + drop, none = bins$count != 0, inner = inner_runs(bins$count != 0), TRUE diff --git a/R/stat-bin2d.R b/R/stat-bin2d.R index bdb69db23a..fe27a41162 100644 --- a/R/stat-bin2d.R +++ b/R/stat-bin2d.R @@ -1,7 +1,4 @@ -#' @param bins numeric vector giving number of bins in both vertical and -#' horizontal directions. Set to 30 by default. -#' @param binwidth Numeric vector giving bin width in both vertical and -#' horizontal directions. Overrides `bins` if both set. +#' @inheritParams stat_bin #' @param drop if `TRUE` removes all cells with 0 counts. #' @export #' @rdname geom_bin_2d @@ -11,11 +8,21 @@ #' ncount = "count, scaled to maximum of 1.", #' ndensity = "density, scaled to a maximum of 1." #' ) +#' @section Controlling binning parameters for the x and y directions: +#' The arguments `bins`, `binwidth`, `breaks`, `center`, and `boundary` can +#' be set separately for the x and y directions. When given as a scalar, one +#' value applies to both directions. When given as a vector of length two, +#' the first is applied to the x direction and the second to the y direction. +#' Alternatively, these can be a named list containing `x` and `y` elements, +#' for example `list(x = 10, y = 20)`. stat_bin_2d <- function(mapping = NULL, data = NULL, geom = "tile", position = "identity", ..., bins = 30, binwidth = NULL, + center = NULL, + boundary = NULL, + breaks = NULL, drop = TRUE, na.rm = FALSE, show.legend = NA, @@ -31,6 +38,9 @@ stat_bin_2d <- function(mapping = NULL, data = NULL, params = list2( bins = bins, binwidth = binwidth, + center = center, + boundary = boundary, + breaks = breaks, drop = drop, na.rm = na.rm, ... @@ -45,48 +55,37 @@ stat_bin_2d <- function(mapping = NULL, data = NULL, stat_bin2d <- stat_bin_2d #' @rdname ggplot2-ggproto +#' @include stat-summary-2d.R #' @format NULL #' @usage NULL #' @export -StatBin2d <- ggproto("StatBin2d", Stat, +StatBin2d <- ggproto( + "StatBin2d", StatSummary2d, default_aes = aes(weight = 1, fill = after_stat(count)), required_aes = c("x", "y"), compute_group = function(data, scales, binwidth = NULL, bins = 30, - breaks = NULL, origin = NULL, drop = TRUE) { + breaks = NULL, origin = NULL, drop = TRUE, + boundary = NULL, closed = NULL, center = NULL) { - origin <- dual_param(origin, list(NULL, NULL)) - binwidth <- dual_param(binwidth, list(NULL, NULL)) - breaks <- dual_param(breaks, list(NULL, NULL)) - bins <- dual_param(bins, list(x = 30, y = 30)) + data$z <- data$weight %||% 1 + data$weight <- NULL - xbreaks <- bin2d_breaks(scales$x, breaks$x, origin$x, binwidth$x, bins$x) - ybreaks <- bin2d_breaks(scales$y, breaks$y, origin$y, binwidth$y, bins$y) + # For backward compatibility, boundary defaults to 0 + boundary <- boundary %||% if (is.null(center)) list(x = 0, y = 0) - xbin <- cut(data$x, xbreaks, include.lowest = TRUE, labels = FALSE) - ybin <- cut(data$y, ybreaks, include.lowest = TRUE, labels = FALSE) - - if (is.null(data$weight)) - data$weight <- 1 - - out <- tapply_df(data$weight, list(xbin = xbin, ybin = ybin), sum, drop = drop) - - xdim <- bin_loc(xbreaks, out$xbin) - out$x <- xdim$mid - out$width <- xdim$length - - ydim <- bin_loc(ybreaks, out$ybin) - out$y <- ydim$mid - out$height <- ydim$length + out <- StatSummary2d$compute_group( + data, scales, binwidth = binwidth, bins = bins, breaks = breaks, + drop = drop, fun = "sum", boundary = boundary, closed = closed, + center = center + ) out$count <- out$value out$ncount <- out$count / max(out$count, na.rm = TRUE) out$density <- out$count / sum(out$count, na.rm = TRUE) out$ndensity <- out$density / max(out$density, na.rm = TRUE) out - }, - - dropped_aes = "weight" # No longer available after transformation + } ) dual_param <- function(x, default = list(x = NULL, y = NULL)) { @@ -102,53 +101,3 @@ dual_param <- function(x, default = list(x = NULL, y = NULL)) { list(x = x, y = x) } } - -bin2d_breaks <- function(scale, breaks = NULL, origin = NULL, binwidth = NULL, - bins = 30, closed = "right") { - # Bins for categorical data should take the width of one level, - # and should show up centered over their tick marks. All other parameters - # are ignored. - if (scale$is_discrete()) { - breaks <- scale$get_breaks() - return(-0.5 + seq_len(length(breaks) + 1)) - } else { - if (!is.null(breaks)) { - breaks <- scale$transform(breaks) - } - } - - if (!is.null(breaks)) - return(breaks) - - range <- scale$get_limits() - - if (is.null(binwidth) || identical(binwidth, NA)) { - binwidth <- diff(range) / bins - } - check_number_decimal(binwidth) - - if (is.null(origin) || identical(origin, NA)) { - origin <- round_any(range[1], binwidth, floor) - } - check_number_decimal(origin) - - breaks <- seq(origin, range[2] + binwidth, binwidth) - - # Check if the last bin lies fully outside the range - if (length(breaks) > 1 && breaks[length(breaks) - 1] >= range[2]) { - breaks <- breaks[-length(breaks)] - } - bins(breaks, closed)$fuzzy -} - -bin_loc <- function(x, id) { - left <- x[-length(x)] - right <- x[-1] - - list( - left = left[id], - right = right[id], - mid = ((left + right) / 2)[id], - length = diff(x)[id] - ) -} diff --git a/R/stat-bindot.R b/R/stat-bindot.R index 85eecc4d54..66184a527c 100644 --- a/R/stat-bindot.R +++ b/R/stat-bindot.R @@ -77,13 +77,11 @@ StatBindot <- ggproto("StatBindot", Stat, } if (method == "histodot") { - closed <- if (right) "right" else "left" - if (!is.null(binwidth)) { - bins <- bin_breaks_width(range, binwidth, boundary = origin, closed = closed) - } else { - bins <- bin_breaks_bins(range, 30, boundary = origin, closed = closed) - } - + bins <- compute_bins( + values, scales[[binaxis]], + breaks = NULL, binwidth = binwidth, bins = 30, center = NULL, + boundary = origin, closed = if (right) "right" else "left" + ) data <- bin_vector(values, bins, weight = data$weight, pad = FALSE) # Change "width" column to "binwidth" for consistency diff --git a/R/stat-binhex.R b/R/stat-binhex.R index 0b5d3991c6..be5b61daf7 100644 --- a/R/stat-binhex.R +++ b/R/stat-binhex.R @@ -7,6 +7,13 @@ #' ncount = "count, scaled to maximum of 1.", #' ndensity = "density, scaled to maximum of 1." #' ) +#' @section Controlling binning parameters for the x and y directions: +#' The arguments `bins` and `binwidth` can +#' be set separately for the x and y directions. When given as a scalar, one +#' value applies to both directions. When given as a vector of length two, +#' the first is applied to the x direction and the second to the y direction. +#' Alternatively, these can be a named list containing `x` and `y` elements, +#' for example `list(x = 10, y = 20)`. stat_bin_hex <- function(mapping = NULL, data = NULL, geom = "hex", position = "identity", ..., diff --git a/R/stat-summary-2d.R b/R/stat-summary-2d.R index 60e5e49813..41d0c5b588 100644 --- a/R/stat-summary-2d.R +++ b/R/stat-summary-2d.R @@ -28,6 +28,7 @@ #' @param drop drop if the output of `fun` is `NA`. #' @param fun function for summary. #' @param fun.args A list of extra arguments to pass to `fun` +#' @inheritSection stat_bin_2d Controlling binning parameters for the x and y directions #' @export #' @examples #' d <- ggplot(diamonds, aes(carat, depth, z = price)) @@ -92,31 +93,50 @@ StatSummary2d <- ggproto("StatSummary2d", Stat, required_aes = c("x", "y", "z"), dropped_aes = "z", # z gets dropped during statistical transformation + setup_params = function(self, data, params) { + + if (is.character(params$drop)) { + params$drop <- !identical(params$drop, "none") + } + + params <- fix_bin_params(params, fun = snake_class(self), version = "3.5.2") + vars <- c("origin", "binwidth", "breaks", "center", "boundary") + params[vars] <- lapply(params[vars], dual_param, default = NULL) + params$closed <- dual_param(params$closed, list(x = "right", y = "right")) + + params + }, + compute_group = function(data, scales, binwidth = NULL, bins = 30, breaks = NULL, origin = NULL, drop = TRUE, - fun = "mean", fun.args = list()) { - origin <- dual_param(origin, list(NULL, NULL)) - binwidth <- dual_param(binwidth, list(NULL, NULL)) - breaks <- dual_param(breaks, list(NULL, NULL)) + fun = "mean", fun.args = list(), + boundary = 0, closed = NULL, center = NULL) { bins <- dual_param(bins, list(x = 30, y = 30)) - xbreaks <- bin2d_breaks(scales$x, breaks$x, origin$x, binwidth$x, bins$x) - ybreaks <- bin2d_breaks(scales$y, breaks$y, origin$y, binwidth$y, bins$y) - - xbin <- cut(data$x, xbreaks, include.lowest = TRUE, labels = FALSE) - ybin <- cut(data$y, ybreaks, include.lowest = TRUE, labels = FALSE) + xbin <- compute_bins( + data$x, scales$x, breaks$x, binwidth$x, bins$x, + center$x, boundary$x, closed$x + ) + ybin <- compute_bins( + data$y, scales$y, breaks$y, binwidth$y, bins$y, + center$y, boundary$y, closed$y + ) + cut_id <- list( + xbin = as.integer(bin_cut(data$x, xbin)), + ybin = as.integer(bin_cut(data$y, ybin)) + ) fun <- as_function(fun) f <- function(x) { inject(fun(x, !!!fun.args)) } - out <- tapply_df(data$z, list(xbin = xbin, ybin = ybin), f, drop = drop) + out <- tapply_df(data$z, cut_id, f, drop = drop) - xdim <- bin_loc(xbreaks, out$xbin) + xdim <- bin_loc(xbin$breaks, out$xbin) out$x <- xdim$mid out$width <- xdim$length - ydim <- bin_loc(ybreaks, out$ybin) + ydim <- bin_loc(ybin$breaks, out$ybin) out$y <- ydim$mid out$height <- ydim$length diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index a56bea189e..e3db18b102 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -79,16 +79,21 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, compute_group = function(data, scales, fun = NULL, bins = 30, binwidth = NULL, breaks = NULL, origin = NULL, right = FALSE, na.rm = FALSE, - flipped_aes = FALSE, width = NULL) { - data <- flip_data(data, flipped_aes) + flipped_aes = FALSE, width = NULL, center = NULL, + boundary = NULL, closed = c("right", "left")) { + x <- flipped_names(flipped_aes)$x - breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, - closed = if (right) "right" else "left") + bins <- compute_bins( + data[[x]], scales[[x]], + breaks = breaks, binwidth = binwidth, bins = bins, + center = center, boundary = boundary, closed = closed + ) + data$bin <- bin_cut(data[[x]], bins) - data$bin <- cut(data$x, breaks, include.lowest = TRUE, labels = FALSE) + data <- flip_data(data, flipped_aes) out <- dapply(data, "bin", fun %||% function(df) mean_se(df$y)) - locs <- bin_loc(breaks, out$bin) + locs <- bin_loc(bins$breaks, out$bin) out$x <- locs$mid out$width <- width %||% if (scales[[x]]$is_discrete()) 0.9 else locs$length out$flipped_aes <- flipped_aes diff --git a/man/geom_bin_2d.Rd b/man/geom_bin_2d.Rd index fa3b32b4ce..dc0b9ce082 100644 --- a/man/geom_bin_2d.Rd +++ b/man/geom_bin_2d.Rd @@ -26,6 +26,9 @@ stat_bin_2d( ..., bins = 30, binwidth = NULL, + center = NULL, + boundary = NULL, + breaks = NULL, drop = TRUE, na.rm = FALSE, show.legend = NA, @@ -115,11 +118,33 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} these connections, see how the \link[=layer_stats]{stat} and \link[=layer_geoms]{geom} arguments work.} -\item{bins}{numeric vector giving number of bins in both vertical and -horizontal directions. Set to 30 by default.} - -\item{binwidth}{Numeric vector giving bin width in both vertical and -horizontal directions. Overrides \code{bins} if both set.} +\item{bins}{Number of bins. Overridden by \code{binwidth}. Defaults to 30.} + +\item{binwidth}{The width of the bins. Can be specified as a numeric value +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. +The default is to use the number of bins in \code{bins}, +covering the range of the data. You should always override +this value, exploring multiple widths to find the best to illustrate the +stories in your data. + +The bin width of a date variable is the number of days in each time; the +bin width of a time variable is the number of seconds.} + +\item{center, boundary}{bin position specifiers. Only one, \code{center} or +\code{boundary}, may be specified for a single plot. \code{center} specifies the +center of one of the bins. \code{boundary} specifies the boundary between two +bins. Note that if either is above or below the range of the data, things +will be shifted by the appropriate integer multiple of \code{binwidth}. +For example, to center on integers use \code{binwidth = 1} and \code{center = 0}, even +if \code{0} is outside the range of the data. Alternatively, this same alignment +can be specified with \code{binwidth = 1} and \code{boundary = 0.5}, even if \code{0.5} is +outside the range of the data.} + +\item{breaks}{Alternatively, you can supply a numeric vector giving +the bin boundaries. Overrides \code{binwidth}, \code{bins}, \code{center}, +and \code{boundary}. Can also be a function that takes group-wise values as input and returns bin boundaries.} \item{drop}{if \code{TRUE} removes all cells with 0 counts.} } @@ -153,6 +178,16 @@ These are calculated by the 'stat' part of layers and can be accessed with \link } } +\section{Controlling binning parameters for the x and y directions}{ + +The arguments \code{bins}, \code{binwidth}, \code{breaks}, \code{center}, and \code{boundary} can +be set separately for the x and y directions. When given as a scalar, one +value applies to both directions. When given as a vector of length two, +the first is applied to the x direction and the second to the y direction. +Alternatively, these can be a named list containing \code{x} and \code{y} elements, +for example \code{list(x = 10, y = 20)}. +} + \examples{ d <- ggplot(diamonds, aes(x, y)) + xlim(4, 10) + ylim(4, 10) d + geom_bin_2d() @@ -160,7 +195,7 @@ d + geom_bin_2d() # You can control the size of the bins by specifying the number of # bins in each direction: d + geom_bin_2d(bins = 10) -d + geom_bin_2d(bins = 30) +d + geom_bin_2d(bins = list(x = 30, y = 10)) # Or by specifying the width of the bins d + geom_bin_2d(binwidth = c(0.1, 0.1)) diff --git a/man/geom_hex.Rd b/man/geom_hex.Rd index 553787761b..da103b0e3c 100644 --- a/man/geom_hex.Rd +++ b/man/geom_hex.Rd @@ -112,11 +112,19 @@ the default plot specification, e.g. \code{\link[=borders]{borders()}}.} \code{stat_bin_hex()}. For more information about overriding these connections, see how the \link[=layer_stats]{stat} and \link[=layer_geoms]{geom} arguments work.} -\item{bins}{numeric vector giving number of bins in both vertical and -horizontal directions. Set to 30 by default.} - -\item{binwidth}{Numeric vector giving bin width in both vertical and -horizontal directions. Overrides \code{bins} if both set.} +\item{bins}{Number of bins. Overridden by \code{binwidth}. Defaults to 30.} + +\item{binwidth}{The width of the bins. Can be specified as a numeric value +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. +The default is to use the number of bins in \code{bins}, +covering the range of the data. You should always override +this value, exploring multiple widths to find the best to illustrate the +stories in your data. + +The bin width of a date variable is the number of days in each time; the +bin width of a time variable is the number of seconds.} } \description{ Divides the plane into regular hexagons, counts the number of cases in @@ -162,6 +170,16 @@ These are calculated by the 'stat' part of layers and can be accessed with \link } } +\section{Controlling binning parameters for the x and y directions}{ + +The arguments \code{bins} and \code{binwidth} can +be set separately for the x and y directions. When given as a scalar, one +value applies to both directions. When given as a vector of length two, +the first is applied to the x direction and the second to the y direction. +Alternatively, these can be a named list containing \code{x} and \code{y} elements, +for example \code{list(x = 10, y = 20)}. +} + \examples{ d <- ggplot(diamonds, aes(carat, price)) d + geom_hex() diff --git a/man/geom_histogram.Rd b/man/geom_histogram.Rd index 32f9c39610..0a27e87c10 100644 --- a/man/geom_histogram.Rd +++ b/man/geom_histogram.Rd @@ -46,7 +46,7 @@ stat_bin( closed = c("right", "left"), pad = FALSE, na.rm = FALSE, - keep.zeroes = "all", + drop = "all", orientation = NA, show.legend = NA, inherit.aes = TRUE @@ -174,10 +174,11 @@ or left edges of bins are included in the bin.} \item{pad}{If \code{TRUE}, adds empty bins at either end of x. This ensures frequency polygons touch 0. Defaults to \code{FALSE}.} -\item{keep.zeroes}{Treatment of zero count bins. If \code{"all"} (default), such +\item{drop}{Treatment of zero count bins. If \code{"all"} (default), such bins are kept as-is. If \code{"none"}, all zero count bins are filtered out. If \code{"inner"} only zero count bins at the flanks are filtered out, but not -in the middle.} +in the middle. \code{TRUE} is shorthand for \code{"all"} and \code{FALSE} is shorthand +for \code{"none"}.} } \description{ Visualise the distribution of a single continuous variable by dividing diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd index ea01c29996..6658fdafb9 100644 --- a/man/ggplot2-ggproto.Rd +++ b/man/ggplot2-ggproto.Rd @@ -19,14 +19,14 @@ % R/position-dodge.R, R/position-dodge2.R, R/position-identity.R, % R/position-jitter.R, R/position-jitterdodge.R, R/position-nudge.R, % R/position-stack.R, R/scale-.R, R/scale-binned.R, R/scale-continuous.R, -% R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, -% R/stat-align.R, R/stat-bin.R, R/stat-bin2d.R, R/stat-bindot.R, +% R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, R/stat-align.R, +% R/stat-bin.R, R/stat-summary-2d.R, R/stat-bin2d.R, R/stat-bindot.R, % R/stat-binhex.R, R/stat-boxplot.R, R/stat-contour.R, R/stat-count.R, % R/stat-density-2d.R, R/stat-density.R, R/stat-ecdf.R, R/stat-ellipse.R, % R/stat-function.R, R/stat-identity.R, R/stat-manual.R, R/stat-qq-line.R, % R/stat-qq.R, R/stat-quantilemethods.R, R/stat-smooth.R, R/stat-sum.R, -% R/stat-summary-2d.R, R/stat-summary-bin.R, R/stat-summary-hex.R, -% R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R +% R/stat-summary-bin.R, R/stat-summary-hex.R, R/stat-summary.R, +% R/stat-unique.R, R/stat-ydensity.R \docType{data} \name{ggplot2-ggproto} \alias{ggplot2-ggproto} @@ -126,6 +126,7 @@ \alias{ScaleContinuousIdentity} \alias{StatAlign} \alias{StatBin} +\alias{StatSummary2d} \alias{StatBin2d} \alias{StatBindot} \alias{StatBinhex} @@ -146,7 +147,6 @@ \alias{StatQuantile} \alias{StatSmooth} \alias{StatSum} -\alias{StatSummary2d} \alias{StatSummaryBin} \alias{StatSummaryHex} \alias{StatSummary} diff --git a/man/stat_summary_2d.Rd b/man/stat_summary_2d.Rd index 9ee4604b65..da62dd0a15 100644 --- a/man/stat_summary_2d.Rd +++ b/man/stat_summary_2d.Rd @@ -113,11 +113,19 @@ lists which parameters it can accept. \link[=draw_key]{key glyphs}, to change the display of the layer in the legend. }} -\item{bins}{numeric vector giving number of bins in both vertical and -horizontal directions. Set to 30 by default.} +\item{bins}{Number of bins. Overridden by \code{binwidth}. Defaults to 30.} -\item{binwidth}{Numeric vector giving bin width in both vertical and -horizontal directions. Overrides \code{bins} if both set.} +\item{binwidth}{The width of the bins. Can be specified as a numeric value +or as a function that takes x after scale transformation as input and +returns a single numeric value. When specifying a function along with a +grouping structure, the function will be called once per group. +The default is to use the number of bins in \code{bins}, +covering the range of the data. You should always override +this value, exploring multiple widths to find the best to illustrate the +stories in your data. + +The bin width of a date variable is the number of days in each time; the +bin width of a time variable is the number of seconds.} \item{drop}{drop if the output of \code{fun} is \code{NA}.} @@ -173,6 +181,16 @@ These are calculated by the 'stat' part of layers and can be accessed with \link } } +\section{Controlling binning parameters for the x and y directions}{ + +The arguments \code{bins}, \code{binwidth}, \code{breaks}, \code{center}, and \code{boundary} can +be set separately for the x and y directions. When given as a scalar, one +value applies to both directions. When given as a vector of length two, +the first is applied to the x direction and the second to the y direction. +Alternatively, these can be a named list containing \code{x} and \code{y} elements, +for example \code{list(x = 10, y = 20)}. +} + \examples{ d <- ggplot(diamonds, aes(carat, depth, z = price)) d + stat_summary_2d() diff --git a/tests/testthat/_snaps/stat-bin.md b/tests/testthat/_snaps/stat-bin.md index 2b5ee05525..db0b8f44c0 100644 --- a/tests/testthat/_snaps/stat-bin.md +++ b/tests/testthat/_snaps/stat-bin.md @@ -23,51 +23,30 @@ # inputs to binning are checked - Computation failed in `stat_bin()`. - Caused by error in `bins()`: - ! `breaks` must be a vector, not a character vector. + `breaks` must be a vector, not a character vector. --- - `x_range` must be a vector of length 2, not length 1. + `binwidth` must be a number, not a character vector. --- - Computation failed in `stat_bin()`. - Caused by error in `bin_breaks_width()`: - ! `binwidth` must be a number, not a character vector. + `binwidth` must be a number larger than or equal to 0, not the number -4. --- - Computation failed in `stat_bin()`. - Caused by error in `bin_breaks_width()`: - ! `binwidth` must be a number larger than or equal to 0, not the number -4. - ---- - - `x_range` must be a vector of length 2, not length 1. - ---- - - Computation failed in `stat_bin()`. - Caused by error in `bin_breaks_bins()`: - ! `bins` must be a whole number larger than or equal to 1, not the number -4. + `bins` must be a whole number larger than or equal to 1, not the number -4. # setting boundary and center - Code - comp_bin(df, boundary = 5, center = 0) - Condition - Error in `stat_bin()`: - ! Problem while computing stat. - i Error occurred in the 1st layer. - Caused by error in `setup_params()`: - ! Only one of `boundary` and `center` may be specified in `stat_bin()`. + Computation failed in `stat_bin()`. + Caused by error in `compute_bins()`: + ! Only one of `boundary` and `center` may be specified. # bin errors at high bin counts Code - bin_breaks_width(c(1, 2e+06), 1) + compute_bins(c(1, 2e+06), binwidth = 1) Condition Error in `bin_breaks_width()`: ! The number of histogram bins must be less than 1,000,000. diff --git a/tests/testthat/_snaps/stat-bin2d.md b/tests/testthat/_snaps/stat-bin2d.md index ffc60d7f92..a0bb2eebc7 100644 --- a/tests/testthat/_snaps/stat-bin2d.md +++ b/tests/testthat/_snaps/stat-bin2d.md @@ -1,12 +1,12 @@ # binwidth is respected Computation failed in `stat_bin2d()`. - Caused by error in `bin2d_breaks()`: + Caused by error in `compute_bins()`: ! `binwidth` must be a number, not a double vector. --- Computation failed in `stat_bin2d()`. - Caused by error in `bin2d_breaks()`: - ! `origin` must be a number, not a double vector. + Caused by error in `compute_bins()`: + ! `boundary` must be a number or `NULL`, not a double vector. diff --git a/tests/testthat/test-stat-bin.R b/tests/testthat/test-stat-bin.R index a114748daf..3df87821b8 100644 --- a/tests/testthat/test-stat-bin.R +++ b/tests/testthat/test-stat-bin.R @@ -118,17 +118,17 @@ test_that("stat_bin() provides width (#3522)", { expect_equal(out$xmax - out$xmin, rep(binwidth, 10)) }) -test_that("stat_bin(keep.zeroes) options work as intended", { +test_that("stat_bin(drop) options work as intended", { p <- ggplot(data.frame(x = c(1, 2, 2, 3, 5, 6, 6, 7)), aes(x)) + scale_x_continuous(limits = c(-1, 9)) - ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "all")) + ld <- layer_data(p + geom_histogram(binwidth = 1, drop = "all")) expect_equal(ld$x, -1:9) - ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "inner")) + ld <- layer_data(p + geom_histogram(binwidth = 1, drop = "inner")) expect_equal(ld$x, c(1:7)) - ld <- layer_data(p + geom_histogram(binwidth = 1, keep.zeroes = "none")) + ld <- layer_data(p + geom_histogram(binwidth = 1, drop = "none")) expect_equal(ld$x, c(1:3, 5:7)) }) @@ -147,19 +147,19 @@ test_that("bins is strictly adhered to", { # Default case nbreaks <- vapply(nbins, function(bins) { - length(bin_breaks_bins(c(0, 10), bins)$breaks) + length(compute_bins(c(0, 10), bins = bins)$breaks) }, numeric(1)) expect_equal(nbreaks, nbins + 1) # Center is provided nbreaks <- vapply(nbins, function(bins) { - length(bin_breaks_bins(c(0, 10), bins, center = 0)$breaks) + length(compute_bins(c(0, 10), bins = bins, center = 0)$breaks) }, numeric(1)) expect_equal(nbreaks, nbins + 1) # Boundary is provided nbreaks <- vapply(nbins, function(bins) { - length(bin_breaks_bins(c(0, 10), bins, boundary = 0)$breaks) + length(compute_bins(c(0, 10), bins = bins, boundary = 0)$breaks) }, numeric(1)) expect_equal(nbreaks, nbins + 1) @@ -172,13 +172,10 @@ comp_bin <- function(df, ...) { test_that("inputs to binning are checked", { dat <- data_frame(x = c(0, 10)) - expect_snapshot_error(comp_bin(dat, breaks = letters)) - expect_snapshot_error(bin_breaks_width(3)) - expect_snapshot_error(comp_bin(dat, binwidth = letters)) - expect_snapshot_error(comp_bin(dat, binwidth = -4)) - - expect_snapshot_error(bin_breaks_bins(3)) - expect_snapshot_error(comp_bin(dat, bins = -4)) + expect_snapshot_error(compute_bins(dat, breaks = letters)) + expect_snapshot_error(compute_bins(dat, binwidth = letters)) + expect_snapshot_error(compute_bins(dat, binwidth = -4)) + expect_snapshot_error(compute_bins(dat, bins = -4)) }) test_that("closed left or right", { @@ -208,14 +205,14 @@ test_that("setting boundary and center", { df <- data_frame(x = c(0, 30)) # Error if both boundary and center are specified - expect_snapshot(comp_bin(df, boundary = 5, center = 0), error = TRUE) + expect_snapshot_warning(comp_bin(df, boundary = 5, center = 0, bins = 30)) res <- comp_bin(df, binwidth = 10, boundary = 0, pad = FALSE) expect_identical(res$count, c(1, 0, 1)) expect_identical(res$xmin[1], 0) expect_identical(res$xmax[3], 30) - res <- comp_bin(df, binwidth = 10, center = 0, pad = FALSE) + res <- comp_bin(df, binwidth = 10, center = 0, boundary = NULL, pad = FALSE) expect_identical(res$count, c(1, 0, 0, 1)) expect_identical(res$xmin[1], df$x[1] - 5) expect_identical(res$xmax[4], df$x[2] + 5) @@ -230,7 +227,7 @@ test_that("weights are added", { }) test_that("bin errors at high bin counts", { - expect_snapshot(bin_breaks_width(c(1, 2e6), 1), error = TRUE) + expect_snapshot(compute_bins(c(1, 2e6), binwidth = 1), error = TRUE) }) # stat_count -------------------------------------------------------------- diff --git a/tests/testthat/test-stat-bin2d.R b/tests/testthat/test-stat-bin2d.R index 54d95679c9..6d83448956 100644 --- a/tests/testthat/test-stat-bin2d.R +++ b/tests/testthat/test-stat-bin2d.R @@ -14,7 +14,7 @@ test_that("binwidth is respected", { expect_snapshot_warning(ggplot_build(p)) p <- ggplot(df, aes(x, y)) + - stat_bin_2d(geom = "tile", origin = c(0.25, 0.5, 0.75)) + stat_bin_2d(geom = "tile", boundary = c(0.25, 0.5, 0.75)) expect_snapshot_warning(ggplot_build(p)) }) From e30642b0b65e5288e8dea0a3ed59f84e63be502a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 16:52:49 +0100 Subject: [PATCH 209/264] Limits of binned scales when data has zero width (#6225) * fallback for zero-range limits * add test * add news bullet --- NEWS.md | 2 ++ R/scale-.R | 10 +++++++++- tests/testthat/test-scale-binned.R | 6 ++++++ 3 files changed, 17 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 2eec9e3b33..c587911c83 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Binned scales with zero-width data expand the default limits by 0.1 + (@teunbrand, #5066) * New default `geom_qq_line(geom = "abline")` for better clipping in the vertical direction. In addition, `slope` and `intercept` are new computed variables in `stat_qq_line()` (@teunbrand, #6087). diff --git a/R/scale-.R b/R/scale-.R index 5ae52f65ab..1ab3381099 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -1292,9 +1292,17 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, new_limits[1] <- breaks[1] breaks <- breaks[-1] } - } else { + } else if (nbreaks == 1) { bin_size <- max(breaks[1] - limits[1], limits[2] - breaks[1]) new_limits <- c(breaks[1] - bin_size, breaks[1] + bin_size) + } else { + new_limits <- limits + if (zero_range(new_limits)) { + # 0.1 is the same width as the expansion `default_expansion()` + # gives for 0-width data + new_limits <- new_limits + c(-0.05, 0.05) + } + breaks <- new_limits } new_limits_trans <- suppressWarnings(transformation$transform(new_limits)) limits[is.finite(new_limits_trans)] <- new_limits[is.finite(new_limits_trans)] diff --git a/tests/testthat/test-scale-binned.R b/tests/testthat/test-scale-binned.R index 527d862339..22ce6ef12a 100644 --- a/tests/testthat/test-scale-binned.R +++ b/tests/testthat/test-scale-binned.R @@ -104,3 +104,9 @@ test_that('binned scales can calculate breaks on date-times', { ))) ) }) + +test_that("binned scales can calculate breaks for zero-width data", { + scale <- scale_x_binned() + scale$train(c(1, 1)) + expect_equal(scale$get_breaks(), c(0.95, 1.05)) +}) From 4b887b713392a3a5fdfdbcf4e7d2c4143098b967 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Mon, 27 Jan 2025 19:45:31 +0100 Subject: [PATCH 210/264] Tweak polar distance (#6226) * add boosts to radius * tweak test * accept snapshots * add news bullet --- NEWS.md | 3 + R/coord-polar.R | 6 +- R/coord-radial.R | 6 +- .../bottom-half-circle-with-rotated-text.svg | 4 +- ...with-axes-placed-at-90-and-225-degrees.svg | 10 +- .../inner-radius-with-all-axes.svg | 44 +-- .../coord-polar/partial-with-all-axes.svg | 46 +-- ...etrack-plot-closed-and-has-center-hole.svg | 6 +- ...cetrack-plot-closed-and-no-center-hole.svg | 6 +- .../rays-circular-arcs-and-spiral-arcs.svg | 285 +++++++++--------- .../rose-plot-with-has-equal-spacing.svg | 4 +- .../coord-polar/three-concentric-circles.svg | 4 +- .../polar-lines-intersect-mid-bars.svg | 12 +- .../open-and-closed-munched-polygons.svg | 8 +- .../_snaps/geom-raster/rectangle-fallback.svg | 8 +- .../_snaps/geom-violin/coord-polar.svg | 2 +- ...xis-theta-with-angle-adapting-to-theta.svg | 96 +++--- .../_snaps/guide-axis/stacked-radial-axes.svg | 42 +-- tests/testthat/test-coord-polar.R | 2 +- 19 files changed, 306 insertions(+), 288 deletions(-) diff --git a/NEWS.md b/NEWS.md index c587911c83..1d4344dc5e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -278,6 +278,9 @@ than `origin`, following in `stat_bin()`'s footsteps (@teunbrand). * `stat_summary_2d()` and `stat_bin_2d()` now deal with zero-range data more elegantly (@teunbrand, #6207). +* Munching in `coord_polar()` and `coord_radial()` now adds more detail, + particularly for data-points with a low radius near the center + (@teunbrand, #5023). # ggplot2 3.5.1 diff --git a/R/coord-polar.R b/R/coord-polar.R index de9453ddb9..b8855f52b9 100644 --- a/R/coord-polar.R +++ b/R/coord-polar.R @@ -84,7 +84,7 @@ CoordPolar <- ggproto("CoordPolar", Coord, is_free = function() TRUE, - distance = function(self, x, y, details) { + distance = function(self, x, y, details, boost = 0.75) { arc <- self$start + c(0, 2 * pi) dir <- self$direction if (self$theta == "x") { @@ -94,8 +94,8 @@ CoordPolar <- ggproto("CoordPolar", Coord, r <- rescale(x, from = details$r.range) theta <- theta_rescale_no_clip(y, details$theta.range, arc, dir) } - - dist_polar(r, theta) + # The ^boost boosts detailed munching when r is small + dist_polar(r^boost, theta) }, backtransform_range = function(self, panel_params) { diff --git a/R/coord-radial.R b/R/coord-radial.R index 1fea09dcde..ef6130fb34 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -120,7 +120,7 @@ CoordRadial <- ggproto("CoordRadial", Coord, is_free = function() TRUE, - distance = function(self, x, y, details) { + distance = function(self, x, y, details, boost = 0.75) { arc <- details$arc %||% c(0, 2 * pi) if (self$theta == "x") { r <- rescale(y, from = details$r.range, to = self$inner_radius / 0.4) @@ -129,8 +129,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, r <- rescale(x, from = details$r.range, to = self$inner_radius / 0.4) theta <- theta_rescale_no_clip(y, details$theta.range, arc) } - - dist_polar(r, theta) + # The ^boost boosts detailed munching when r is small + dist_polar(r^boost, theta) }, backtransform_range = function(self, panel_params) { diff --git a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg index c01f91abbc..6349bcb350 100644 --- a/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg +++ b/tests/testthat/_snaps/coord-polar/bottom-half-circle-with-rotated-text.svg @@ -33,8 +33,8 @@ - - + + diff --git a/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg index 497db8dcf4..46607ddecd 100644 --- a/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg +++ b/tests/testthat/_snaps/coord-polar/full-circle-with-axes-placed-at-90-and-225-degrees.svg @@ -29,15 +29,15 @@ - - - + + + - - + + diff --git a/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg b/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg index b75d829d47..7fddfe8e83 100644 --- a/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg +++ b/tests/testthat/_snaps/coord-polar/inner-radius-with-all-axes.svg @@ -28,26 +28,26 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - - - + + + + @@ -97,8 +97,8 @@ - - + + 10 15 20 @@ -111,7 +111,7 @@ - + diff --git a/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg b/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg index 03d06791cf..2f1de17be0 100644 --- a/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg +++ b/tests/testthat/_snaps/coord-polar/partial-with-all-axes.svg @@ -28,26 +28,26 @@ - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -105,8 +105,8 @@ - - + + 100 200 300 @@ -115,7 +115,7 @@ - + diff --git a/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-has-center-hole.svg b/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-has-center-hole.svg index 8bf3cc6ec2..60045c846f 100644 --- a/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-has-center-hole.svg +++ b/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-has-center-hole.svg @@ -44,9 +44,9 @@ - - - + + + 1 2 0/3 diff --git a/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-no-center-hole.svg b/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-no-center-hole.svg index d145a1e446..32bb41821f 100644 --- a/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-no-center-hole.svg +++ b/tests/testthat/_snaps/coord-polar/racetrack-plot-closed-and-no-center-hole.svg @@ -44,9 +44,9 @@ - - - + + + 1 2 0/3 diff --git a/tests/testthat/_snaps/coord-polar/rays-circular-arcs-and-spiral-arcs.svg b/tests/testthat/_snaps/coord-polar/rays-circular-arcs-and-spiral-arcs.svg index dfc63cb3d9..0c255f0bb8 100644 --- a/tests/testthat/_snaps/coord-polar/rays-circular-arcs-and-spiral-arcs.svg +++ b/tests/testthat/_snaps/coord-polar/rays-circular-arcs-and-spiral-arcs.svg @@ -47,115 +47,130 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -303,32 +318,32 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/coord-polar/rose-plot-with-has-equal-spacing.svg b/tests/testthat/_snaps/coord-polar/rose-plot-with-has-equal-spacing.svg index b9d09b1835..c82603f417 100644 --- a/tests/testthat/_snaps/coord-polar/rose-plot-with-has-equal-spacing.svg +++ b/tests/testthat/_snaps/coord-polar/rose-plot-with-has-equal-spacing.svg @@ -44,8 +44,8 @@ - - + + A B diff --git a/tests/testthat/_snaps/coord-polar/three-concentric-circles.svg b/tests/testthat/_snaps/coord-polar/three-concentric-circles.svg index e00a3d6a7c..b54b3afc35 100644 --- a/tests/testthat/_snaps/coord-polar/three-concentric-circles.svg +++ b/tests/testthat/_snaps/coord-polar/three-concentric-circles.svg @@ -47,8 +47,8 @@ - - + + 0.25 0.50 diff --git a/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg b/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg index 2f67080988..4bd4970011 100644 --- a/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg +++ b/tests/testthat/_snaps/geom-hline-vline-abline/polar-lines-intersect-mid-bars.svg @@ -36,10 +36,10 @@ - - - - + + + + @@ -47,8 +47,8 @@ - - + + A B C diff --git a/tests/testthat/_snaps/geom-polygon/open-and-closed-munched-polygons.svg b/tests/testthat/_snaps/geom-polygon/open-and-closed-munched-polygons.svg index b970c9f317..5080746f6c 100644 --- a/tests/testthat/_snaps/geom-polygon/open-and-closed-munched-polygons.svg +++ b/tests/testthat/_snaps/geom-polygon/open-and-closed-munched-polygons.svg @@ -25,10 +25,10 @@ - - - - + + + + colour diff --git a/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg b/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg index efb96b5c87..9a3ee13ab3 100644 --- a/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg +++ b/tests/testthat/_snaps/geom-raster/rectangle-fallback.svg @@ -36,10 +36,10 @@ - - - - + + + + 1.0 1.5 2.0 diff --git a/tests/testthat/_snaps/geom-violin/coord-polar.svg b/tests/testthat/_snaps/geom-violin/coord-polar.svg index 02ae1107df..5da2c31990 100644 --- a/tests/testthat/_snaps/geom-violin/coord-polar.svg +++ b/tests/testthat/_snaps/geom-violin/coord-polar.svg @@ -38,7 +38,7 @@ - + A B C diff --git a/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg b/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg index 48b903c6f3..79f3e27b8c 100644 --- a/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg +++ b/tests/testthat/_snaps/guide-axis/guide-axis-theta-with-angle-adapting-to-theta.svg @@ -28,53 +28,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + @@ -176,8 +176,8 @@ - - + + 10 15 20 diff --git a/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg b/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg index 9b4cf580e7..d8399aeb76 100644 --- a/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg +++ b/tests/testthat/_snaps/guide-axis/stacked-radial-axes.svg @@ -28,21 +28,21 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -95,15 +95,15 @@ - + 100 200 300 - - + + 100 200 300 @@ -112,7 +112,7 @@ - + 100 200 300 @@ -121,7 +121,7 @@ - + @@ -130,7 +130,7 @@ 200 300 400 - + diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index 2b07d96b21..1f662d2322 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -9,7 +9,7 @@ test_that("polar distance is calculated correctly", { ) coord <- coord_polar() panel_params <- coord$setup_panel_params(scales$x, scales$y) - dists <- coord$distance(dat$theta, dat$r, panel_params) + dists <- coord$distance(dat$theta, dat$r, panel_params, boost = 1) # dists is normalized by dividing by this value, so we'll add it back # The maximum length of a spiral arc, from (t,r) = (0,0) to (2*pi,1) From 212224dfcf934181ce88f846609be04b1e5e031d Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 09:16:38 +0100 Subject: [PATCH 211/264] Scale name function (#6200) * `Scale$make_title()` can uses functions * Disentangle `Layout$resolve_label()` * pre-resolve functions in `labs()` * rework how guides make titles * add test * add news bullet --- NEWS.md | 2 ++ R/axis-secondary.R | 4 +-- R/guide-bins.R | 2 +- R/guide-colorbar.R | 2 +- R/guide-colorsteps.R | 4 +-- R/guide-legend.R | 2 +- R/guide-old.R | 2 +- R/labels.R | 9 +++++++ R/layout.R | 48 +++++++++++++++++++----------------- R/scale-.R | 19 +++++++++++--- R/scale-continuous.R | 6 ++--- R/scale-date.R | 12 ++++----- R/scale-view.R | 6 ++--- tests/testthat/test-labels.R | 23 +++++++++++++++++ 14 files changed, 95 insertions(+), 46 deletions(-) diff --git a/NEWS.md b/NEWS.md index 1d4344dc5e..9340b73a2f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Scale names, guide titles and aesthetic labels can now accept functions + (@teunbrand, #4313) * Binned scales with zero-width data expand the default limits by 0.1 (@teunbrand, #5066) * New default `geom_qq_line(geom = "abline")` for better clipping in the diff --git a/R/axis-secondary.R b/R/axis-secondary.R index 23d36092b6..c1d024e288 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -329,7 +329,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, scale$train(range) scale }, - make_title = function(title) { - title + make_title = function(...) { + ScaleContinuous$make_title(...) } ) diff --git a/R/guide-bins.R b/R/guide-bins.R index c03d5179d6..b83494fb77 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -218,7 +218,7 @@ GuideBins <- ggproto( key$.value <- 1 - key$.value } - params$title <- scale$make_title(params$title %|W|% scale$name %|W|% title) + params$title <- scale$make_title(params$title, scale$name, title) params$key <- key params }, diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index c7c424c2ac..287b0087b8 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -259,7 +259,7 @@ GuideColourbar <- ggproto( extract_params = function(scale, params, title = waiver(), ...) { - params$title <- scale$make_title(params$title %|W|% scale$name %|W|% title) + params$title <- scale$make_title(params$title, scale$name, title) limits <- params$decor$value[c(1L, nrow(params$decor))] to <- switch( params$display, diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index 240a1e607c..14cca8563d 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -191,9 +191,7 @@ GuideColoursteps <- ggproto( params$key <- key } - params$title <- scale$make_title( - params$title %|W|% scale$name %|W|% title - ) + params$title <- scale$make_title(params$title, scale$name, title) limits <- c(params$decor$min[1], params$decor$max[nrow(params$decor)]) if (params$reverse) { diff --git a/R/guide-legend.R b/R/guide-legend.R index 37aad2e3f0..9355ae5a70 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -185,7 +185,7 @@ GuideLegend <- ggproto( extract_params = function(scale, params, title = waiver(), ...) { - params$title <- scale$make_title(params$title %|W|% scale$name %|W|% title) + params$title <- scale$make_title(params$title, scale$name, title) if (isTRUE(params$reverse %||% FALSE)) { params$key <- params$key[nrow(params$key):1, , drop = FALSE] } diff --git a/R/guide-old.R b/R/guide-old.R index de870965fd..d20fec0e3e 100644 --- a/R/guide-old.R +++ b/R/guide-old.R @@ -89,7 +89,7 @@ GuideOld <- ggproto( train = function(self, params, scale, aesthetic = NULL, title = waiver(), direction = NULL) { - params$title <- scale$make_title(params$title %|W|% scale$name %|W|% title) + params$title <- scale$make_title(params$title, scale$name, title) params$direction <- params$direction %||% direction %||% "vertical" params <- guide_train(params, scale, aesthetic) params diff --git a/R/labels.R b/R/labels.R index 14d7f32a41..a736e2bf54 100644 --- a/R/labels.R +++ b/R/labels.R @@ -84,6 +84,15 @@ setup_plot_labels <- function(plot, layers, data) { )) } + # User labels can be functions, so apply these to the default labels + plot_labels <- lapply(setNames(nm = names(plot_labels)), function(nm) { + label <- plot_labels[[nm]] + if (!is.function(label)) { + return(label) + } + label(labels[[nm]] %||% "") + }) + dict <- plot_labels$dictionary if (length(dict) > 0) { labels <- lapply(labels, function(x) { diff --git a/R/layout.R b/R/layout.R index d3cad0ffeb..92a28216d7 100644 --- a/R/layout.R +++ b/R/layout.R @@ -244,35 +244,39 @@ Layout <- ggproto("Layout", NULL, }, resolve_label = function(self, scale, labels) { - # General order is: guide title > scale name > labels - aes <- scale$aesthetics[[1]] - primary <- scale$name %|W|% labels[[aes]] - secondary <- if (is.null(scale$secondary.axis)) { - waiver() - } else { - scale$sec_name() - } %|W|% labels[[paste0("sec.", aes)]] - if (is.derived(secondary)) secondary <- primary + aes <- scale$aesthetics[[1]] + + prim_scale <- scale$name + seco_scale <- (scale$sec_name %||% waiver)() + + prim_label <- labels[[aes]] + seco_label <- labels[[paste0("sec. aes")]] + + prim_guide <- seco_guide <- waiver() + order <- scale$axis_order() - if (!is.null(self$panel_params[[1]]$guides)) { - if ((scale$position) %in% c("left", "right")) { - guides <- c("y", "y.sec") - } else { - guides <- c("x", "x.sec") - } - params <- self$panel_params[[1]]$guides$get_params(guides) + panel <- self$panel_params[[1]]$guides + if (!is.null(panel)) { + position <- scale$position + aes <- switch(position, left = , right = "y", "x") + params <- panel$get_params(paste0(aes, c("", ".sec"))) if (!is.null(params)) { - primary <- params[[1]]$title %|W|% primary - secondary <- params[[2]]$title %|W|% secondary - position <- params[[1]]$position %||% scale$position - if (position != scale$position) { + prim_guide <- params[[1]]$title + seco_guide <- params[[2]]$title + position <- scale$position + if ((params[[1]]$position %||% position) != position) { order <- rev(order) } } } - primary <- scale$make_title(primary) - secondary <- scale$make_sec_title(secondary) + + primary <- scale$make_title(prim_guide, prim_scale, prim_label) + secondary <- scale$make_sec_title(seco_guide, seco_scale, seco_label) + if (is.derived(secondary)) { + secondary <- primary + } + list(primary = primary, secondary = secondary)[order] }, diff --git a/R/scale-.R b/R/scale-.R index 1ab3381099..f6e42a7e1e 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -612,12 +612,25 @@ Scale <- ggproto("Scale", NULL, ord }, - make_title = function(title) { + make_title = function(self, guide_title = waiver(), scale_title = waiver(), label_title = waiver()) { + title <- label_title + scale_title <- allow_lambda(scale_title) + if (is.function(scale_title)) { + title <- scale_title(title) + } else { + title <- scale_title %|W|% title + } + guide_title <- allow_lambda(guide_title) + if (is.function(guide_title)) { + title <- guide_title(title) + } else { + title <- guide_title %|W|% title + } title }, - make_sec_title = function(title) { - title + make_sec_title = function(self, ...) { + self$make_title(...) } ) diff --git a/R/scale-continuous.R b/R/scale-continuous.R index 39b5203565..8a681c2f20 100644 --- a/R/scale-continuous.R +++ b/R/scale-continuous.R @@ -159,11 +159,11 @@ ScaleContinuousPosition <- ggproto("ScaleContinuousPosition", ScaleContinuous, self$secondary.axis$name } }, - make_sec_title = function(self, title) { + make_sec_title = function(self, ...) { if (!is.waiver(self$secondary.axis)) { - self$secondary.axis$make_title(title) + self$secondary.axis$make_title(...) } else { - ggproto_parent(ScaleContinuous, self)$make_sec_title(title) + ggproto_parent(ScaleContinuous, self)$make_sec_title(...) } } ) diff --git a/R/scale-date.R b/R/scale-date.R index 436b9b129d..dff564e71e 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -392,11 +392,11 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous, self$secondary.axis$name } }, - make_sec_title = function(self, title) { + make_sec_title = function(self, ...) { if (!is.waiver(self$secondary.axis)) { - self$secondary.axis$make_title(title) + self$secondary.axis$make_title(...) } else { - ggproto_parent(ScaleContinuous, self)$make_sec_title(title) + ggproto_parent(ScaleContinuous, self)$make_sec_title(...) } } @@ -443,11 +443,11 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous, self$secondary.axis$name } }, - make_sec_title = function(self, title) { + make_sec_title = function(self, ...) { if (!is.waiver(self$secondary.axis)) { - self$secondary.axis$make_title(title) + self$secondary.axis$make_title(...) } else { - ggproto_parent(ScaleContinuous, self)$make_sec_title(title) + ggproto_parent(ScaleContinuous, self)$make_sec_title(...) } } ) diff --git a/R/scale-view.R b/R/scale-view.R index 350d27e9c0..cf9d4195d5 100644 --- a/R/scale-view.R +++ b/R/scale-view.R @@ -76,7 +76,7 @@ view_scale_secondary <- function(scale, limits = scale$get_limits(), # different breaks and labels in a different data space aesthetics = scale$aesthetics, name = scale$sec_name(), - make_title = function(self, title) self$scale$make_sec_title(title), + make_title = function(self, ...) self$scale$make_sec_title(...), continuous_range = sort(continuous_range), dimension = function(self) self$break_info$range, get_limits = function(self) self$break_info$range, @@ -127,8 +127,8 @@ ViewScale <- ggproto("ViewScale", NULL, x } }, - make_title = function(self, title) { - self$scale$make_title(title) + make_title = function(self, ...) { + self$scale$make_title(...) }, mapped_breaks = function(self) { self$map(self$get_breaks()) diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index 0b1fc5df50..172eca6364 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -199,6 +199,29 @@ test_that("position axis label hierarchy works as intended", { ) }) +test_that("labels can be derived using functions", { + + p <- ggplot(mtcars, aes(disp, mpg, colour = drat, shape = factor(cyl))) + + geom_point() + + labs( + y = to_upper_ascii, + shape = function(x) gsub("factor", "foo", x) + ) + + scale_shape_discrete( + name = to_upper_ascii, + guide = guide_legend(title = function(x) paste0(x, "!!!")) + ) + + scale_x_continuous(name = to_upper_ascii) + + guides(colour = guide_colourbar(title = to_upper_ascii)) + + labs <- get_labs(p) + expect_equal(labs$shape, "FOO(CYL)!!!") + expect_equal(labs$colour, "DRAT") + expect_equal(labs$x, "DISP") + expect_equal(labs$y, "MPG") + +}) + test_that("moving guide positions lets titles follow", { df <- data_frame(foo = c(1e1, 1e5), bar = c(0, 100)) From fdaa19510f58165878c44f1d7b021e03e0ec17fe Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 09:32:55 +0100 Subject: [PATCH 212/264] link blog (#6246) --- README.Rmd | 10 ++++++++-- README.md | 17 ++++++++++------- 2 files changed, 18 insertions(+), 9 deletions(-) diff --git a/README.Rmd b/README.Rmd index f546e5dc22..8c601f59ea 100644 --- a/README.Rmd +++ b/README.Rmd @@ -70,7 +70,7 @@ If you are looking for innovation, look to ggplot2's rich ecosystem of extension ## Learning ggplot2 -If you are new to ggplot2 you are better off starting with a systematic introduction, rather than trying to learn from reading individual documentation pages. Currently, there are three good places to start: +If you are new to ggplot2 you are better off starting with a systematic introduction, rather than trying to learn from reading individual documentation pages. Currently, there are several good places to start: 1. The [Data Visualization][r4ds-vis] and [Communication][r4ds-comm] chapters in @@ -92,7 +92,12 @@ If you are new to ggplot2 you are better off starting with a systematic introduc by Winston Chang. It provides a set of recipes to solve common graphics problems. -If you've mastered the basics and want to learn more, read [ggplot2: Elegant Graphics for Data Analysis][ggplot2-book]. It describes the theoretical underpinnings of ggplot2 and shows you how all the pieces fit together. This book helps you understand the theory that underpins ggplot2, and will help you create new types of graphics specifically tailored to your needs. +1. If you've mastered the basics and want to learn more, read [ggplot2: Elegant Graphics for Data Analysis][ggplot2-book]. + It describes the theoretical underpinnings of ggplot2 and shows you how all the pieces fit together. + This book helps you understand the theory that underpins ggplot2, + and will help you create new types of graphics specifically tailored to your needs. + +1. For articles about announcements and deep-dives you can visit the [tidyverse blog][blog]. ## Getting help @@ -114,3 +119,4 @@ There are two main places to get help with ggplot2: [r4ds-vis]: https://r4ds.hadley.nz/data-visualize [r4ds-comm]: https://r4ds.hadley.nz/communication [oreilly]: https://learning.oreilly.com/videos/data-visualization-in/9781491963661/ +[blog]: https://www.tidyverse.org/tags/ggplot2/ diff --git a/README.md b/README.md index 7fa139829b..3683108c63 100644 --- a/README.md +++ b/README.md @@ -74,7 +74,7 @@ extensions. See a community maintained list at If you are new to ggplot2 you are better off starting with a systematic introduction, rather than trying to learn from reading individual -documentation pages. Currently, there are three good places to start: +documentation pages. Currently, there are several good places to start: 1. The [Data Visualization](https://r4ds.hadley.nz/data-visualize) and [Communication](https://r4ds.hadley.nz/communication) chapters in [R @@ -97,12 +97,15 @@ documentation pages. Currently, there are three good places to start: Cookbook](https://r-graphics.org) by Winston Chang. It provides a set of recipes to solve common graphics problems. -If you’ve mastered the basics and want to learn more, read [ggplot2: -Elegant Graphics for Data Analysis](https://ggplot2-book.org). It -describes the theoretical underpinnings of ggplot2 and shows you how all -the pieces fit together. This book helps you understand the theory that -underpins ggplot2, and will help you create new types of graphics -specifically tailored to your needs. +5. If you’ve mastered the basics and want to learn more, read [ggplot2: + Elegant Graphics for Data Analysis](https://ggplot2-book.org). It + describes the theoretical underpinnings of ggplot2 and shows you how + all the pieces fit together. This book helps you understand the + theory that underpins ggplot2, and will help you create new types of + graphics specifically tailored to your needs. + +6. For articles about announcements and deep-dives you can visit the + [tidyverse blog](https://www.tidyverse.org/tags/ggplot2/). ## Getting help From fa7e2c1b5c6a8f24c7c9e1520600b6f11cb6b112 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 09:34:30 +0100 Subject: [PATCH 213/264] Include image of shape table (#6236) * add news bullet * add images * include in docs * Revert "add news bullet" This reverts commit e16ae8b600180c1b3d95a0da39bdaa3e43296373. --- R/scale-shape.R | 7 +++ man/figures/shape_table.pdf | Bin 0 -> 5370 bytes man/figures/shape_table.svg | 120 ++++++++++++++++++++++++++++++++++++ man/scale_shape.Rd | 7 +++ 4 files changed, 134 insertions(+) create mode 100644 man/figures/shape_table.pdf create mode 100644 man/figures/shape_table.svg diff --git a/R/scale-shape.R b/R/scale-shape.R index effa0a0b2f..39687022fc 100644 --- a/R/scale-shape.R +++ b/R/scale-shape.R @@ -12,6 +12,13 @@ #' @inheritParams scale_x_discrete #' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @rdname scale_shape +#' @details +#' Shapes can be referred to by number or name. Shapes in \[0, 20\] do not +#' support a fill aesthetic, whereas shapes in \[21, 25\] do. +#' +#' \if{html}{\figure{shape_table.svg}{All shapes by number and name}} +#' \if{latex}{\figure{shape_table.pdf}} +#' #' @seealso #' The documentation for [differentiation related aesthetics][aes_linetype_size_shape]. #' diff --git a/man/figures/shape_table.pdf b/man/figures/shape_table.pdf new file mode 100644 index 0000000000000000000000000000000000000000..8e7f539dc2c72736cc80d3062e92ec3ef343ccfb GIT binary patch literal 5370 zcmZ`-XH=6}yQK(7q(}#)ydY?(Apt_DN|oLrbiojcLJ}eL-jOyG>CzDtWDx1yLPv^# z2r5WXs&oXT=uMn)zHhGgzWH_bdCED@%36D$EnuLkE(#Ts1PO%Bhc1K;hmKjhgP?#o zfW3JOBrgwwsJNr;@h(`5sy!YJfK_E-;xI`ljPQfPB%soQAc!v3;s4z;alyM1vW$T1 z?)Erm7nBE}?}^8G;t6R6?pOy;6xyA*D=8)^1|wiUdtr%?AV^UWgvK}!PXYVqGyufJ z7l#HQD)xALSF95NF|c<+djJxI03+Z(3DUnM5aWo^?r04D?{J6;7K0}&Jpjbdbchk! z1MBIIBGi-oU-gIqzs8}1#yH`f0jQLWBmhx&am5pE08w`(3`Z4>!aAUd=k~x8X66R+ zxj${8ZOkuC(|%C3#Xz@xw7$VPrDddMYLs@(ly026mxL5X-a<3}{Zu2}p@nLHj?*J^ zCS9~I|G{udPTi`Bg=dwb?&f~*iF*5IX*o_OODmSsIvwHY z17k|3{)M!i{MAr4-(Yywd}DB4+Yj1wI=#R=F~w&$k*TI-TP^vn+XrjRZMLoMyepaG zMHw1@l&xvz>S|e-i@)kut0+dc1o1m(D1l_j zmL`j@O_^A|xZJKO^scr36_Z%K&D@NRQ)p14}Et_NUiMnFPR0rLm zgJDnwhaNxH`i*#7K=yp^s{)J2=yFg_Qh%#mNj96$UCer>NLUM|rzU+`vPO6jbO zNkT?fR6mVr7)iPPu_kF{^lEc*K|&g)(@a?{rCATWJHFCsRx;nR7QtG6hvrTCRxFkP zn=etbz5f%3EzRk7YMFgk$7D&4(Oru$?LO7kLmwz#x|{qdbFsnGmQM$IkGY!ujoBJeoA>!lWN!^^2V1b(9}Z<>eDEjD%>I55)2xXinHL7GegQF) z?Y?3{aqra~NXpe29R+$Z0^HPGWxna)0WXp9_1=)KydEzci|`pyTg~N3k(!98FMf|3 z1s}ImcT$Z?p!`MYMX0a5P&%6_>^8~1r_`NR*fef%eokxMEw_!re^JA$k@vA7?i74m zK*%tu{&EqiH&jK6yV>By#caLF@#-Z>>N@?Q4uguBQyMDG+>hY*V&6Y2!L0M?>^RtWNdM5A8sGb9k-cpLQA1`KGBUAvABjppEHN)X@eMt^ytri`x`Sef$}{LF*M}7hR1_SN%3~6{ znkhan?4z$HnS%}E){yjd*x(!DTP?>wgw zaET?H>Wo!0tuVWa+IYrhGUbAD(H#R#N;;4+b0aGw?*+lfI6X%2v(uRpF}Z~=UnY1S zJ(`ehZS*2RK#!+Cd&v!r(sdh;GKIXr8h?R+~8}3 zEzgWbzw>kiVEwYfID9VYj+yX6J$-Y6hlbByHeY;7WE zCvUQIBtT+?=e|Sh3upbH@nMLmLU!SN?v5W9K`W)j;+dIT@r64aWa-0+9MNpz-4d1x za|0f{MJ>tmE)qKfgNJN~*l8;IB(4*xp&!T6r{~hzgHH&=_cw?9O@Ty)`-_2oQQ%+9 z2hnzM@Bpj;BI6kWHUwtGdJ-583P5zx4lee}SRcSjoUkV;0RvzNgw21EB$4EPks5)E zQO0OIUyZ0~_~0N}(Zn_o0fT>ZME5|LLi#3m3`w3iDC zO)Lu0BTzTwZvuu%$-w_l0w$j69|F!z_ck$}VvQbdlWsFeIUjp(40y?LSt9spOgH^zt?2J2PHAcj9=P0oU-O%>q96Y?+Y~O_hr^g z>JEu(4e?oo!OT)Uc0{ZK_OsCRGP|${d5!^(p?UPyrw>;a5@Zxx?qNo%wEKGF4mt@5a_B#QfDT(*S+f&?`$Z zM*gxGj?31@Q3$e=7*k|(9;x~ZdRHy0KXn>A8{mec4#I|xba z({@j~z&qT{0k%e+^CC{d6(2rWYm?^R7KAKs9_7;otK0|}Hfo>V{A};Dn~F%mLse|0 zF^+zvs-3+<^SEy`i}}%qJXGI3xmg)b_}gP3_taDeN_7C8^g63vrWlGW<)~|i`Pql` zFTa;eHKpHucgQf3Zcg@q_rkRxZW6E%13>NXAUv`ec&__8`M1Hi*IAjl$HQUY1Cfn7 z-+Nj4gA-BLRbh>chC^SnPb|qK0TQ)q%E|W7oJ5&FRp^=1smYhrp9CPN59dtH~ zIf+yiU}FxcD`3ADR%v(TA*E*lgJd`y$Bqw0%}OGu#6kz`&U_#>5~s@x5!?d3x^_My zviCfTQ8XS<>E(PHX`XcP6FG$ng8}EgvjQs08e}Zj)(VUsa+XJ}7CJ6lEranFnn`F? 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Use a continuous variable to shape unless \code{scale_shape_binned()} is used. Still, as shape has no inherent order, this use is not advised. } +\details{ +Shapes can be referred to by number or name. Shapes in [0, 20] do not +support a fill aesthetic, whereas shapes in [21, 25] do. + +\if{html}{\figure{shape_table.svg}{All shapes by number and name}} +\if{latex}{\figure{shape_table.pdf}} +} \examples{ set.seed(596) dsmall <- diamonds[sample(nrow(diamonds), 100), ] From 7356fe3029ade295dd53589d96869b8a64f17bf5 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 11:35:02 +0100 Subject: [PATCH 214/264] Coord sf breaks fallback (#6232) * add news bullet * fallback * avoid duplicated labels * add test * add news bullet --- NEWS.md | 4 ++++ R/coord-sf.R | 8 ++++++++ tests/testthat/test-coord_sf.R | 12 ++++++++++++ 3 files changed, 24 insertions(+) diff --git a/NEWS.md b/NEWS.md index 9340b73a2f..e2e2d0c607 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* Axis labels are now preserved better when using `coord_sf(expand = TRUE)` and + graticule lines are straight but do not meet the edge (@teunbrand, #2985). +* Attempt to boost detail in `coord_polar()` and `coord_radial()` near the + center (@teunbrand, #5023) * Scale names, guide titles and aesthetic labels can now accept functions (@teunbrand, #4313) * Binned scales with zero-width data expand the default limits by 0.1 diff --git a/R/coord-sf.R b/R/coord-sf.R index 3f96ff6aaf..d603d57de7 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -721,6 +721,14 @@ view_scales_from_graticule <- function(graticule, scale, aesthetic, accept_start <- graticule[[orth_start]] < thres accept_end <- graticule[[orth_end]] < thres } + if (!any(accept_start | accept_end)) { + eps <- sqrt(.Machine$double.xmin) + subtract <- switch(position, top = , bottom = 90, 0) + straight <- + abs(graticule$angle_start - subtract) < eps & + abs(graticule$angle_end - subtract) < eps + accept_start <- straight + } # Parsing the information of the `label_axes` argument: # should we label the meridians ("E") or parallels ("N")? diff --git a/tests/testthat/test-coord_sf.R b/tests/testthat/test-coord_sf.R index 516d2fa9ec..a684bea20b 100644 --- a/tests/testthat/test-coord_sf.R +++ b/tests/testthat/test-coord_sf.R @@ -425,3 +425,15 @@ test_that("coord_sf() can render with empty graticules", { p <- suppressWarnings(layer_grob(ggplot(df) + geom_sf())[[1]]) expect_length(p$x, 1) }) + +test_that("coord_sf() can calculate breaks when expansion is on", { + skip_if_not_installed("sf") + df <- sf::st_multipoint(cbind(c(-180, 180), c(-90, 90))) + df <- sf::st_sfc(df, crs = 4326) + b <- ggplot_build(ggplot(df) + geom_sf()) + + x <- get_guide_data(b, "x") + y <- get_guide_data(b, "y") + expect_equal(nrow(x), 5L) + expect_equal(nrow(y), 3L) +}) From c052d8123440a18d6d132d2143757c74e61b6305 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 11:35:34 +0100 Subject: [PATCH 215/264] Scales expose `aesthetics` argument (#6227) * add news bullet * add `aesthetics` as parameter * redocument * add news bullet --- NEWS.md | 1 + R/scale-alpha.R | 20 ++++++++++---------- R/scale-identity.R | 25 +++++++++++++++---------- R/scale-linetype.R | 10 +++++----- R/scale-linewidth.R | 21 +++++++++++---------- R/scale-manual.R | 22 +++++++++++----------- R/scale-shape.R | 10 +++++----- R/scale-size.R | 34 ++++++++++++++++++---------------- R/zxx.R | 20 ++++++++++++-------- man/scale_alpha.Rd | 15 +++++++++++---- man/scale_identity.Rd | 30 +++++++++++++++++++++++++----- man/scale_linetype.Rd | 19 +++++++++++++++---- man/scale_linewidth.Rd | 8 ++++++-- man/scale_manual.Rd | 40 +++++++++++++++++++++++++++++++++++----- man/scale_shape.Rd | 7 ++++--- man/scale_size.Rd | 15 ++++++++++----- 16 files changed, 194 insertions(+), 103 deletions(-) diff --git a/NEWS.md b/NEWS.md index e2e2d0c607..c0f7809db6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -287,6 +287,7 @@ * Munching in `coord_polar()` and `coord_radial()` now adds more detail, particularly for data-points with a low radius near the center (@teunbrand, #5023). +* All scales now expose the `aesthetics` parameter (@teunbrand, #5841) # ggplot2 3.5.1 diff --git a/R/scale-alpha.R b/R/scale-alpha.R index 5e22937e88..c9155db9aa 100644 --- a/R/scale-alpha.R +++ b/R/scale-alpha.R @@ -31,9 +31,9 @@ #' #' # Changing the title #' p + scale_alpha("cylinders") -scale_alpha <- function(name = waiver(), ..., range = NULL) { +scale_alpha <- function(name = waiver(), ..., range = NULL, aesthetics = "alpha") { palette <- if (!is.null(range)) pal_rescale(range) else NULL - continuous_scale("alpha", name = name, palette = palette, ...) + continuous_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_alpha @@ -42,9 +42,9 @@ scale_alpha_continuous <- scale_alpha #' @rdname scale_alpha #' @export -scale_alpha_binned <- function(name = waiver(), ..., range = NULL) { +scale_alpha_binned <- function(name = waiver(), ..., range = NULL, aesthetics = "alpha") { palette <- if (!is.null(range)) pal_rescale(range) else NULL - binned_scale("alpha", name = name, palette = palette, ...) + binned_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_alpha @@ -58,22 +58,22 @@ scale_alpha_discrete <- function(...) { #' @rdname scale_alpha #' @export -scale_alpha_ordinal <- function(name = waiver(), ..., range = NULL) { +scale_alpha_ordinal <- function(name = waiver(), ..., range = NULL, aesthetics = "alpha") { palette <- if (!is.null(range)) { function(n) seq(range[1], range[2], length.out = n) } else { NULL } - discrete_scale("alpha", name = name, palette = palette, ...) + discrete_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_alpha #' @export #' @usage NULL -scale_alpha_datetime <- function(name = waiver(), ..., range = NULL) { +scale_alpha_datetime <- function(name = waiver(), ..., range = NULL, aesthetics = "alpha") { palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( - aesthetics = "alpha", transform = "time", name = name, + aesthetics = aesthetics, transform = "time", name = name, palette = palette, ... ) } @@ -81,10 +81,10 @@ scale_alpha_datetime <- function(name = waiver(), ..., range = NULL) { #' @rdname scale_alpha #' @export #' @usage NULL -scale_alpha_date <- function(name = waiver(), ..., range = NULL){ +scale_alpha_date <- function(name = waiver(), ..., range = NULL, aesthetics = "alpha"){ palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( - aesthetics = "alpha", transform = "date", name = name, + aesthetics = aesthetics, transform = "date", name = name, palette = palette, ... ) } diff --git a/R/scale-identity.R b/R/scale-identity.R index d86f6ae360..3ab2de5c43 100644 --- a/R/scale-identity.R +++ b/R/scale-identity.R @@ -89,9 +89,10 @@ scale_fill_identity <- function(name = waiver(), ..., guide = "none", #' @seealso #' Other shape scales: [scale_shape()], [scale_shape_manual()]. #' @export -scale_shape_identity <- function(name = waiver(), ..., guide = "none") { +scale_shape_identity <- function(name = waiver(), ..., guide = "none", + aesthetics = "shape") { continuous_scale( - "shape", name = name, + aesthetics, name = name, palette = pal_identity(), ..., guide = guide, super = ScaleContinuousIdentity ) @@ -101,9 +102,10 @@ scale_shape_identity <- function(name = waiver(), ..., guide = "none") { #' @seealso #' Other linetype scales: [scale_linetype()], [scale_linetype_manual()]. #' @export -scale_linetype_identity <- function(name = waiver(), ..., guide = "none") { +scale_linetype_identity <- function(name = waiver(), ..., guide = "none", + aesthetics = "linetype") { discrete_scale( - "linetype", name = name, + aesthetics, name = name, palette = pal_identity(), ..., guide = guide, super = ScaleDiscreteIdentity ) @@ -113,9 +115,10 @@ scale_linetype_identity <- function(name = waiver(), ..., guide = "none") { #' @seealso #' Other alpha scales: [scale_alpha()], [scale_alpha_manual()]. #' @export -scale_linewidth_identity <- function(name = waiver(), ..., guide = "none") { +scale_linewidth_identity <- function(name = waiver(), ..., guide = "none", + aesthetics = "linewidth") { continuous_scale( - "linewidth", name = name, + aesthetics, name = name, palette = pal_identity(), ..., guide = guide, super = ScaleContinuousIdentity ) @@ -123,9 +126,10 @@ scale_linewidth_identity <- function(name = waiver(), ..., guide = "none") { #' @rdname scale_identity #' @export -scale_alpha_identity <- function(name = waiver(), ..., guide = "none") { +scale_alpha_identity <- function(name = waiver(), ..., guide = "none", + aesthetics = "alpha") { continuous_scale( - "alpha", name = name, + aesthetics, name = name, palette = pal_identity(), ..., guide = guide, super = ScaleContinuousIdentity ) @@ -135,9 +139,10 @@ scale_alpha_identity <- function(name = waiver(), ..., guide = "none") { #' @seealso #' Other size scales: [scale_size()], [scale_size_manual()]. #' @export -scale_size_identity <- function(name = waiver(), ..., guide = "none") { +scale_size_identity <- function(name = waiver(), ..., guide = "none", + aesthetics = "size") { continuous_scale( - "size", name = name, + aesthetics, name = name, palette = pal_identity(), ..., guide = guide, super = ScaleContinuousIdentity ) diff --git a/R/scale-linetype.R b/R/scale-linetype.R index 8f8c62e30e..a53f660c72 100644 --- a/R/scale-linetype.R +++ b/R/scale-linetype.R @@ -5,7 +5,7 @@ #' line types unless `scale_linetype_binned()` is used. Still, as linetypes has #' no inherent order, this use is not advised. #' -#' @inheritParams scale_x_discrete +#' @inheritParams discrete_scale #' @inheritDotParams discrete_scale -expand -position -na.value -scale_name -palette #' @param na.value The linetype to use for `NA` values. #' @rdname scale_linetype @@ -35,9 +35,9 @@ #' scale_linetype_identity() + #' facet_grid(linetype ~ .) + #' theme_void(20) -scale_linetype <- function(name = waiver(), ..., na.value = NA) { +scale_linetype <- function(name = waiver(), ..., na.value = NA, aesthetics = "linetype") { discrete_scale( - "linetype", name = name, + aesthetics, name = name, palette = NULL, na.value = na.value, ... @@ -46,9 +46,9 @@ scale_linetype <- function(name = waiver(), ..., na.value = NA) { #' @rdname scale_linetype #' @export -scale_linetype_binned <- function(name = waiver(), ..., na.value = NA) { +scale_linetype_binned <- function(name = waiver(), ..., na.value = NA, aesthetics = "linetype") { binned_scale( - "linetype", name = name, + aesthetics, name = name, palette = NULL, na.value = na.value, ... diff --git a/R/scale-linewidth.R b/R/scale-linewidth.R index 9bf05b3913..f9cec8856f 100644 --- a/R/scale-linewidth.R +++ b/R/scale-linewidth.R @@ -33,9 +33,10 @@ scale_linewidth_continuous <- function(name = waiver(), breaks = waiver(), labels = waiver(), limits = NULL, range = NULL, transform = "identity", trans = deprecated(), - guide = "legend") { + guide = "legend", + aesthetics = "linewidth") { palette <- if (!is.null(range)) pal_rescale(range) else NULL - continuous_scale("linewidth", palette = palette, name = name, + continuous_scale(aesthetics, palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, guide = guide) } @@ -49,9 +50,9 @@ scale_linewidth <- scale_linewidth_continuous scale_linewidth_binned <- function(name = waiver(), breaks = waiver(), labels = waiver(), limits = NULL, range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", - trans = deprecated(), guide = "bins") { + trans = deprecated(), guide = "bins", aesthetics = "linewidth") { palette <- if (!is.null(range)) pal_rescale(range) else NULL - binned_scale("linewidth", palette = palette, name = name, + binned_scale(aesthetics, palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, n.breaks = n.breaks, nice.breaks = nice.breaks, guide = guide) @@ -70,22 +71,22 @@ scale_linewidth_discrete <- function(...) { #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_ordinal <- function(name = waiver(), ..., range = NULL) { +scale_linewidth_ordinal <- function(name = waiver(), ..., range = NULL, aesthetics = "linewidth") { palette <- if (!is.null(range)) { function(n) seq(range[1], range[2], length.out = n) } else { NULL } - discrete_scale("linewidth", name = name, palette = palette, ...) + discrete_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_datetime <- function(name = waiver(), ..., range = NULL) { +scale_linewidth_datetime <- function(name = waiver(), ..., range = NULL, aesthetics = "linewidth") { palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( - "linewidth", transform = "time", name = name, + aesthetics, transform = "time", name = name, palette = palette, ... ) } @@ -93,10 +94,10 @@ scale_linewidth_datetime <- function(name = waiver(), ..., range = NULL) { #' @rdname scale_linewidth #' @export #' @usage NULL -scale_linewidth_date <- function(name = waiver(), ..., range = NULL) { +scale_linewidth_date <- function(name = waiver(), ..., range = NULL, aesthetics = "linewidth") { palette <- if (!is.null(range)) pal_rescale(range) else NULL datetime_scale( - "linewidth", transform = "date", name = name, + aesthetics, transform = "date", name = name, palette = palette, ... ) } diff --git a/R/scale-manual.R b/R/scale-manual.R index 47c647fc02..9f6284361b 100644 --- a/R/scale-manual.R +++ b/R/scale-manual.R @@ -11,7 +11,7 @@ #' `scale_discrete_manual()` is a generic scale that can work with any aesthetic or set #' of aesthetics provided via the `aesthetics` argument. #' -#' @inheritParams scale_x_discrete +#' @inheritParams discrete_scale #' @inheritDotParams discrete_scale -expand -position -aesthetics -palette -scale_name #' @param aesthetics Character string or vector of character strings listing the #' name(s) of the aesthetic(s) that this scale works with. This can be useful, for @@ -103,38 +103,38 @@ scale_fill_manual <- function(..., values, aesthetics = "fill", breaks = waiver( #' @seealso #' Other size scales: [scale_size()], [scale_size_identity()]. #' @export -scale_size_manual <- function(..., values, breaks = waiver(), na.value = NA) { - manual_scale("size", values, breaks, ..., na.value = na.value) +scale_size_manual <- function(..., values, breaks = waiver(), na.value = NA, aesthetics = "size") { + manual_scale(aesthetics, values, breaks, ..., na.value = na.value) } #' @rdname scale_manual #' @seealso #' Other shape scales: [scale_shape()], [scale_shape_identity()]. #' @export -scale_shape_manual <- function(..., values, breaks = waiver(), na.value = NA) { - manual_scale("shape", values, breaks, ..., na.value = na.value) +scale_shape_manual <- function(..., values, breaks = waiver(), na.value = NA, aesthetics = "shape") { + manual_scale(aesthetics, values, breaks, ..., na.value = na.value) } #' @rdname scale_manual #' @seealso #' Other linetype scales: [scale_linetype()], [scale_linetype_identity()]. #' @export -scale_linetype_manual <- function(..., values, breaks = waiver(), na.value = NA) { - manual_scale("linetype", values, breaks, ..., na.value = na.value) +scale_linetype_manual <- function(..., values, breaks = waiver(), na.value = NA, aesthetics = "linetype") { + manual_scale(aesthetics, values, breaks, ..., na.value = na.value) } #' @rdname scale_manual #' @seealso #' Other alpha scales: [scale_alpha()], [scale_alpha_identity()]. #' @export -scale_linewidth_manual <- function(..., values, breaks = waiver(), na.value = NA) { - manual_scale("linewidth", values, breaks, ..., na.value = na.value) +scale_linewidth_manual <- function(..., values, breaks = waiver(), na.value = NA, aesthetics = "linewidth") { + manual_scale(aesthetics, values, breaks, ..., na.value = na.value) } #' @rdname scale_manual #' @export -scale_alpha_manual <- function(..., values, breaks = waiver(), na.value = NA) { - manual_scale("alpha", values, breaks, ..., na.value = na.value) +scale_alpha_manual <- function(..., values, breaks = waiver(), na.value = NA, aesthetics = "alpha") { + manual_scale(aesthetics, values, breaks, ..., na.value = na.value) } #' @rdname scale_manual diff --git a/R/scale-shape.R b/R/scale-shape.R index 39687022fc..bde6756840 100644 --- a/R/scale-shape.R +++ b/R/scale-shape.R @@ -9,7 +9,7 @@ #' #' @param solid Should the shapes be solid, `TRUE`, or hollow, #' `FALSE`? -#' @inheritParams scale_x_discrete +#' @inheritParams discrete_scale #' @inheritDotParams discrete_scale -expand -position -scale_name -palette #' @rdname scale_shape #' @details @@ -49,16 +49,16 @@ #' scale_shape_identity() + #' facet_wrap(~shape) + #' theme_void() -scale_shape <- function(name = waiver(), ..., solid = NULL) { +scale_shape <- function(name = waiver(), ..., solid = NULL, aesthetics = "shape") { palette <- if (!is.null(solid)) pal_shape(solid) else NULL - discrete_scale("shape", name = name, palette = palette, ...) + discrete_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_shape #' @export -scale_shape_binned <- function(name = waiver(), ..., solid = TRUE) { +scale_shape_binned <- function(name = waiver(), ..., solid = TRUE, aesthetics = "shape") { palette <- if (!is.null(solid)) pal_binned(pal_shape(solid)) else NULL - binned_scale("shape", name = name, palette = palette, ...) + binned_scale(aesthetics, name = name, palette = palette, ...) } #' @rdname scale_shape diff --git a/R/scale-size.R b/R/scale-size.R index 525f378e15..964abf16a6 100644 --- a/R/scale-size.R +++ b/R/scale-size.R @@ -55,9 +55,10 @@ scale_size_continuous <- function(name = waiver(), breaks = waiver(), labels = w limits = NULL, range = NULL, transform = "identity", trans = deprecated(), - guide = "legend") { + guide = "legend", + aesthetics = "size") { palette <- if (!is.null(range)) pal_area(range) else NULL - continuous_scale("size", palette = palette, name = name, + continuous_scale(aesthetics, palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, guide = guide) } @@ -71,8 +72,8 @@ scale_size <- scale_size_continuous scale_radius <- function(name = waiver(), breaks = waiver(), labels = waiver(), limits = NULL, range = c(1, 6), transform = "identity", trans = deprecated(), - guide = "legend") { - continuous_scale("size", palette = pal_rescale(range), name = name, + guide = "legend", aesthetics = "size") { + continuous_scale(aesthetics, palette = pal_rescale(range), name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, guide = guide) } @@ -82,9 +83,10 @@ scale_radius <- function(name = waiver(), breaks = waiver(), labels = waiver(), scale_size_binned <- function(name = waiver(), breaks = waiver(), labels = waiver(), limits = NULL, range = NULL, n.breaks = NULL, nice.breaks = TRUE, transform = "identity", - trans = deprecated(), guide = "bins") { + trans = deprecated(), guide = "bins", + aesthetics = "size") { palette <- if (!is.null(range)) pal_area(range) else NULL - binned_scale("size", palette = palette, name = name, + binned_scale(aesthetics, palette = palette, name = name, breaks = breaks, labels = labels, limits = limits, transform = transform, trans = trans, n.breaks = n.breaks, nice.breaks = nice.breaks, guide = guide) @@ -103,22 +105,22 @@ scale_size_discrete <- function(...) { #' @rdname scale_size #' @export #' @usage NULL -scale_size_ordinal <- function(name = waiver(), ..., range = NULL) { +scale_size_ordinal <- function(name = waiver(), ..., range = NULL, aesthetics = "size") { palette <- if (!is.null(range)) { function(n) sqrt(seq(range[1]^2, range[2]^2, length.out = n)) } else { NULL } - discrete_scale("size", name = name, palette = palette, ...) + discrete_scale(aesthetics, name = name, palette = palette, ...) } #' @inheritDotParams continuous_scale -aesthetics -scale_name -palette -rescaler -expand -position #' @param max_size Size of largest points. #' @export #' @rdname scale_size -scale_size_area <- function(name = waiver(), ..., max_size = 6) { +scale_size_area <- function(name = waiver(), ..., max_size = 6, aesthetics = "size") { continuous_scale( - "size", name = name, + aesthetics, name = name, palette = abs_area(max_size), rescaler = rescale_max, ... ) @@ -126,9 +128,9 @@ scale_size_area <- function(name = waiver(), ..., max_size = 6) { #' @export #' @rdname scale_size -scale_size_binned_area <- function(name = waiver(), ..., max_size = 6) { +scale_size_binned_area <- function(name = waiver(), ..., max_size = 6, aesthetics = "size") { binned_scale( - "size", name = name, + aesthetics, name = name, palette = abs_area(max_size), rescaler = rescale_max, ... ) @@ -137,15 +139,15 @@ scale_size_binned_area <- function(name = waiver(), ..., max_size = 6) { #' @rdname scale_size #' @export #' @usage NULL -scale_size_datetime <- function(name = waiver(), ..., range = NULL) { +scale_size_datetime <- function(name = waiver(), ..., range = NULL, aesthetics = "size") { palette <- if (!is.null(range)) pal_area(range) else NULL - datetime_scale("size", "time", name = name, palette = palette, ...) + datetime_scale(aesthetics, "time", name = name, palette = palette, ...) } #' @rdname scale_size #' @export #' @usage NULL -scale_size_date <- function(name = waiver(), ..., range = NULL) { +scale_size_date <- function(name = waiver(), ..., range = NULL, aesthetics = "size") { palette <- if (!is.null(range)) pal_area(range) else NULL - datetime_scale("size", "date", name = name, palette = palette, ...) + datetime_scale(aesthetics, "date", name = name, palette = palette, ...) } diff --git a/R/zxx.R b/R/zxx.R index 59b3812e56..7c10940491 100644 --- a/R/zxx.R +++ b/R/zxx.R @@ -36,9 +36,10 @@ scale_colour_datetime <- function(name = waiver(), ..., high = "#56B1F7", space = "Lab", na.value = "grey50", - guide = "colourbar") { + guide = "colourbar", + aesthetics = "colour") { datetime_scale( - aesthetics = "colour", transform = "time", name = name, + aesthetics = aesthetics, transform = "time", name = name, palette = pal_seq_gradient(low, high, space), na.value = na.value, guide = guide, @@ -60,9 +61,10 @@ scale_colour_date <- function(name = waiver(), high = "#56B1F7", space = "Lab", na.value = "grey50", - guide = "colourbar") { + guide = "colourbar", + aesthetics = "colour") { datetime_scale( - aesthetics = "colour", transform = "date", name = name, + aesthetics = aesthetics, transform = "date", name = name, palette = pal_seq_gradient(low, high, space), na.value = na.value, guide = guide, @@ -114,9 +116,10 @@ scale_fill_datetime <- function(name = waiver(), ..., high = "#56B1F7", space = "Lab", na.value = "grey50", - guide = "colourbar") { + guide = "colourbar", + aesthetics = "fill") { datetime_scale( - aesthetics = "fill", transform = "time", name = name, + aesthetics = aesthetics, transform = "time", name = name, palette = pal_seq_gradient(low, high, space), na.value = na.value, guide = guide, @@ -132,9 +135,10 @@ scale_fill_date <- function(name = waiver(), ..., high = "#56B1F7", space = "Lab", na.value = "grey50", - guide = "colourbar") { + guide = "colourbar", + aesthetics = "fill") { datetime_scale( - aesthetics = "fill", transform = "date", name = name, + aesthetics = aesthetics, transform = "date", name = name, palette = pal_seq_gradient(low, high, space), na.value = na.value, guide = guide, diff --git a/man/scale_alpha.Rd b/man/scale_alpha.Rd index 6833a08002..7c4a5784df 100644 --- a/man/scale_alpha.Rd +++ b/man/scale_alpha.Rd @@ -10,15 +10,20 @@ \alias{scale_alpha_date} \title{Alpha transparency scales} \usage{ -scale_alpha(name = waiver(), ..., range = NULL) +scale_alpha(name = waiver(), ..., range = NULL, aesthetics = "alpha") -scale_alpha_continuous(name = waiver(), ..., range = NULL) +scale_alpha_continuous( + name = waiver(), + ..., + range = NULL, + aesthetics = "alpha" +) -scale_alpha_binned(name = waiver(), ..., range = NULL) +scale_alpha_binned(name = waiver(), ..., range = NULL, aesthetics = "alpha") scale_alpha_discrete(...) -scale_alpha_ordinal(name = waiver(), ..., range = NULL) +scale_alpha_ordinal(name = waiver(), ..., range = NULL, aesthetics = "alpha") } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If @@ -31,6 +36,8 @@ or \code{\link[=discrete_scale]{discrete_scale()}} as appropriate, to control na breaks, labels and so forth.} \item{range}{Output range of alpha values. Must lie between 0 and 1.} + +\item{aesthetics}{The names of the aesthetics that this scale works with.} } \description{ Alpha-transparency scales are not tremendously useful, but can be a diff --git a/man/scale_identity.Rd b/man/scale_identity.Rd index 2f3a877cfd..68100940e0 100644 --- a/man/scale_identity.Rd +++ b/man/scale_identity.Rd @@ -22,15 +22,35 @@ scale_colour_identity( scale_fill_identity(name = waiver(), ..., guide = "none", aesthetics = "fill") -scale_shape_identity(name = waiver(), ..., guide = "none") +scale_shape_identity( + name = waiver(), + ..., + guide = "none", + aesthetics = "shape" +) -scale_linetype_identity(name = waiver(), ..., guide = "none") +scale_linetype_identity( + name = waiver(), + ..., + guide = "none", + aesthetics = "linetype" +) -scale_linewidth_identity(name = waiver(), ..., guide = "none") +scale_linewidth_identity( + name = waiver(), + ..., + guide = "none", + aesthetics = "linewidth" +) -scale_alpha_identity(name = waiver(), ..., guide = "none") +scale_alpha_identity( + name = waiver(), + ..., + guide = "none", + aesthetics = "alpha" +) -scale_size_identity(name = waiver(), ..., guide = "none") +scale_size_identity(name = waiver(), ..., guide = "none", aesthetics = "size") scale_discrete_identity(aesthetics, name = waiver(), ..., guide = "none") diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index cc5fa67cb4..5707bd9f90 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -7,13 +7,23 @@ \alias{scale_linetype_discrete} \title{Scale for line patterns} \usage{ -scale_linetype(name = waiver(), ..., na.value = NA) +scale_linetype(name = waiver(), ..., na.value = NA, aesthetics = "linetype") -scale_linetype_binned(name = waiver(), ..., na.value = NA) +scale_linetype_binned( + name = waiver(), + ..., + na.value = NA, + aesthetics = "linetype" +) scale_linetype_continuous(...) -scale_linetype_discrete(name = waiver(), ..., na.value = NA) +scale_linetype_discrete( + name = waiver(), + ..., + na.value = NA, + aesthetics = "linetype" +) } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If @@ -49,7 +59,6 @@ every level in a legend, the layer should use \code{show.legend = TRUE}.} \item{\code{na.translate}}{Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify \code{na.translate = FALSE}.} - \item{\code{aesthetics}}{The names of the aesthetics that this scale works with.} \item{\code{minor_breaks}}{One of: \itemize{ \item \code{NULL} for no minor breaks @@ -79,6 +88,8 @@ notation. }} \item{na.value}{The linetype to use for \code{NA} values.} + +\item{aesthetics}{The names of the aesthetics that this scale works with.} } \description{ Default line types based on a set supplied by Richard Pearson, diff --git a/man/scale_linewidth.Rd b/man/scale_linewidth.Rd index 5c9a842da9..86e414a8a6 100644 --- a/man/scale_linewidth.Rd +++ b/man/scale_linewidth.Rd @@ -18,7 +18,8 @@ scale_linewidth( range = NULL, transform = "identity", trans = deprecated(), - guide = "legend" + guide = "legend", + aesthetics = "linewidth" ) scale_linewidth_binned( @@ -31,7 +32,8 @@ scale_linewidth_binned( nice.breaks = TRUE, transform = "identity", trans = deprecated(), - guide = "bins" + guide = "bins", + aesthetics = "linewidth" ) } \arguments{ @@ -99,6 +101,8 @@ You can create your own transformation with \code{\link[scales:new_transform]{sc \item{guide}{A function used to create a guide or its name. See \code{\link[=guides]{guides()}} for more information.} +\item{aesthetics}{The names of the aesthetics that this scale works with.} + \item{n.breaks}{An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if \code{breaks = waiver()}. Use \code{NULL} to use the default diff --git a/man/scale_manual.Rd b/man/scale_manual.Rd index d49cd0f526..b2723888d4 100644 --- a/man/scale_manual.Rd +++ b/man/scale_manual.Rd @@ -28,15 +28,45 @@ scale_fill_manual( na.value = "grey50" ) -scale_size_manual(..., values, breaks = waiver(), na.value = NA) +scale_size_manual( + ..., + values, + breaks = waiver(), + na.value = NA, + aesthetics = "size" +) -scale_shape_manual(..., values, breaks = waiver(), na.value = NA) +scale_shape_manual( + ..., + values, + breaks = waiver(), + na.value = NA, + aesthetics = "shape" +) -scale_linetype_manual(..., values, breaks = waiver(), na.value = NA) +scale_linetype_manual( + ..., + values, + breaks = waiver(), + na.value = NA, + aesthetics = "linetype" +) -scale_linewidth_manual(..., values, breaks = waiver(), na.value = NA) +scale_linewidth_manual( + ..., + values, + breaks = waiver(), + na.value = NA, + aesthetics = "linewidth" +) -scale_alpha_manual(..., values, breaks = waiver(), na.value = NA) +scale_alpha_manual( + ..., + values, + breaks = waiver(), + na.value = NA, + aesthetics = "alpha" +) scale_discrete_manual(aesthetics, ..., values, breaks = waiver()) } diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index 4f90b5c0d6..64f831c75d 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -8,9 +8,9 @@ \alias{scale_shape_continuous} \title{Scales for shapes, aka glyphs} \usage{ -scale_shape(name = waiver(), ..., solid = NULL) +scale_shape(name = waiver(), ..., solid = NULL, aesthetics = "shape") -scale_shape_binned(name = waiver(), ..., solid = TRUE) +scale_shape_binned(name = waiver(), ..., solid = TRUE, aesthetics = "shape") } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If @@ -49,7 +49,6 @@ from a discrete scale, specify \code{na.translate = FALSE}.} \item{\code{na.value}}{If \code{na.translate = TRUE}, what aesthetic value should the missing values be displayed as? Does not apply to position scales where \code{NA} is always placed at the far right.} - \item{\code{aesthetics}}{The names of the aesthetics that this scale works with.} \item{\code{minor_breaks}}{One of: \itemize{ \item \code{NULL} for no minor breaks @@ -80,6 +79,8 @@ notation. \item{solid}{Should the shapes be solid, \code{TRUE}, or hollow, \code{FALSE}?} + +\item{aesthetics}{The names of the aesthetics that this scale works with.} } \description{ \code{scale_shape()} maps discrete variables to six easily discernible shapes. diff --git a/man/scale_size.Rd b/man/scale_size.Rd index 2ba6a1e295..028d5b8490 100644 --- a/man/scale_size.Rd +++ b/man/scale_size.Rd @@ -21,7 +21,8 @@ scale_size( range = NULL, transform = "identity", trans = deprecated(), - guide = "legend" + guide = "legend", + aesthetics = "size" ) scale_radius( @@ -32,7 +33,8 @@ scale_radius( range = c(1, 6), transform = "identity", trans = deprecated(), - guide = "legend" + guide = "legend", + aesthetics = "size" ) scale_size_binned( @@ -45,12 +47,13 @@ scale_size_binned( nice.breaks = TRUE, transform = "identity", trans = deprecated(), - guide = "bins" + guide = "bins", + aesthetics = "size" ) -scale_size_area(name = waiver(), ..., max_size = 6) +scale_size_area(name = waiver(), ..., max_size = 6, aesthetics = "size") -scale_size_binned_area(name = waiver(), ..., max_size = 6) +scale_size_binned_area(name = waiver(), ..., max_size = 6, aesthetics = "size") } \arguments{ \item{name}{The name of the scale. Used as the axis or legend title. If @@ -117,6 +120,8 @@ You can create your own transformation with \code{\link[scales:new_transform]{sc \item{guide}{A function used to create a guide or its name. See \code{\link[=guides]{guides()}} for more information.} +\item{aesthetics}{The names of the aesthetics that this scale works with.} + \item{n.breaks}{An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if \code{breaks = waiver()}. Use \code{NULL} to use the default From 1b9ee73e55261f38060b441091d8280a87f81b1c Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 11:38:41 +0100 Subject: [PATCH 216/264] Encourage specifying `breaks` when giving labels as a vector (#6237) --- R/scale-.R | 4 +++- man/binned_scale.Rd | 4 +++- man/continuous_scale.Rd | 4 +++- man/datetime_scale.Rd | 4 +++- man/discrete_scale.Rd | 4 +++- man/scale_binned.Rd | 4 +++- man/scale_continuous.Rd | 4 +++- man/scale_date.Rd | 4 +++- man/scale_discrete.Rd | 4 +++- man/scale_gradient.Rd | 4 +++- man/scale_grey.Rd | 4 +++- man/scale_hue.Rd | 4 +++- man/scale_linetype.Rd | 4 +++- man/scale_linewidth.Rd | 4 +++- man/scale_manual.Rd | 4 +++- man/scale_shape.Rd | 4 +++- man/scale_size.Rd | 4 +++- man/scale_steps.Rd | 4 +++- 18 files changed, 54 insertions(+), 18 deletions(-) diff --git a/R/scale-.R b/R/scale-.R index f6e42a7e1e..7cae5da74b 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -34,7 +34,9 @@ #' may choose a slightly different number to ensure nice break labels. Will #' only have an effect if `breaks = waiver()`. Use `NULL` to use the default #' number of breaks given by the transformation. -#' @param labels One of: +#' @param labels One of the options below. Please note that when `labels` is a +#' vector, it is highly recommended to also set the `breaks` argument as a +#' vector to protect against unintended mismatches. #' - `NULL` for no labels #' - `waiver()` for the default labels computed by the #' transformation object diff --git a/man/binned_scale.Rd b/man/binned_scale.Rd index c1bbd50404..203cd66bb4 100644 --- a/man/binned_scale.Rd +++ b/man/binned_scale.Rd @@ -55,7 +55,9 @@ Note that for position scales, limits are provided after scale expansion. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/continuous_scale.Rd b/man/continuous_scale.Rd index a572ec2bf7..76d7492ba6 100644 --- a/man/continuous_scale.Rd +++ b/man/continuous_scale.Rd @@ -70,7 +70,9 @@ may choose a slightly different number to ensure nice break labels. Will only have an effect if \code{breaks = waiver()}. Use \code{NULL} to use the default number of breaks given by the transformation.} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/datetime_scale.Rd b/man/datetime_scale.Rd index d0a1afeec2..c843dc0706 100644 --- a/man/datetime_scale.Rd +++ b/man/datetime_scale.Rd @@ -61,7 +61,9 @@ values between 0 and 1 returns the corresponding output values output }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/discrete_scale.Rd b/man/discrete_scale.Rd index ae349cdf1f..cf76226a67 100644 --- a/man/discrete_scale.Rd +++ b/man/discrete_scale.Rd @@ -60,7 +60,9 @@ the function has two arguments, it will be given the limits and major break positions. }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_binned.Rd b/man/scale_binned.Rd index ad98d61969..f75f8a16f9 100644 --- a/man/scale_binned.Rd +++ b/man/scale_binned.Rd @@ -68,7 +68,9 @@ Note that for position scales, limits are provided after scale expansion. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_continuous.Rd b/man/scale_continuous.Rd index 153bb325f5..5fa4a0fb44 100644 --- a/man/scale_continuous.Rd +++ b/man/scale_continuous.Rd @@ -92,7 +92,9 @@ may choose a slightly different number to ensure nice break labels. Will only have an effect if \code{breaks = waiver()}. Use \code{NULL} to use the default number of breaks given by the transformation.} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_date.Rd b/man/scale_date.Rd index 86c82e0271..bce3946d9a 100644 --- a/man/scale_date.Rd +++ b/man/scale_date.Rd @@ -122,7 +122,9 @@ weeks", or "10 years". If both \code{breaks} and \code{date_breaks} are specified, \code{date_breaks} wins. Valid specifications are 'sec', 'min', 'hour', 'day', 'week', 'month' or 'year', optionally followed by 's'.} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_discrete.Rd b/man/scale_discrete.Rd index 19e1df99fb..d6a3b99378 100644 --- a/man/scale_discrete.Rd +++ b/man/scale_discrete.Rd @@ -76,7 +76,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_gradient.Rd b/man/scale_gradient.Rd index 619e71f3ef..6d0b5c8c15 100644 --- a/man/scale_gradient.Rd +++ b/man/scale_gradient.Rd @@ -129,7 +129,9 @@ break positions. may choose a slightly different number to ensure nice break labels. Will only have an effect if \code{breaks = waiver()}. Use \code{NULL} to use the default number of breaks given by the transformation.} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_grey.Rd b/man/scale_grey.Rd index 0ee97a15de..9d838508dc 100644 --- a/man/scale_grey.Rd +++ b/man/scale_grey.Rd @@ -69,7 +69,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_hue.Rd b/man/scale_hue.Rd index 1280e741bb..0a0aba8fcd 100644 --- a/man/scale_hue.Rd +++ b/man/scale_hue.Rd @@ -75,7 +75,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_linetype.Rd b/man/scale_linetype.Rd index 5707bd9f90..d0b2fb9349 100644 --- a/man/scale_linetype.Rd +++ b/man/scale_linetype.Rd @@ -70,7 +70,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_linewidth.Rd b/man/scale_linewidth.Rd index 86e414a8a6..2efb7378d3 100644 --- a/man/scale_linewidth.Rd +++ b/man/scale_linewidth.Rd @@ -54,7 +54,9 @@ Note that for position scales, limits are provided after scale expansion. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_manual.Rd b/man/scale_manual.Rd index b2723888d4..75677d54d0 100644 --- a/man/scale_manual.Rd +++ b/man/scale_manual.Rd @@ -105,7 +105,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_shape.Rd b/man/scale_shape.Rd index 64f831c75d..4ec9ba9894 100644 --- a/man/scale_shape.Rd +++ b/man/scale_shape.Rd @@ -60,7 +60,9 @@ accepts rlang \link[rlang:as_function]{lambda} function notation. When the function has two arguments, it will be given the limits and major break positions. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_size.Rd b/man/scale_size.Rd index 028d5b8490..0756ed4483 100644 --- a/man/scale_size.Rd +++ b/man/scale_size.Rd @@ -73,7 +73,9 @@ Note that for position scales, limits are provided after scale expansion. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} -\item{labels}{One of: +\item{labels}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the diff --git a/man/scale_steps.Rd b/man/scale_steps.Rd index 1206c159f9..9f6740a561 100644 --- a/man/scale_steps.Rd +++ b/man/scale_steps.Rd @@ -129,7 +129,9 @@ as output (e.g., a function returned by \code{\link[scales:breaks_extended]{scal Note that for position scales, limits are provided after scale expansion. Also accepts rlang \link[rlang:as_function]{lambda} function notation. }} - \item{\code{labels}}{One of: + \item{\code{labels}}{One of the options below. Please note that when \code{labels} is a +vector, it is highly recommended to also set the \code{breaks} argument as a +vector to protect against unintended mismatches. \itemize{ \item \code{NULL} for no labels \item \code{waiver()} for the default labels computed by the From f8d98257fff4e71cb93494db5ca11573779e5c2f Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 12:05:38 +0100 Subject: [PATCH 217/264] Deprecate `fatten` (#6238) * deprecate fatten * `fatten` isn't a formal argument to `geom_boxplot()` * document * add news bullet --- NEWS.md | 2 ++ R/geom-boxplot.R | 9 +++++++++ R/geom-crossbar.R | 11 ++++++++++- R/geom-linerange.R | 6 +++--- R/geom-pointrange.R | 8 +++++++- man/geom_linerange.Rd | 10 +++++----- 6 files changed, 36 insertions(+), 10 deletions(-) diff --git a/NEWS.md b/NEWS.md index c0f7809db6..d8167c66c9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* The `fatten` argument has been deprecated in `geom_boxplot()`, + `geom_crossbar()` and `geom_pointrange()` (@teunbrand, #4881). * Axis labels are now preserved better when using `coord_sf(expand = TRUE)` and graticule lines are straight but do not meet the edge (@teunbrand, #2985). * Attempt to boost detail in `coord_polar()` and `coord_radial()` near the diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R index edd6117538..96c6ed9d35 100644 --- a/R/geom-boxplot.R +++ b/R/geom-boxplot.R @@ -239,6 +239,15 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom, extra_params = c("na.rm", "orientation", "outliers"), setup_params = function(data, params) { + if ("fatten" %in% names(params)) { + deprecate_soft0( + "3.6.0", "geom_boxplot(fatten)", + "geom_boxplot(median.linewidth)" + ) + } else { + # For backward compatibility reasons + params$fatten <- 2 + } params$flipped_aes <- has_flipped_aes(data, params) params }, diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index 7316033de6..8f9d8ccd74 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -17,7 +17,7 @@ geom_crossbar <- function(mapping = NULL, data = NULL, box.color = NULL, box.linetype = NULL, box.linewidth = NULL, - fatten = 2.5, + fatten = deprecated(), na.rm = FALSE, orientation = NA, show.legend = NA, @@ -60,6 +60,15 @@ geom_crossbar <- function(mapping = NULL, data = NULL, #' @export GeomCrossbar <- ggproto("GeomCrossbar", Geom, setup_params = function(data, params) { + if (lifecycle::is_present(params$fatten)) { + deprecate_soft0( + "3.6.0", "geom_crossbar(fatten)", + "geom_crossbar(middle.linewidth)" + ) + } else { + # For backward compatibility reasons + params$fatten <- 2.5 + } GeomErrorbar$setup_params(data, params) }, diff --git a/R/geom-linerange.R b/R/geom-linerange.R index 085d8f98a9..71c0799971 100644 --- a/R/geom-linerange.R +++ b/R/geom-linerange.R @@ -6,9 +6,9 @@ #' @eval rd_orientation() #' #' @eval rd_aesthetics("geom", "linerange", "Note that `geom_pointrange()` also understands `size` for the size of the points.") -#' @param fatten A multiplicative factor used to increase the size of the -#' middle bar in `geom_crossbar()` and the middle point in -#' `geom_pointrange()`. +#' @param fatten `r lifecycle::badge("deprecated")` A multiplicative factor +#' used to increase the size of the middle bar in `geom_crossbar()` and the +#' middle point in `geom_pointrange()`. #' @seealso #' [stat_summary()] for examples of these guys in use, #' [geom_smooth()] for continuous analogue diff --git a/R/geom-pointrange.R b/R/geom-pointrange.R index d0e5194311..1943bb4f4c 100644 --- a/R/geom-pointrange.R +++ b/R/geom-pointrange.R @@ -3,7 +3,7 @@ geom_pointrange <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity", ..., - fatten = 4, + fatten = deprecated(), na.rm = FALSE, orientation = NA, show.legend = NA, @@ -42,6 +42,12 @@ GeomPointrange <- ggproto("GeomPointrange", Geom, required_aes = c("x", "y", "ymin|xmin", "ymax|xmax"), setup_params = function(data, params) { + if (lifecycle::is_present(params$fatten)) { + deprecate_soft0("3.6.0", "geom_pointrange(fatten)", I("the `size` aesthetic")) + } else { + # For backward compatibility reasons + params$fatten <- 4 + } GeomLinerange$setup_params(data, params) }, diff --git a/man/geom_linerange.Rd b/man/geom_linerange.Rd index 93f340656e..0c77084236 100644 --- a/man/geom_linerange.Rd +++ b/man/geom_linerange.Rd @@ -23,7 +23,7 @@ geom_crossbar( box.color = NULL, box.linetype = NULL, box.linewidth = NULL, - fatten = 2.5, + fatten = deprecated(), na.rm = FALSE, orientation = NA, show.legend = NA, @@ -72,7 +72,7 @@ geom_pointrange( stat = "identity", position = "identity", ..., - fatten = 4, + fatten = deprecated(), na.rm = FALSE, orientation = NA, show.legend = NA, @@ -160,9 +160,9 @@ data's aesthetics.} \item{box.colour, box.color, box.linetype, box.linewidth}{Default aesthetics for the boxes. Set to \code{NULL} to inherit from the data's aesthetics.} -\item{fatten}{A multiplicative factor used to increase the size of the -middle bar in \code{geom_crossbar()} and the middle point in -\code{geom_pointrange()}.} +\item{fatten}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} A multiplicative factor +used to increase the size of the middle bar in \code{geom_crossbar()} and the +middle point in \code{geom_pointrange()}.} \item{na.rm}{If \code{FALSE}, the default, missing values are removed with a warning. If \code{TRUE}, missing values are silently removed.} From 12d1c98fd4efd60f05d0e50409c2244c701255b9 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 12:06:11 +0100 Subject: [PATCH 218/264] Document guide theme argument (#6268) * mention ignored arguments * No need to fuss over these specifics with axes * document --- R/guide-axis.R | 3 +++ R/guide-legend.R | 6 +++++- man/guide_axis.Rd | 2 +- man/guide_axis_logticks.Rd | 2 +- man/guide_axis_stack.Rd | 2 +- man/guide_axis_theta.Rd | 2 +- man/guide_bins.Rd | 6 +++++- man/guide_colourbar.Rd | 6 +++++- man/guide_coloursteps.Rd | 6 +++++- man/guide_custom.Rd | 6 +++++- man/guide_legend.Rd | 6 +++++- 11 files changed, 37 insertions(+), 10 deletions(-) diff --git a/R/guide-axis.R b/R/guide-axis.R index 70ac3da43f..d445900071 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -6,6 +6,9 @@ #' [scale_(x|y)_discrete()][scale_x_discrete()]. #' #' @inheritParams guide_legend +#' @param theme A [`theme`][theme()] object to style the guide individually or +#' differently from the plot's theme settings. The `theme` argument in the +#' guide partially overrides, and is combined with, the plot's theme. #' @param check.overlap silently remove overlapping labels, #' (recursively) prioritizing the first, last, and middle labels. #' @param angle Compared to setting the angle in [theme()] / [element_text()], diff --git a/R/guide-legend.R b/R/guide-legend.R index 9355ae5a70..b875fa1950 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -15,7 +15,11 @@ #' specified in [labs()] is used for the title. #' @param theme A [`theme`][theme()] object to style the guide individually or #' differently from the plot's theme settings. The `theme` argument in the -#' guide overrides, and is combined with, the plot's theme. +#' guide partially overrides, and is combined with, the plot's theme. +#' Arguments that apply to a single legend are respected, most of which have +#' the `legend`-prefix. Arguments that apply to combined legends +#' (the legend box) are ignored, including `legend.position`, +#' `legend.justification.*`, `legend.location` and `legend.box.*`. #' @param position A character string indicating where the legend should be #' placed relative to the plot panels. #' @param direction A character string indicating the direction of the guide. diff --git a/man/guide_axis.Rd b/man/guide_axis.Rd index 4d4ba4f166..baf05cebe6 100644 --- a/man/guide_axis.Rd +++ b/man/guide_axis.Rd @@ -24,7 +24,7 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme.} \item{check.overlap}{silently remove overlapping labels, (recursively) prioritizing the first, last, and middle labels.} diff --git a/man/guide_axis_logticks.Rd b/man/guide_axis_logticks.Rd index b6f7d55737..7398f24890 100644 --- a/man/guide_axis_logticks.Rd +++ b/man/guide_axis_logticks.Rd @@ -51,7 +51,7 @@ and \code{FALSE} are shorthand for \code{"both"} and \code{"none"} respectively. \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme.} \item{prescale_base, negative_small, short_theme}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} diff --git a/man/guide_axis_stack.Rd b/man/guide_axis_stack.Rd index 4a18fc3fdb..542f4eb44b 100644 --- a/man/guide_axis_stack.Rd +++ b/man/guide_axis_stack.Rd @@ -30,7 +30,7 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme.} \item{spacing}{A \code{\link[=unit]{unit()}} objects that determines how far separate guides are spaced apart.} diff --git a/man/guide_axis_theta.Rd b/man/guide_axis_theta.Rd index 6e18e57a60..79f4b61cad 100644 --- a/man/guide_axis_theta.Rd +++ b/man/guide_axis_theta.Rd @@ -22,7 +22,7 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme.} \item{angle}{Compared to setting the angle in \code{\link[=theme]{theme()}} / \code{\link[=element_text]{element_text()}}, this also uses some heuristics to automatically pick the \code{hjust} and \code{vjust} that diff --git a/man/guide_bins.Rd b/man/guide_bins.Rd index 8ee5311445..d9fd873cdb 100644 --- a/man/guide_bins.Rd +++ b/man/guide_bins.Rd @@ -25,7 +25,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme. +Arguments that apply to a single legend are respected, most of which have +the \code{legend}-prefix. Arguments that apply to combined legends +(the legend box) are ignored, including \code{legend.position}, +\verb{legend.justification.*}, \code{legend.location} and \verb{legend.box.*}.} \item{angle}{Overrules the theme settings to automatically apply appropriate \code{hjust} and \code{vjust} for angled legend text. Can be a single number diff --git a/man/guide_colourbar.Rd b/man/guide_colourbar.Rd index 9a441f39cc..95546aa21c 100644 --- a/man/guide_colourbar.Rd +++ b/man/guide_colourbar.Rd @@ -49,7 +49,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme. +Arguments that apply to a single legend are respected, most of which have +the \code{legend}-prefix. Arguments that apply to combined legends +(the legend box) are ignored, including \code{legend.position}, +\verb{legend.justification.*}, \code{legend.location} and \verb{legend.box.*}.} \item{nbin}{A numeric specifying the number of bins for drawing the colourbar. A smoother colourbar results from a larger value.} diff --git a/man/guide_coloursteps.Rd b/man/guide_coloursteps.Rd index 5bec4a8d73..dc5806929a 100644 --- a/man/guide_coloursteps.Rd +++ b/man/guide_coloursteps.Rd @@ -43,7 +43,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme. +Arguments that apply to a single legend are respected, most of which have +the \code{legend}-prefix. Arguments that apply to combined legends +(the legend box) are ignored, including \code{legend.position}, +\verb{legend.justification.*}, \code{legend.location} and \verb{legend.box.*}.} \item{alpha}{A numeric between 0 and 1 setting the colour transparency of the bar. Use \code{NA} to preserve the alpha encoded in the colour itself diff --git a/man/guide_custom.Rd b/man/guide_custom.Rd index 74c8a9f00a..f13559cae2 100644 --- a/man/guide_custom.Rd +++ b/man/guide_custom.Rd @@ -25,7 +25,11 @@ If \code{NULL} (default), no title is shown.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme. +Arguments that apply to a single legend are respected, most of which have +the \code{legend}-prefix. Arguments that apply to combined legends +(the legend box) are ignored, including \code{legend.position}, +\verb{legend.justification.*}, \code{legend.location} and \verb{legend.box.*}.} \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} diff --git a/man/guide_legend.Rd b/man/guide_legend.Rd index 67465c9877..366005c99f 100644 --- a/man/guide_legend.Rd +++ b/man/guide_legend.Rd @@ -25,7 +25,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} \item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or differently from the plot's theme settings. The \code{theme} argument in the -guide overrides, and is combined with, the plot's theme.} +guide partially overrides, and is combined with, the plot's theme. +Arguments that apply to a single legend are respected, most of which have +the \code{legend}-prefix. Arguments that apply to combined legends +(the legend box) are ignored, including \code{legend.position}, +\verb{legend.justification.*}, \code{legend.location} and \verb{legend.box.*}.} \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} From 09776db1488a85f370b0203b20e64fea660ef11d Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 12:44:13 +0100 Subject: [PATCH 219/264] =?UTF-8?q?=F0=9F=90=9B=20Deal=20with=20empty=20ra?= =?UTF-8?q?dial=20axes=20=20(#6272)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Avoid assigning NULL to list, thereby deleting the element * protect theta guide better against empty keys * add test * add news bullet * Fix partial match * fix another partial match --- NEWS.md | 2 ++ R/coord-radial.R | 40 ++++++++++++++++++------------- R/guide-axis-theta.R | 26 +++++++++++--------- R/guides-.R | 6 ++--- tests/testthat/test-coord-polar.R | 12 ++++++++++ 5 files changed, 56 insertions(+), 30 deletions(-) diff --git a/NEWS.md b/NEWS.md index d8167c66c9..3090a3fa3b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* `coord_radial()` now displays no axis instead of throwing an error when + a scale has no breaks (@teunbrand, #6271). * The `fatten` argument has been deprecated in `geom_boxplot()`, `geom_crossbar()` and `geom_pointrange()` (@teunbrand, #4881). * Axis labels are now preserved better when using `coord_sf(expand = TRUE)` and diff --git a/R/coord-radial.R b/R/coord-radial.R index ef6130fb34..bc933ea1d7 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -250,11 +250,18 @@ CoordRadial <- ggproto("CoordRadial", Coord, names(gdefs) <- aesthetics # Train theta guide - for (t in intersect(c("theta", "theta.sec"), aesthetics[!empty])) { - gdefs[[t]] <- guides[[t]]$train(gdefs[[t]], panel_params[[t]]) - gdefs[[t]] <- guides[[t]]$transform(gdefs[[t]], self, panel_params) - gdefs[[t]] <- guides[[t]]$get_layer_key(gdefs[[t]], layers) - } + t <- intersect(c("theta", "theta.sec"), aesthetics[!empty]) + gdefs[t] <- Map( + function(guide, guide_param, scale) { + guide_param$theme_suffix <- "theta" + guide_param <- guide$train(guide_param, scale) + guide_param <- guide$transform(guide_param, self, panel_params) + guide_param <- guide$get_layer_key(guide_param, layers) + }, + guide = guides[t], + guide_param = gdefs[t], + scale = panel_params[t] + ) if (!isFALSE(self$r_axis_inside)) { # For radial axis, we need to pretend that rotation starts at 0 and @@ -269,17 +276,18 @@ CoordRadial <- ggproto("CoordRadial", Coord, temp <- modify_list(panel_params, mod) # Train radial guide - for (r in intersect(c("r", "r.sec"), aesthetics[!empty])) { - gdefs[[r]] <- guides[[r]]$train(gdefs[[r]], panel_params[[r]]) - gdefs[[r]] <- guides[[r]]$transform(gdefs[[r]], self, temp) # Use temp - gdefs[[r]] <- guides[[r]]$get_layer_key(gdefs[[r]], layers) - } - - # Set theme suffixes - gdefs$theta$theme_suffix <- "theta" - gdefs$theta.sec$theme_suffix <- "theta" - gdefs$r$theme_suffix <- "r" - gdefs$r.sec$theme_suffix <- "r" + r <- intersect(c("r", "r.sec"), aesthetics[!empty]) + gdefs[r] <- Map( + function(guide, guide_param, scale) { + guide_param$theme_suffix <- "r" + guide_param <- guide$train(guide_param, scale) + guide_param <- guide$transform(guide_param, self, temp) + guide_param <- guide$get_layer_key(guide_param, layers) + }, + guide = guides[r], + guide_param = gdefs[r], + scale = panel_params[r] + ) panel_params$guides$update_params(gdefs) panel_params diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index 7f4c3c9246..af96a337b6 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -63,22 +63,26 @@ GuideAxisTheta <- ggproto( transform = function(params, coord, panel_params) { - opposite_var <- setdiff(c("x", "y"), params$aesthetic) - opposite_value <- switch(params$position, top = , right = , theta.sec = -Inf, Inf) - if (is.unsorted(panel_params$inner_radius %||% NA)) { - opposite_value <- -opposite_value - } - if (nrow(params$key) > 0) { - params$key[[opposite_var]] <- opposite_value - } - if (nrow(params$decor) > 0) { - params$decor[[opposite_var]] <- opposite_value + position <- params$position + + if (!is.null(position)) { + opposite_var <- setdiff(c("x", "y"), params$aesthetic) + opposite_value <- switch(position, top = , right = , theta.sec = -Inf, Inf) + if (is.unsorted(panel_params$inner_radius %||% NA)) { + opposite_value <- -opposite_value + } + if (nrow(params$key) > 0) { + params$key[[opposite_var]] <- opposite_value + } + if (nrow(params$decor) > 0) { + params$decor[[opposite_var]] <- opposite_value + } } params <- GuideAxis$transform(params, coord, panel_params) key <- params$key - n <- nrow(key) + n <- vec_size(key) if (n < 1) { return(params) } diff --git a/R/guides-.R b/R/guides-.R index 63a17cc430..3ea09c7104 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -525,7 +525,7 @@ Guides <- ggproto( coord <- coord %||% default_inside_position %||% just groups$justs[[i]] <- just - groups$coord[[i]] <- coord + groups$coords[[i]] <- coord } groups <- vec_group_loc(vec_slice(groups, keep)) @@ -540,10 +540,10 @@ Guides <- ggproto( # prepare output for (i in vec_seq_along(groups)) { adjust <- NULL - position <- groups$key$position[i] + position <- groups$key$positions[i] if (position == "inside") { adjust <- theme( - legend.position.inside = groups$key$coord[[i]], + legend.position.inside = groups$key$coords[[i]], legend.justification.inside = groups$key$justs[[i]] ) } diff --git a/tests/testthat/test-coord-polar.R b/tests/testthat/test-coord-polar.R index 1f662d2322..466162b0f5 100644 --- a/tests/testthat/test-coord-polar.R +++ b/tests/testthat/test-coord-polar.R @@ -197,6 +197,18 @@ test_that("radial coords can be reversed", { expect_equal(as.numeric(fwd$y), rev(as.numeric(rev$y))) }) +test_that("coord_radial can deal with empty breaks (#6271)", { + p <- ggplot_build( + ggplot(mtcars, aes(mpg, disp)) + + geom_point() + + coord_radial() + + scale_x_continuous(breaks = numeric()) + + scale_y_continuous(breaks = numeric()) + ) + guides <- p$layout$panel_params[[1]]$guides$guides + is_none <- vapply(guides, inherits, logical(1), what = "GuideNone") + expect_true(all(is_none)) +}) # Visual tests ------------------------------------------------------------ From b9d1c79da0f59405ffef2279ebe44b18a8dad697 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 12:44:59 +0100 Subject: [PATCH 220/264] =?UTF-8?q?=E2=9C=A8=20Justification=20for=20legen?= =?UTF-8?q?d=20keys=20(#6279)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * combine glyph layers into a single key earlier * new `key.justification` theme element * apply key justification * add test * add news bullet --- NEWS.md | 2 + R/guide-legend.R | 54 +++++-- R/theme-elements.R | 1 + R/theme.R | 5 + man/theme.Rd | 6 + .../guide-legend/legend-key-justification.svg | 136 ++++++++++++++++++ tests/testthat/test-guide-legend.R | 16 +++ 7 files changed, 205 insertions(+), 15 deletions(-) create mode 100644 tests/testthat/_snaps/guide-legend/legend-key-justification.svg diff --git a/NEWS.md b/NEWS.md index 3090a3fa3b..d38fbc670d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -292,6 +292,8 @@ particularly for data-points with a low radius near the center (@teunbrand, #5023). * All scales now expose the `aesthetics` parameter (@teunbrand, #5841) +* New `theme(legend.key.justification)` to control the alignment of legend keys + (@teunbrand, #3669). # ggplot2 3.5.1 diff --git a/R/guide-legend.R b/R/guide-legend.R index b875fa1950..c8bf395f0a 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -178,6 +178,7 @@ GuideLegend <- ggproto( key = "legend.key", key_height = "legend.key.height", key_width = "legend.key.width", + key_just = "legend.key.justification", text = "legend.text", theme.title = "legend.title", spacing_x = "legend.key.spacing.x", @@ -275,7 +276,6 @@ GuideLegend <- ggproto( c("horizontal", "vertical"), arg_nm = "direction" ) params$n_breaks <- n_breaks <- nrow(params$key) - params$n_key_layers <- length(params$decor) + 1 # +1 is key background # Resolve shape if (!is.null(params$nrow) && !is.null(params$ncol) && @@ -378,6 +378,9 @@ GuideLegend <- ggproto( elements$key <- ggname("legend.key", element_grob(elements$key)) } + if (!is.null(elements$key_just)) { + elements$key_just <- valid.just(elements$key_just) + } elements$text <- label_angle_heuristic(elements$text, elements$text_position, params$angle) @@ -391,22 +394,39 @@ GuideLegend <- ggproto( build_decor = function(decor, grobs, elements, params) { - key_size <- c(elements$width_cm, elements$height_cm) * 10 - - draw <- function(i) { - bg <- elements$key - keys <- lapply(decor, function(g) { - data <- vec_slice(g$data, i) - if (data$.draw %||% TRUE) { - key <- g$draw_key(data, g$params, key_size) - set_key_size(key, data$linewidth, data$size, key_size / 10) - } else { - zeroGrob() + key_size <- c(elements$width_cm, elements$height_cm) + just <- elements$key_just + idx <- seq_len(params$n_breaks) + + key_glyphs <- lapply(idx, function(i) { + glyph <- lapply(decor, function(dec) { + data <- vec_slice(dec$data, i) + if (!(data$.draw %||% TRUE)) { + return(zeroGrob()) } + key <- dec$draw_key(data, dec$params, key_size * 10) + set_key_size(key, data$linewidth, data$size, key_size) }) - c(list(bg), keys) - } - unlist(lapply(seq_len(params$n_breaks), draw), FALSE) + + width <- vapply(glyph, get_attr, which = "width", default = 0, numeric(1)) + width <- max(width, 0, key_size[1], na.rm = TRUE) + height <- vapply(glyph, get_attr, which = "height", default = 0, numeric(1)) + height <- max(height, 0, key_size[2], na.rm = TRUE) + + vp <- NULL + if (!is.null(just)) { + vp <- viewport( + x = just[1], y = just[2], just = just, + width = unit(width, "cm"), height = unit(height, "cm") + ) + } + + grob <- gTree(children = inject(gList(elements$key, !!!glyph)), vp = vp) + attr(grob, "width") <- width + attr(grob, "height") <- height + grob + }) + key_glyphs }, build_labels = function(key, elements, params) { @@ -795,3 +815,7 @@ deprecated_guide_args <- function( } theme } + +get_attr <- function(x, which, exact = TRUE, default = NULL) { + attr(x, which = which, exact = exact) %||% default +} diff --git a/R/theme-elements.R b/R/theme-elements.R index b83822ed3a..833da1b192 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -625,6 +625,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { legend.key.spacing = el_def(c("unit", "rel"), "spacing"), legend.key.spacing.x = el_def(c("unit", "rel"), "legend.key.spacing"), legend.key.spacing.y = el_def(c("unit", "rel"), "legend.key.spacing"), + legend.key.justification = el_def(c("character", "numeric", "integer")), legend.frame = el_def("element_rect", "rect"), legend.axis.line = el_def("element_line", "line"), legend.ticks = el_def("element_line", "legend.axis.line"), diff --git a/R/theme.R b/R/theme.R index cb7859dfe2..bf65c565a9 100644 --- a/R/theme.R +++ b/R/theme.R @@ -84,6 +84,10 @@ #' between legend keys given as a `unit`. Spacing in the horizontal (x) and #' vertical (y) direction inherit from `legend.key.spacing` or can be #' specified separately. `legend.key.spacing` inherits from `spacing`. +#' @param legend.key.justification Justification for positioning legend keys +#' when more space is available than needed for display. The default, `NULL`, +#' stretches keys into the available space. Can be a location like `"center"` +#' or `"top"`, or a two-element numeric vector. #' @param legend.frame frame drawn around the bar ([element_rect()]). #' @param legend.ticks tick marks shown along bars or axes ([element_line()]) #' @param legend.ticks.length length of tick marks in legend @@ -393,6 +397,7 @@ theme <- function(..., legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y, + legend.key.justification, legend.frame, legend.ticks, legend.ticks.length, diff --git a/man/theme.Rd b/man/theme.Rd index 51f92e1f96..0a4941266e 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -84,6 +84,7 @@ theme( legend.key.spacing, legend.key.spacing.x, legend.key.spacing.y, + legend.key.justification, legend.frame, legend.ticks, legend.ticks.length, @@ -229,6 +230,11 @@ between legend keys given as a \code{unit}. Spacing in the horizontal (x) and vertical (y) direction inherit from \code{legend.key.spacing} or can be specified separately. \code{legend.key.spacing} inherits from \code{spacing}.} +\item{legend.key.justification}{Justification for positioning legend keys +when more space is available than needed for display. The default, \code{NULL}, +stretches keys into the available space. Can be a location like \code{"center"} +or \code{"top"}, or a two-element numeric vector.} + \item{legend.frame}{frame drawn around the bar (\code{\link[=element_rect]{element_rect()}}).} \item{legend.ticks}{tick marks shown along bars or axes (\code{\link[=element_line]{element_line()}})} diff --git a/tests/testthat/_snaps/guide-legend/legend-key-justification.svg b/tests/testthat/_snaps/guide-legend/legend-key-justification.svg new file mode 100644 index 0000000000..25880c7d29 --- /dev/null +++ b/tests/testthat/_snaps/guide-legend/legend-key-justification.svg @@ -0,0 +1,136 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +100 +200 +300 +400 + + + + + + + + + + +10 +15 +20 +25 +30 +35 +mpg +disp + +drat + + + + + + +3 +4 +5 + +factor(cyl) + + + + + + +one line +up +to +four +lines +up +to +five +whole +lines +legend key justification + + diff --git a/tests/testthat/test-guide-legend.R b/tests/testthat/test-guide-legend.R index d4a47c145e..c68ab03297 100644 --- a/tests/testthat/test-guide-legend.R +++ b/tests/testthat/test-guide-legend.R @@ -212,3 +212,19 @@ test_that("legend.byrow works in `guide_legend()`", { expect_doppelganger("legend.byrow = TRUE", p) }) +test_that("legend.key.justification works as intended", { + + p <- ggplot(mtcars, aes(mpg, disp, colour = factor(cyl), size = drat)) + + geom_point() + + scale_size_continuous( + range = c(0, 20), breaks = c(3, 4, 5), limits = c(2.5, 5) + ) + + scale_colour_discrete( + labels = c("one line", "up\nto\nfour\nlines", "up\nto\nfive\nwhole\nlines") + ) + + theme(legend.key.justification = c(1, 0)) + + expect_doppelganger("legend key justification", p) + +}) + From a85c6a268699721e3fbb12e53b08a3d82c89c272 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:18:35 +0100 Subject: [PATCH 221/264] =?UTF-8?q?=F0=9F=A9=B9=20Turn=20off=20`size`=20fa?= =?UTF-8?q?llback=20from=20`GeomBar`=20(#6281)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * turn off `size` fallback mechanism * add news bullet --- NEWS.md | 2 ++ R/geom-bar.R | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index d38fbc670d..1419f620be 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Turned off fallback for `size` to `linewidth` translation in + `geom_bar()`/`geom_col()` (#4848). * `coord_radial()` now displays no axis instead of throwing an error when a scale has no breaks (@teunbrand, #6271). * The `fatten` argument has been deprecated in `geom_boxplot()`, diff --git a/R/geom-bar.R b/R/geom-bar.R index 19c86dfbb1..b0901502d9 100644 --- a/R/geom-bar.R +++ b/R/geom-bar.R @@ -155,5 +155,5 @@ GeomBar <- ggproto("GeomBar", GeomRect, flip_data(data, params$flipped_aes) }, - rename_size = TRUE + rename_size = FALSE ) From f2ad9484b2c92fee84a002ba12898510cb7ec4da Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:19:10 +0100 Subject: [PATCH 222/264] =?UTF-8?q?=F0=9F=93=9D=20Mention=20(`fill=5F`)`al?= =?UTF-8?q?pha()`=20in=20theme=20element=20docs=20(#6283)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * mention alpha/fill_alpha in params * sprinkle comments in examples --- R/theme-elements.R | 8 +++++++- man/element.Rd | 10 ++++++++-- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/R/theme-elements.R b/R/theme-elements.R index 833da1b192..7d3ceb47dd 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -14,8 +14,10 @@ #' `margin()`, `margin_part()` and `margin_auto()` are all used to specify the #' margins of elements. #' -#' @param fill Fill colour. +#' @param fill Fill colour. `fill_alpha()` can be used to set the transparency +#' of the fill. #' @param colour,color Line/border colour. Color is an alias for colour. +#' `alpha()` can be used to set the transparency of the colour. #' @param linewidth,borderwidth Line/border size in mm. #' @param size,fontsize text size in pts. #' @param arrow.fill Fill colour for arrows. @@ -26,17 +28,21 @@ #' calculating final element state. #' @return An S3 object of class `element`, `rel`, or `margin`. #' @examples +#' # A standard plot #' plot <- ggplot(mpg, aes(displ, hwy)) + geom_point() #' +#' # Turning off theme elements by setting them to blank #' plot + theme( #' panel.background = element_blank(), #' axis.text = element_blank() #' ) #' +#' # Text adjustments #' plot + theme( #' axis.text = element_text(colour = "red", size = rel(1.5)) #' ) #' +#' # Turning on the axis line with an arrow #' plot + theme( #' axis.line = element_line(arrow = arrow()) #' ) diff --git a/man/element.Rd b/man/element.Rd index c43fadfed2..041bf794f5 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -74,9 +74,11 @@ margin_part(t = NA, r = NA, b = NA, l = NA, unit = "pt") margin_auto(t = 0, r = t, b = t, l = r, unit = "pt") } \arguments{ -\item{fill}{Fill colour.} +\item{fill}{Fill colour. \code{fill_alpha()} can be used to set the transparency +of the fill.} -\item{colour, color}{Line/border colour. Color is an alias for colour.} +\item{colour, color}{Line/border colour. Color is an alias for colour. +\code{alpha()} can be used to set the transparency of the colour.} \item{linewidth, borderwidth}{Line/border size in mm.} @@ -155,17 +157,21 @@ specify the display of how non-data components of the plot are drawn. margins of elements. } \examples{ +# A standard plot plot <- ggplot(mpg, aes(displ, hwy)) + geom_point() +# Turning off theme elements by setting them to blank plot + theme( panel.background = element_blank(), axis.text = element_blank() ) +# Text adjustments plot + theme( axis.text = element_text(colour = "red", size = rel(1.5)) ) +# Turning on the axis line with an arrow plot + theme( axis.line = element_line(arrow = arrow()) ) From f82879419f93b192cf2d0a4040ece2dafb0d6f16 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:25:24 +0100 Subject: [PATCH 223/264] =?UTF-8?q?=E2=9C=A8=20Using=20date=20breaks/minor?= =?UTF-8?q?=20breaks/labels=20in=20time=20scales.=20(#6282)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Allow `transform = "hms"` in `datetime_scale()` * add date arguments to time scales * use `datetime_scale()` in time scales * allow for additional underscore args * inherit position scale * `label_time()` can handle both *and* classes * add test * add news bullet * redocument * work in a skip * Revert "`label_time()` can handle both *and* classes" This reverts commit adcd2cb13ee94048af044e46a9abe832dac6ff9c. * separate labelling logic --- NEWS.md | 2 + R/scale-date.R | 56 +++++++++++++------ man/scale_date.Rd | 6 ++ tests/testthat/_snaps/prohibited-functions.md | 6 +- tests/testthat/test-scale-date.R | 14 +++++ 5 files changed, 65 insertions(+), 19 deletions(-) diff --git a/NEWS.md b/NEWS.md index 1419f620be..c8abcc17de 100644 --- a/NEWS.md +++ b/NEWS.md @@ -296,6 +296,8 @@ * All scales now expose the `aesthetics` parameter (@teunbrand, #5841) * New `theme(legend.key.justification)` to control the alignment of legend keys (@teunbrand, #3669). +* Added `scale_{x/y}_time(date_breaks, date_minor_breaks, date_labels)` + (@teunbrand, #4335). # ggplot2 3.5.1 diff --git a/R/scale-date.R b/R/scale-date.R index dff564e71e..e518c7ac11 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -223,8 +223,11 @@ scale_y_datetime <- function(name = waiver(), #' @rdname scale_date scale_x_time <- function(name = waiver(), breaks = waiver(), + date_breaks = waiver(), minor_breaks = waiver(), + date_minor_breaks = waiver(), labels = waiver(), + date_labels = waiver(), limits = NULL, expand = waiver(), oob = censor, @@ -233,20 +236,25 @@ scale_x_time <- function(name = waiver(), position = "bottom", sec.axis = waiver()) { - scale_x_continuous( + sc <- datetime_scale( + ggplot_global$x_aes, + "hms", name = name, + palette = identity, breaks = breaks, + date_breaks = date_breaks, labels = labels, + date_labels = date_labels, minor_breaks = minor_breaks, + date_minor_breaks = date_minor_breaks, + guide = guide, limits = limits, expand = expand, oob = oob, - na.value = na.value, - guide = guide, - position = position, - transform = scales::transform_hms(), - sec.axis = sec.axis + position = position ) + + set_sec_axis(sec.axis, sc) } @@ -254,8 +262,11 @@ scale_x_time <- function(name = waiver(), #' @export scale_y_time <- function(name = waiver(), breaks = waiver(), + date_breaks = waiver(), minor_breaks = waiver(), + date_minor_breaks = waiver(), labels = waiver(), + date_labels = waiver(), limits = NULL, expand = waiver(), oob = censor, @@ -264,20 +275,25 @@ scale_y_time <- function(name = waiver(), position = "left", sec.axis = waiver()) { - scale_y_continuous( + sc <- datetime_scale( + ggplot_global$y_aes, + "hms", name = name, + palette = identity, breaks = breaks, + date_breaks = date_breaks, labels = labels, + date_labels = date_labels, minor_breaks = minor_breaks, + date_minor_breaks = date_minor_breaks, + guide = guide, limits = limits, expand = expand, oob = oob, - na.value = na.value, - guide = guide, - position = position, - transform = scales::transform_hms(), - sec.axis = sec.axis + position = position ) + + set_sec_axis(sec.axis, sc) } #' Date/time scale constructor @@ -312,9 +328,13 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), } if (!is.waiver(date_labels)) { check_string(date_labels) - labels <- function(self, x) { - tz <- self$timezone %||% "UTC" - label_date(date_labels, tz)(x) + if (transform == "hms") { + labels <- label_time(date_labels) + } else { + labels <- function(self, x) { + tz <- self$timezone %||% "UTC" + label_date(date_labels, tz)(x) + } } } @@ -324,7 +344,8 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), scale_class <- switch( transform, date = ScaleContinuousDate, - time = ScaleContinuousDatetime + time = ScaleContinuousDatetime, + ScaleContinuousPosition ) } else { scale_class <- ScaleContinuous @@ -332,7 +353,8 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), transform <- switch(transform, date = transform_date(), - time = transform_time(timezone) + time = transform_time(timezone), + hms = transform_hms() ) sc <- continuous_scale( diff --git a/man/scale_date.Rd b/man/scale_date.Rd index bce3946d9a..9eb6643130 100644 --- a/man/scale_date.Rd +++ b/man/scale_date.Rd @@ -78,8 +78,11 @@ scale_y_datetime( scale_x_time( name = waiver(), breaks = waiver(), + date_breaks = waiver(), minor_breaks = waiver(), + date_minor_breaks = waiver(), labels = waiver(), + date_labels = waiver(), limits = NULL, expand = waiver(), oob = censor, @@ -92,8 +95,11 @@ scale_x_time( scale_y_time( name = waiver(), breaks = waiver(), + date_breaks = waiver(), minor_breaks = waiver(), + date_minor_breaks = waiver(), labels = waiver(), + date_labels = waiver(), limits = NULL, expand = waiver(), oob = censor, diff --git a/tests/testthat/_snaps/prohibited-functions.md b/tests/testthat/_snaps/prohibited-functions.md index 4612a484bf..34e58d5d14 100644 --- a/tests/testthat/_snaps/prohibited-functions.md +++ b/tests/testthat/_snaps/prohibited-functions.md @@ -143,7 +143,8 @@ [4] "date_minor_breaks" $scale_x_time - [1] "minor_breaks" + [1] "date_breaks" "minor_breaks" "date_minor_breaks" + [4] "date_labels" $scale_y_continuous [1] "minor_breaks" @@ -157,7 +158,8 @@ [4] "date_minor_breaks" $scale_y_time - [1] "minor_breaks" + [1] "date_breaks" "minor_breaks" "date_minor_breaks" + [4] "date_labels" $sf_transform_xy [1] "target_crs" "source_crs" "authority_compliant" diff --git a/tests/testthat/test-scale-date.R b/tests/testthat/test-scale-date.R index a90d203eba..48259e3261 100644 --- a/tests/testthat/test-scale-date.R +++ b/tests/testthat/test-scale-date.R @@ -47,6 +47,20 @@ test_that("not cached across calls", { expect_equal(get_panel_scales(p2)$x$timezone, "Australia/Lord_Howe") }) +test_that("time scale date breaks and labels work", { + skip_if_not_installed("hms") + + d <- c(base_time(), base_time() + 5 * 24 * 3600) - base_time() + + sc <- scale_x_time(date_breaks = "1 day", date_labels = "%d") + sc$train(d) + + breaks <- sc$get_breaks() + expect_length(breaks, 6) + labels <- sc$get_labels(breaks) + expect_equal(labels, paste0("0", 1:6)) +}) + test_that("datetime size scales work", { p <- ggplot(df, aes(y = y)) + geom_point(aes(time1, size = time1)) From aeaed9a4896b1315410c7df26ba44e0641f49f89 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:26:32 +0100 Subject: [PATCH 224/264] =?UTF-8?q?=F0=9F=9A=91=20Fix=20for=20revdep=20pro?= =?UTF-8?q?blem=20with=20adding=20`NULL`=20to=20theme=20(#6296)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * use `add_theme()` directly * fallback for invalid `legend.position` --- R/guides-.R | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/R/guides-.R b/R/guides-.R index 3ea09c7104..44ed7fb383 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -480,7 +480,7 @@ Guides <- ggproto( if (length(default_position) == 2) { default_position <- "inside" } - if (default_position == "none") { + if (!default_position %in% c(.trbl, "inside")) { return(zeroGrob()) } @@ -547,7 +547,8 @@ Guides <- ggproto( legend.justification.inside = groups$key$justs[[i]] ) } - grobs[[i]] <- self$package_box(grobs[[i]], position, theme + adjust) + adjust <- add_theme(theme, adjust, "internal theme settings") + grobs[[i]] <- self$package_box(grobs[[i]], position, adjust) } # merge inside grobs into single gtable @@ -598,11 +599,7 @@ Guides <- ggproto( } # Determine default direction - direction <- switch( - position, - inside = , left = , right = "vertical", - top = , bottom = "horizontal" - ) + direction <- switch(position, top = , bottom = "horizontal", "vertical") # Populate missing theme arguments theme$legend.box <- theme$legend.box %||% direction From 8ef9c6ef3d3b9e26c862829f8cf6a0821b46c190 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:26:54 +0100 Subject: [PATCH 225/264] replace `vec_slice()` (#6297) --- R/facet-grid-.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/facet-grid-.R b/R/facet-grid-.R index be11524541..ff5cdf0d81 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -309,7 +309,9 @@ FacetGrid <- ggproto("FacetGrid", Facet, params$margins ) # Apply recycling on original data to fit margins - data <- vec_slice(data, facet_vals$.index) + # We're using base subsetting here because `data` might have a superclass + # that isn't handled well by vctrs::vec_slice + data <- data[facet_vals$.index, , drop = FALSE] facet_vals$.index <- NULL } From 66d6ee422e450ba7e6c050a8ea90db257bc93649 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 13:27:38 +0100 Subject: [PATCH 226/264] repair names that might have become lost (#6298) --- R/plot-construction.R | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/R/plot-construction.R b/R/plot-construction.R index b021b630e9..cd18fc8310 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -195,13 +195,20 @@ ggplot_add.by <- function(object, plot, object_name) { #' @export ggplot_add.Layer <- function(object, plot, object_name) { - layers_names <- new_layer_names(object, names(plot$layers)) + layers_names <- new_layer_names(object, names2(plot$layers)) plot$layers <- append(plot$layers, object) names(plot$layers) <- layers_names plot } new_layer_names <- function(layer, existing) { + + empty <- !nzchar(existing) + if (any(empty)) { + existing[empty] <- "unknown" + existing <- vec_as_names(existing, repair = "unique", quiet = TRUE) + } + new_name <- layer$name if (is.null(new_name)) { # Construct a name from the layer's call From df315af8e2a2b48b965a979ba4c80fade3247f62 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 14:20:08 +0100 Subject: [PATCH 227/264] protect if-clause (#6302) --- R/geom-ribbon.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 4365c122d5..746684afbe 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -132,7 +132,7 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, strsplit(self$required_aes, "|", fixed = TRUE), `[[`, i = 1, character(1) ) - if (params$flipped_aes || any(data$flipped_aes) %||% FALSE) { + if (isTRUE(params$flipped_aes || any(data$flipped_aes) %||% FALSE)) { vars <- switch_orientation(vars) } vars <- c(vars, self$non_missing_aes) From df0e150249474f1d465a45b01ad16a6771091cc8 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 14:20:45 +0100 Subject: [PATCH 228/264] =?UTF-8?q?=E2=9C=A8=20Point=20and=20polygon=20the?= =?UTF-8?q?me=20elements=20(#6249)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * `translate_shape_string()` deals with non-character input * new element constructors * document new elements * add `element_grob()` methods * include `point` and `polygon` in theme * include template in default themes * :technologist: deal with `pathGrob()`'s id-logic. * add tests * add news bullet --- NAMESPACE | 4 + NEWS.md | 2 + R/geom-point.R | 11 +-- R/geom-sf.R | 4 +- R/legend-draw.R | 6 +- R/theme-defaults.R | 22 +++++ R/theme-elements.R | 84 +++++++++++++++++-- R/theme.R | 4 + man/element.Rd | 37 ++++++-- man/theme.Rd | 6 ++ man/translate_shape_string.Rd | 3 +- .../testthat/_snaps/theme/point-elements.svg | 27 ++++++ .../_snaps/theme/polygon-elements.svg | 24 ++++++ tests/testthat/test-theme.R | 41 +++++++++ 14 files changed, 247 insertions(+), 28 deletions(-) create mode 100644 tests/testthat/_snaps/theme/point-elements.svg create mode 100644 tests/testthat/_snaps/theme/polygon-elements.svg diff --git a/NAMESPACE b/NAMESPACE index 690b9fb0ed..b58765ecc1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -20,6 +20,8 @@ S3method(c,mapped_discrete) S3method(drawDetails,zeroGrob) S3method(element_grob,element_blank) S3method(element_grob,element_line) +S3method(element_grob,element_point) +S3method(element_grob,element_polygon) S3method(element_grob,element_rect) S3method(element_grob,element_text) S3method(format,ggproto) @@ -346,6 +348,8 @@ export(element_blank) export(element_geom) export(element_grob) export(element_line) +export(element_point) +export(element_polygon) export(element_rect) export(element_render) export(element_text) diff --git a/NEWS.md b/NEWS.md index c8abcc17de..5497358548 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* New `element_point()` and `element_polygon()` that can be given to + `theme(point, polygon)` as an extension point (@teunbrand, #6248). * Turned off fallback for `size` to `linewidth` translation in `geom_bar()`/`geom_col()` (#4848). * `coord_radial()` now displays no axis instead of throwing an error when diff --git a/R/geom-point.R b/R/geom-point.R index bf73cf8749..47f3fc6fc2 100644 --- a/R/geom-point.R +++ b/R/geom-point.R @@ -148,10 +148,7 @@ GeomPoint <- ggproto("GeomPoint", Geom, ), draw_panel = function(self, data, panel_params, coord, na.rm = FALSE) { - if (is.character(data$shape)) { - data$shape <- translate_shape_string(data$shape) - } - + data$shape <- translate_shape_string(data$shape) coords <- coord$transform(data, panel_params) ggname("geom_point", pointsGrob( @@ -176,7 +173,8 @@ GeomPoint <- ggproto("GeomPoint", Geom, #' given as a character vector into integers that are interpreted by the #' grid system. #' -#' @param shape_string A character vector giving point shapes. +#' @param shape_string A character vector giving point shapes. Non-character +#' input will be returned. #' #' @return An integer vector with translated shapes. #' @export @@ -188,6 +186,9 @@ GeomPoint <- ggproto("GeomPoint", Geom, #' # Strings with 1 or less characters are interpreted as symbols #' translate_shape_string(c("a", "b", "?")) translate_shape_string <- function(shape_string) { + if (!is.character(shape_string)) { + return(shape_string) + } # strings of length 0 or 1 are interpreted as symbols by grid if (nchar(shape_string[1]) <= 1) { return(shape_string) diff --git a/R/geom-sf.R b/R/geom-sf.R index 4b61300108..78c543a50d 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -209,9 +209,7 @@ GeomSf <- ggproto("GeomSf", Geom, if (!inherits(coord, "CoordSf")) { cli::cli_abort("{.fn {snake_class(self)}} can only be used with {.fn coord_sf}.") } - if (is.character(data$shape)) { - data$shape <- translate_shape_string(data$shape) - } + data$shape <- translate_shape_string(data$shape) data <- coord$transform(data, panel_params) diff --git a/R/legend-draw.R b/R/legend-draw.R index eb33cc24d7..533e9e111f 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -24,11 +24,7 @@ NULL #' @export #' @rdname draw_key draw_key_point <- function(data, params, size) { - if (is.null(data$shape)) { - data$shape <- 19 - } else if (is.character(data$shape)) { - data$shape <- translate_shape_string(data$shape) - } + data$shape <- translate_shape_string(data$shape %||% 19) # NULL means the default stroke size, and NA means no stroke. pointsGrob(0.5, 0.5, diff --git a/R/theme-defaults.R b/R/theme-defaults.R index e6efd2a783..7fe9742f5e 100644 --- a/R/theme-defaults.R +++ b/R/theme-defaults.R @@ -145,6 +145,17 @@ theme_grey <- function(base_size = 11, base_family = "", spacing = unit(half_line, "pt"), margins = margin_auto(half_line), + point = element_point( + colour = ink, shape = 19, fill = paper, + size = (base_size / 11) * 1.5, + stroke = base_line_size + ), + + polygon = element_polygon( + fill = paper, colour = ink, + linewidth = base_rect_size, linetype = 1 + ), + geom = element_geom( ink = ink, paper = paper, accent = "#3366FF", linewidth = base_line_size, borderwidth = base_line_size, @@ -549,6 +560,8 @@ theme_void <- function(base_size = 11, base_family = "", t <- theme( line = element_blank(), rect = element_blank(), + polygon = element_blank(), + point = element_blank(), text = element_text( family = base_family, face = "plain", colour = ink, size = base_size, @@ -639,6 +652,15 @@ theme_test <- function(base_size = 11, base_family = "", lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE ), + point = element_point( + colour = ink, shape = 19, fill = paper, + size = (base_size / 11) * 1.5, + stroke = base_line_size + ), + polygon = element_polygon( + fill = paper, colour = ink, + linewidth = base_rect_size, linetype = 1 + ), title = element_text(family = header_family), spacing = unit(half_line, "pt"), margins = margin_auto(half_line), diff --git a/R/theme-elements.R b/R/theme-elements.R index 7d3ceb47dd..c3b6ded319 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -8,6 +8,8 @@ #' - `element_rect()`: borders and backgrounds. #' - `element_line()`: lines. #' - `element_text()`: text. +#' - `element_polygon()`: polygons. +#' - `element_point()`: points. #' - `element_geom()`: defaults for drawing layers. #' #' `rel()` is used to specify sizes relative to the parent, @@ -18,8 +20,13 @@ #' of the fill. #' @param colour,color Line/border colour. Color is an alias for colour. #' `alpha()` can be used to set the transparency of the colour. -#' @param linewidth,borderwidth Line/border size in mm. -#' @param size,fontsize text size in pts. +#' @param linewidth,borderwidth,stroke Line/border size in mm. +#' @param size,fontsize,pointsize text size in pts, point size in mm. +#' @param linetype,bordertype Line type for lines and borders respectively. An +#' integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, +#' twodash), or a string with an even number (up to eight) of hexadecimal +#' digits which give the lengths in consecutive positions in the string. +#' @param shape,pointshape Shape for points (1-25). #' @param arrow.fill Fill colour for arrows. #' @param inherit.blank Should this element inherit the existence of an #' `element_blank` among its parents? If `TRUE` the existence of @@ -27,6 +34,10 @@ #' well. If `FALSE` any blank parent element will be ignored when #' calculating final element state. #' @return An S3 object of class `element`, `rel`, or `margin`. +#' @details +#' The `element_polygon()` and `element_point()` functions are not rendered +#' in standard plots and just serve as extension points. +#' #' @examples #' # A standard plot #' plot <- ggplot(mpg, aes(displ, hwy)) + geom_point() @@ -97,10 +108,6 @@ element_rect <- function(fill = NULL, colour = NULL, linewidth = NULL, #' @export #' @rdname element -#' @param linetype,bordertype Line type for lines and borders respectively. An -#' integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, -#' twodash), or a string with an even number (up to eight) of hexadecimal -#' digits which give the lengths in consecutive positions in the string. #' @param lineend Line end Line end style (round, butt, square) #' @param arrow Arrow specification, as created by [grid::arrow()] element_line <- function(colour = NULL, linewidth = NULL, linetype = NULL, @@ -164,11 +171,36 @@ element_text <- function(family = NULL, face = NULL, colour = NULL, ) } +#' @export +#' @rdname element +element_polygon <- function(fill = NULL, colour = NULL, linewidth = NULL, + linetype = NULL, color = NULL, + inherit.blank = FALSE) { + structure( + list( + fill = fill, colour = color %||% colour, linewidth = linewidth, + linetype = linetype, inherit.blank = inherit.blank + ), + class = c("element_polygon", "element") + ) +} + +#' @export +#' @rdname element +element_point <- function(colour = NULL, shape = NULL, size = NULL, fill = NULL, + stroke = NULL, color = NULL, inherit.blank = FALSE) { + structure( + list( + colour = color %||% colour, fill = fill, shape = shape, size = size, + stroke = stroke, inherit.blank = inherit.blank + ), + class = c("element_point", "element") + ) +} + #' @param ink Foreground colour. #' @param paper Background colour. #' @param accent Accent colour. -#' @param pointsize Size for points in mm. -#' @param pointshape Shape for points (1-25). #' @export #' @rdname element element_geom <- function( @@ -357,6 +389,40 @@ element_grob.element_line <- function(element, x = 0:1, y = 0:1, ) } +#' @export +element_grob.element_polygon <- function(element, x = c(0, 0.5, 1, 0.5), + y = c(0.5, 1, 0.5, 0), fill = NULL, + colour = NULL, linewidth = NULL, + linetype = NULL, ..., + id = NULL, id.lengths = NULL, + pathId = NULL, pathId.lengths = NULL) { + + gp <- gg_par(lwd = linewidth, col = colour, fill = fill, lty = linetype) + element_gp <- gg_par(lwd = element$linewidth, col = element$colour, + fill = element$fill, lty = element$linetype) + pathGrob( + x = x, y = y, gp = modify_list(element_gp, gp), ..., + # We swap the id logic so that `id` is always the (super)group id + # (consistent with `polygonGrob()`) and `pathId` always the subgroup id. + pathId = id, pathId.lengths = id.lengths, + id = pathId, id.lengths = pathId.lengths + ) +} + +#' @export +element_grob.element_point <- function(element, x = 0.5, y = 0.5, colour = NULL, + shape = NULL, fill = NULL, size = NULL, + stroke = NULL, ..., + default.units = "npc") { + + gp <- gg_par(col = colour, fill = fill, pointsize = size, stroke = stroke) + element_gp <- gg_par(col = element$colour, fill = element$fill, + pointsize = element$size, stroke = element$stroke) + shape <- translate_shape_string(shape %||% element$shape %||% 19) + pointsGrob(x = x, y = y, pch = shape, gp = modify_list(element_gp, gp), + default.units = default.units, ...) +} + #' Define and register new theme elements #' #' The underlying structure of a ggplot2 theme is defined via the element tree, which @@ -532,6 +598,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) { line = el_def("element_line"), rect = el_def("element_rect"), text = el_def("element_text"), + point = el_def("element_point"), + polygon = el_def("element_polygon"), geom = el_def("element_geom"), title = el_def("element_text", "text"), spacing = el_def("unit"), diff --git a/R/theme.R b/R/theme.R index bf65c565a9..dfe986fc62 100644 --- a/R/theme.R +++ b/R/theme.R @@ -25,6 +25,8 @@ #' @param text all text elements ([element_text()]) #' @param title all title elements: plot, axes, legends ([element_text()]; #' inherits from `text`) +#' @param point all point elements ([element_point()]) +#' @param polygon all polygon elements ([element_polygon()]) #' @param geom defaults for geoms ([element_geom()]) #' @param spacing all spacings ([`unit()`][grid::unit]) #' @param margins all margins ([margin()]) @@ -323,6 +325,8 @@ theme <- function(..., rect, text, title, + point, + polygon, geom, spacing, margins, diff --git a/man/element.Rd b/man/element.Rd index 041bf794f5..99e56f0e94 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -5,6 +5,8 @@ \alias{element_rect} \alias{element_line} \alias{element_text} +\alias{element_polygon} +\alias{element_point} \alias{element_geom} \alias{rel} \alias{margin} @@ -51,6 +53,25 @@ element_text( inherit.blank = FALSE ) +element_polygon( + fill = NULL, + colour = NULL, + linewidth = NULL, + linetype = NULL, + color = NULL, + inherit.blank = FALSE +) + +element_point( + colour = NULL, + shape = NULL, + size = NULL, + fill = NULL, + stroke = NULL, + color = NULL, + inherit.blank = FALSE +) + element_geom( ink = NULL, paper = NULL, @@ -80,7 +101,7 @@ of the fill.} \item{colour, color}{Line/border colour. Color is an alias for colour. \code{alpha()} can be used to set the transparency of the colour.} -\item{linewidth, borderwidth}{Line/border size in mm.} +\item{linewidth, borderwidth, stroke}{Line/border size in mm.} \item{linetype, bordertype}{Line type for lines and borders respectively. An integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, @@ -93,7 +114,7 @@ a blank element among its parents will cause this element to be blank as well. If \code{FALSE} any blank parent element will be ignored when calculating final element state.} -\item{size, fontsize}{text size in pts.} +\item{size, fontsize, pointsize}{text size in pts, point size in mm.} \item{lineend}{Line end Line end style (round, butt, square)} @@ -121,16 +142,14 @@ side of the text facing towards the center of the plot.} rectangle behind the complete text area, and a point where each label is anchored.} +\item{shape, pointshape}{Shape for points (1-25).} + \item{ink}{Foreground colour.} \item{paper}{Background colour.} \item{accent}{Accent colour.} -\item{pointsize}{Size for points in mm.} - -\item{pointshape}{Shape for points (1-25).} - \item{x}{A single number specifying size relative to parent element.} \item{t, r, b, l}{Dimensions of each margin. (To remember order, think trouble).} @@ -149,6 +168,8 @@ specify the display of how non-data components of the plot are drawn. \item \code{element_rect()}: borders and backgrounds. \item \code{element_line()}: lines. \item \code{element_text()}: text. +\item \code{element_polygon()}: polygons. +\item \code{element_point()}: points. \item \code{element_geom()}: defaults for drawing layers. } @@ -156,6 +177,10 @@ specify the display of how non-data components of the plot are drawn. \code{margin()}, \code{margin_part()} and \code{margin_auto()} are all used to specify the margins of elements. } +\details{ +The \code{element_polygon()} and \code{element_point()} functions are not rendered +in standard plots and just serve as extension points. +} \examples{ # A standard plot plot <- ggplot(mpg, aes(displ, hwy)) + geom_point() diff --git a/man/theme.Rd b/man/theme.Rd index 0a4941266e..2766a3f8ca 100644 --- a/man/theme.Rd +++ b/man/theme.Rd @@ -10,6 +10,8 @@ theme( rect, text, title, + point, + polygon, geom, spacing, margins, @@ -165,6 +167,10 @@ these should also be defined in the \verb{element tree} argument. \link[rlang:sp \item{title}{all title elements: plot, axes, legends (\code{\link[=element_text]{element_text()}}; inherits from \code{text})} +\item{point}{all point elements (\code{\link[=element_point]{element_point()}})} + +\item{polygon}{all polygon elements (\code{\link[=element_polygon]{element_polygon()}})} + \item{geom}{defaults for geoms (\code{\link[=element_geom]{element_geom()}})} \item{spacing}{all spacings (\code{\link[grid:unit]{unit()}})} diff --git a/man/translate_shape_string.Rd b/man/translate_shape_string.Rd index f6d205cf79..cbbcad05a7 100644 --- a/man/translate_shape_string.Rd +++ b/man/translate_shape_string.Rd @@ -7,7 +7,8 @@ translate_shape_string(shape_string) } \arguments{ -\item{shape_string}{A character vector giving point shapes.} +\item{shape_string}{A character vector giving point shapes. Non-character +input will be returned.} } \value{ An integer vector with translated shapes. diff --git a/tests/testthat/_snaps/theme/point-elements.svg b/tests/testthat/_snaps/theme/point-elements.svg new file mode 100644 index 0000000000..f810f35c3b --- /dev/null +++ b/tests/testthat/_snaps/theme/point-elements.svg @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/theme/polygon-elements.svg b/tests/testthat/_snaps/theme/polygon-elements.svg new file mode 100644 index 0000000000..e6e0de8c72 --- /dev/null +++ b/tests/testthat/_snaps/theme/polygon-elements.svg @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R index eba47a0c75..8d74b4038f 100644 --- a/tests/testthat/test-theme.R +++ b/tests/testthat/test-theme.R @@ -712,6 +712,47 @@ test_that("margin_part() mechanics work as expected", { # Visual tests ------------------------------------------------------------ +test_that("element_polygon() can render a grob", { + + t <- theme_gray() + theme(polygon = element_polygon(fill = "orchid")) + e <- calc_element("polygon", t) + g <- element_grob( + e, + x = c(0, 0.5, 1, 0.5, 0.15, 0.85, 0.85, 0.15), + y = c(0.5, 0, 0.5, 1, 0.15, 0.15, 0.85, 0.85), + id = c(1, 1, 1, 1, 2, 2, 2, 2), + colour = c("orange", "limegreen") + ) + + expect_s3_class(g, "pathgrob") + expect_equal(g$gp$fill, "orchid") + + expect_doppelganger( + "polygon elements", + function() {grid.newpage(); grid.draw(g)} + ) +}) + +test_that("element_point() can render a grob", { + + t <- theme_gray() + theme(point = element_point(shape = 21, size = 5)) + e <- calc_element("point", t) + g <- element_grob( + e, + x = seq(0.1, 0.9, length.out = 5), + y = seq(0.9, 0.1, length.out = 5), + fill = c("orange", "limegreen", "orchid", "turquoise", "grey") + ) + + expect_s3_class(g, "points") + expect_equal(g$pch, 21) + + expect_doppelganger( + "point elements", + function() {grid.newpage(); grid.draw(g)} + ) +}) + test_that("aspect ratio is honored", { df <- cbind(data_frame(x = 1:8, y = 1:8, f = gl(2,4)), expand.grid(f1 = 1:2, f2 = 1:2, rep = 1:2)) p <- ggplot(df, aes(x, y)) + From 6e0664b78a7a9208f6b09df7ec7d149da00b90d4 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 14:21:29 +0100 Subject: [PATCH 229/264] prepopulate theme (#6304) --- R/guides-.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/guides-.R b/R/guides-.R index 44ed7fb383..83ced80cd7 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -274,7 +274,7 @@ Guides <- ggproto( # # The resulting guide is then drawn in ggplot_gtable - build = function(self, scales, layers, labels, layer_data, theme) { + build = function(self, scales, layers, labels, layer_data, theme = theme()) { # Empty guides list custom <- self$get_custom() From 1bfb3c9b26a046a878d97a15cccf108973a8150a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 28 Jan 2025 15:05:47 +0100 Subject: [PATCH 230/264] Additional settings for `geom_label()` (#6307) * replace `geom_label(label.size)` with `linewidth` aesthetic * add `linetype` aesthetic * add border and text colours * vectorise some operations * preserve thinner linewidth * apply to `geom_sf_labels()` too * adapt legend key * document new params * add test * add news bullet --- NEWS.md | 6 + R/geom-label.R | 50 ++++++-- R/geom-sf.R | 17 ++- R/legend-draw.R | 9 +- ggplot2.Rproj | 1 + man/geom_text.Rd | 17 ++- man/ggsf.Rd | 17 ++- .../geom-label-with-line-parameters.svg | 121 ++++++++++++++++++ tests/testthat/test-geom-label.R | 11 ++ 9 files changed, 227 insertions(+), 22 deletions(-) create mode 100644 tests/testthat/_snaps/geom-label/geom-label-with-line-parameters.svg diff --git a/NEWS.md b/NEWS.md index 5497358548..74b049ace5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,11 @@ # ggplot2 (development version) +* New parameters for `geom_label()` (@teunbrand and @steveharoz, #5365): + * The `linewidth` aesthetic is now applied and replaces the `label.size` + argument. + * The `linetype` aesthetic is now applied. + * New `border.colour` argument to set the colour of borders. + * New `text.colour` argument to set the colour of text. * New `element_point()` and `element_polygon()` that can be given to `theme(point, polygon)` as an extension point (@teunbrand, #6248). * Turned off fallback for `size` to `linewidth` translation in diff --git a/R/geom-label.R b/R/geom-label.R index 68f4549b6e..ae21a48df3 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -2,19 +2,36 @@ #' @rdname geom_text #' @param label.padding Amount of padding around label. Defaults to 0.25 lines. #' @param label.r Radius of rounded corners. Defaults to 0.15 lines. -#' @param label.size Size of label border, in mm. +#' @param label.size `r lifecycle::badge("deprecated")` Replaced by the +#' `linewidth` aesthetic. Size of label border, in mm. +#' @param border.colour,border.color Colour of label border. When `NULL` +#' (default), the `colour` aesthetic determines the colour of the label border. +#' `border.color` is an alias for `border.colour`. +#' @param text.colour,text.color Colour of the text. When `NULL` (default), the +#' `colour` aesthetic determines the colour of the text. `text.color` is an +#' alias for `text.colour`. geom_label <- function(mapping = NULL, data = NULL, stat = "identity", position = "nudge", ..., parse = FALSE, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), - label.size = 0.25, + label.size = deprecated(), + border.colour = NULL, + border.color = NULL, + text.colour = NULL, + text.color = NULL, size.unit = "mm", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { + extra_args <- list2(...) + if (lifecycle::is_present(label.size)) { + deprecate_warn0("3.5.0", "geom_label(label.size)", "geom_label(linewidth)") + extra_args$linewidth <- extra_args$linewidth %||% label.size + } + layer( data = data, mapping = mapping, @@ -27,10 +44,11 @@ geom_label <- function(mapping = NULL, data = NULL, parse = parse, label.padding = label.padding, label.r = label.r, - label.size = label.size, size.unit = size.unit, + border.colour = border.color %||% border.colour, + text.colour = text.color %||% text.colour, na.rm = na.rm, - ... + !!!extra_args ) ) } @@ -49,14 +67,17 @@ GeomLabel <- ggproto("GeomLabel", Geom, size = from_theme(fontsize), angle = 0, hjust = 0.5, vjust = 0.5, alpha = NA, fontface = 1, - lineheight = 1.2 + lineheight = 1.2, + linewidth = from_theme(borderwidth * 0.5), + linetype = from_theme(bordertype) ), draw_panel = function(self, data, panel_params, coord, parse = FALSE, na.rm = FALSE, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), - label.size = 0.25, + border.colour = NULL, + text.colour = NULL, size.unit = "mm") { lab <- data$label if (parse) { @@ -71,6 +92,12 @@ GeomLabel <- ggproto("GeomLabel", Geom, } size.unit <- resolve_text_unit(size.unit) + data$text.colour <- text.colour %||% data$colour + data$border.colour <- border.colour %||% data$colour + data$border.colour[data$linewidth == 0] <- NA + data$fill <- fill_alpha(data$fill, data$alpha) + data$size <- data$size * size.unit + grobs <- lapply(seq_len(nrow(data)), function(i) { row <- data[i, , drop = FALSE] @@ -82,16 +109,17 @@ GeomLabel <- ggproto("GeomLabel", Geom, r = label.r, angle = row$angle, text.gp = gg_par( - col = row$colour, - fontsize = row$size * size.unit, + col = row$text.colour, + fontsize = row$size, fontfamily = row$family, fontface = row$fontface, lineheight = row$lineheight ), rect.gp = gg_par( - col = if (isTRUE(all.equal(label.size, 0))) NA else row$colour, - fill = fill_alpha(row$fill, row$alpha), - lwd = label.size + col = row$border.colour, + fill = row$fill, + lwd = row$linewidth, + lty = row$linetype ) ) }) diff --git a/R/geom-sf.R b/R/geom-sf.R index 78c543a50d..5ba2b3d846 100644 --- a/R/geom-sf.R +++ b/R/geom-sf.R @@ -317,12 +317,22 @@ geom_sf_label <- function(mapping = aes(), data = NULL, parse = FALSE, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), - label.size = 0.25, + label.size = deprecated(), + border.colour = NULL, + border.color = NULL, + text.colour = NULL, + text.color = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, fun.geometry = NULL) { + extra_args <- list2(...) + if (lifecycle::is_present(label.size)) { + deprecate_warn0("3.5.0", "geom_label(label.size)", "geom_label(linewidth)") + extra_args$linewidth <- extra_args$linewidth %||% label.size + } + layer_sf( data = data, mapping = mapping, @@ -335,10 +345,11 @@ geom_sf_label <- function(mapping = aes(), data = NULL, parse = parse, label.padding = label.padding, label.r = label.r, - label.size = label.size, na.rm = na.rm, fun.geometry = fun.geometry, - ... + border.colour = border.color %||% border.colour, + text.colour = text.color %||% text.colour, + !!!extra_args ) ) } diff --git a/R/legend-draw.R b/R/legend-draw.R index 533e9e111f..9a1b607a2e 100644 --- a/R/legend-draw.R +++ b/R/legend-draw.R @@ -328,7 +328,6 @@ draw_key_text <- function(data, params, size) { #' @rdname draw_key draw_key_label <- function(data, params, size) { data <- replace_null(unclass(data), label = "a", angle = 0) - params$label.size <- params$label.size %||% 0.25 hjust <- compute_just(data$hjust %||% 0.5) vjust <- compute_just(data$vjust %||% 0.5) just <- rotate_just(data$angle, hjust, vjust) @@ -338,6 +337,7 @@ draw_key_label <- function(data, params, size) { face = data$fontface %||% 1, size = data$size %||% 3.88 ) + lwd <- data$linewidth %||% 0.25 grob <- labelGrob( data$label, x = unit(just$hjust, "npc"), @@ -347,15 +347,16 @@ draw_key_label <- function(data, params, size) { padding = padding, r = params$label.r %||% unit(0.15, "lines"), text.gp = gg_par( - col = data$colour %||% "black", + col = params$text.colour %||% data$colour %||% "black", fontfamily = data$family %||% "", fontface = data$fontface %||% 1, fontsize = (data$size %||% 3.88) * .pt ), rect.gp = gg_par( - col = if (isTRUE(all.equal(params$label.size, 0))) NA else data$colour, + col = if (isTRUE(all.equal(lwd, 0))) NA else params$border.colour %||% data$colour %||% "black", fill = alpha(data$fill %||% "white", data$alpha), - lwd = params$label.size + lwd = lwd, + lty = data$linetype %||% 1L ) ) angle <- deg2rad(data$angle %||% 0) diff --git a/ggplot2.Rproj b/ggplot2.Rproj index 30db3b4433..5215454023 100644 --- a/ggplot2.Rproj +++ b/ggplot2.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: f500cb87-e0be-413f-b396-3eb022932f55 RestoreWorkspace: Default SaveWorkspace: Default diff --git a/man/geom_text.Rd b/man/geom_text.Rd index e92e3fe3d8..ea698af3c1 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -14,7 +14,11 @@ geom_label( parse = FALSE, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), - label.size = 0.25, + label.size = deprecated(), + border.colour = NULL, + border.color = NULL, + text.colour = NULL, + text.color = NULL, size.unit = "mm", na.rm = FALSE, show.legend = NA, @@ -117,7 +121,16 @@ displayed as described in \code{?plotmath}.} \item{label.r}{Radius of rounded corners. Defaults to 0.15 lines.} -\item{label.size}{Size of label border, in mm.} +\item{label.size}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Replaced by the +\code{linewidth} aesthetic. Size of label border, in mm.} + +\item{border.colour, border.color}{Colour of label border. When \code{NULL} +(default), the \code{colour} aesthetic determines the colour of the label border. +\code{border.color} is an alias for \code{border.colour}.} + +\item{text.colour, text.color}{Colour of the text. When \code{NULL} (default), the +\code{colour} aesthetic determines the colour of the text. \code{text.color} is an +alias for \code{text.colour}.} \item{size.unit}{How the \code{size} aesthetic is interpreted: as millimetres (\code{"mm"}, default), points (\code{"pt"}), centimetres (\code{"cm"}), inches (\code{"in"}), diff --git a/man/ggsf.Rd b/man/ggsf.Rd index 1ab15f232a..f7790f5abb 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -49,7 +49,11 @@ geom_sf_label( parse = FALSE, label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), - label.size = 0.25, + label.size = deprecated(), + border.colour = NULL, + border.color = NULL, + text.colour = NULL, + text.color = NULL, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, @@ -277,7 +281,16 @@ displayed as described in \code{?plotmath}.} \item{label.r}{Radius of rounded corners. Defaults to 0.15 lines.} -\item{label.size}{Size of label border, in mm.} +\item{label.size}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Replaced by the +\code{linewidth} aesthetic. Size of label border, in mm.} + +\item{border.colour, border.color}{Colour of label border. When \code{NULL} +(default), the \code{colour} aesthetic determines the colour of the label border. +\code{border.color} is an alias for \code{border.colour}.} + +\item{text.colour, text.color}{Colour of the text. When \code{NULL} (default), the +\code{colour} aesthetic determines the colour of the text. \code{text.color} is an +alias for \code{text.colour}.} \item{fun.geometry}{A function that takes a \code{sfc} object and returns a \code{sfc_POINT} with the same length as the input. If \code{NULL}, \code{function(x) sf::st_point_on_surface(sf::st_zm(x))} diff --git a/tests/testthat/_snaps/geom-label/geom-label-with-line-parameters.svg b/tests/testthat/_snaps/geom-label/geom-label-with-line-parameters.svg new file mode 100644 index 0000000000..b7c5c9717f --- /dev/null +++ b/tests/testthat/_snaps/geom-label/geom-label-with-line-parameters.svg @@ -0,0 +1,121 @@ + + + + + + + + + + + + + + + + + + + + + + +foo + +bar + +baz + +foo + +bar + +baz + + + +1.00 +1.25 +1.50 +1.75 +2.00 + + + + + + + + + + +1.0 +1.5 +2.0 +2.5 +3.0 +x +y + +labels + + +a + +a + + +a + +a + + +a + +a +bar +baz +foo + +x + + +a + +a + + +a + +a + + +a + +a + + +a + +a + + +a + +a +1.0 +1.5 +2.0 +2.5 +3.0 +geom_label with line parameters + + diff --git a/tests/testthat/test-geom-label.R b/tests/testthat/test-geom-label.R index c80be5e38b..ec94fe7c4b 100644 --- a/tests/testthat/test-geom-label.R +++ b/tests/testthat/test-geom-label.R @@ -22,3 +22,14 @@ test_that("geom_label() rotates labels", { angle_out <- unname(vapply(vps, `[[`, numeric(1), "angle")) expect_equal(angle_in, angle_out) }) + +test_that("geom_label handles line parameters and colours", { + df <- data.frame(x = 1:3, labels = c("foo", "bar", "baz")) + + p <- ggplot(df, aes(x, label = labels, colour = labels, linewidth = x)) + + geom_label(aes(y = 1), border.colour = "black", linetype = 1) + + geom_label(aes(y = 2), text.colour = "black", linetype = 2) + + scale_linewidth(range = c(0.1, 1)) + + expect_doppelganger("geom_label with line parameters", p) +}) From b87a6e354d19fef05e6d20a24e7b62482ac80b5a Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 4 Feb 2025 11:50:56 +0100 Subject: [PATCH 231/264] Demote errors in legend modified expressions (#6267) * handle after scale errors * add test * add news bullet * tweak message * conditional test --- NEWS.md | 2 ++ R/geom-.R | 13 +++++++++---- tests/testthat/_snaps/guide-legend.md | 6 ++++++ tests/testthat/test-guide-legend.R | 9 +++++++++ 4 files changed, 26 insertions(+), 4 deletions(-) create mode 100644 tests/testthat/_snaps/guide-legend.md diff --git a/NEWS.md b/NEWS.md index 74b049ace5..ef806483df 100644 --- a/NEWS.md +++ b/NEWS.md @@ -302,6 +302,8 @@ particularly for data-points with a low radius near the center (@teunbrand, #5023). * All scales now expose the `aesthetics` parameter (@teunbrand, #5841) +* Staged expressions are handled more gracefully if legends cannot resolve them + (@teunbrand, #6264). * New `theme(legend.key.justification)` to control the alignment of legend keys (@teunbrand, #3669). * Added `scale_{x/y}_time(date_breaks, date_minor_breaks, date_labels)` diff --git a/R/geom-.R b/R/geom-.R index f8b5027438..843bd4c11c 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -163,10 +163,15 @@ Geom <- ggproto("Geom", # If any after_scale mappings are detected they will be resolved here # This order means that they will have access to all default aesthetics if (length(modifiers) != 0) { - # Set up evaluation environment - modified_aes <- eval_aesthetics( - substitute_aes(modifiers), data, - mask = list(stage = stage_scaled) + modified_aes <- try_fetch( + eval_aesthetics( + substitute_aes(modifiers), data, + mask = list(stage = stage_scaled) + ), + error = function(cnd) { + cli::cli_warn("Unable to apply staged modifications.", parent = cnd) + data_frame0() + } ) # Check that all output are valid data diff --git a/tests/testthat/_snaps/guide-legend.md b/tests/testthat/_snaps/guide-legend.md new file mode 100644 index 0000000000..7369171c92 --- /dev/null +++ b/tests/testthat/_snaps/guide-legend.md @@ -0,0 +1,6 @@ +# unresolved, modified expressions throw a warning (#6264) + + Unable to apply staged modifications. + Caused by error: + ! object 'prop' not found + diff --git a/tests/testthat/test-guide-legend.R b/tests/testthat/test-guide-legend.R index c68ab03297..cd2311ee93 100644 --- a/tests/testthat/test-guide-legend.R +++ b/tests/testthat/test-guide-legend.R @@ -136,6 +136,15 @@ test_that("legends can be forced to display unrelated geoms", { ) }) +test_that("unresolved, modified expressions throw a warning (#6264)", { + # Snapshot is unstable in lesser R versions + skip_if_not(getRversion() >= "4.3.0") + p <- ggplot(mpg, aes(drv)) + + geom_bar( + aes(fill = stage(drv, after_scale = alpha(fill, prop))) + ) + expect_snapshot_warning(ggplot_build(p)) +}) # Visual tests ------------------------------------------------------------ From d835cfe2ffb0ff68c9a4b224ec1fcb4caba83892 Mon Sep 17 00:00:00 2001 From: Randall Boyes <33524191+rdboyes@users.noreply.github.com> Date: Thu, 13 Feb 2025 13:04:41 -0500 Subject: [PATCH 232/264] Fixes a small typo in docstring for scale_linewidth (#6331) * Update scale-linewidth.R fixes a small typo * document --------- Co-authored-by: Teun van den Brand --- R/scale-linewidth.R | 2 +- man/scale_linewidth.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/scale-linewidth.R b/R/scale-linewidth.R index f9cec8856f..2a062e0e73 100644 --- a/R/scale-linewidth.R +++ b/R/scale-linewidth.R @@ -2,7 +2,7 @@ #' #' `scale_linewidth` scales the width of lines and polygon strokes. Due to #' historical reasons, it is also possible to control this with the `size` -#' aesthetic, but using `linewidth` is encourage to clearly differentiate area +#' aesthetic, but using `linewidth` is encouraged to clearly differentiate area #' aesthetics from stroke width aesthetics. #' #' @name scale_linewidth diff --git a/man/scale_linewidth.Rd b/man/scale_linewidth.Rd index 2efb7378d3..ffce8ffa0f 100644 --- a/man/scale_linewidth.Rd +++ b/man/scale_linewidth.Rd @@ -119,7 +119,7 @@ breaks are given explicitly.} \description{ \code{scale_linewidth} scales the width of lines and polygon strokes. Due to historical reasons, it is also possible to control this with the \code{size} -aesthetic, but using \code{linewidth} is encourage to clearly differentiate area +aesthetic, but using \code{linewidth} is encouraged to clearly differentiate area aesthetics from stroke width aesthetics. } \examples{ From d1fb5506bd99ef983b5e7c1c2f766f4f056074b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Thomas=20M=2E=20Sch=C3=B6ller?= <7847075+MaxAtoms@users.noreply.github.com> Date: Tue, 25 Feb 2025 09:09:26 +0000 Subject: [PATCH 233/264] Document vector passing to nudge_y/nudge_x/position_nudge (#6335) * Document vector passing to position_nudge * Put nudge_y into aes call As discussed in #6355. * Update documentation * redocument --------- Co-authored-by: Teun van den Brand --- R/position-nudge.R | 5 +++++ man/position_nudge.Rd | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/R/position-nudge.R b/R/position-nudge.R index 6bf8a81f01..cd28360d79 100644 --- a/R/position-nudge.R +++ b/R/position-nudge.R @@ -27,6 +27,11 @@ #' ggplot(df, aes(x, y)) + #' geom_point() + #' geom_text(aes(label = y), nudge_y = -0.1) +#' +#' # For each text individually +#' ggplot(df, aes(x, y)) + +#' geom_point() + +#' geom_text(aes(label = y, nudge_y = c(-0.1, 0.1, -0.1, 0.1))) position_nudge <- function(x = NULL, y = NULL) { ggproto(NULL, PositionNudge, x = x, diff --git a/man/position_nudge.Rd b/man/position_nudge.Rd index 0db66c8035..89b5a14326 100644 --- a/man/position_nudge.Rd +++ b/man/position_nudge.Rd @@ -43,6 +43,11 @@ ggplot(df, aes(x, y)) + ggplot(df, aes(x, y)) + geom_point() + geom_text(aes(label = y), nudge_y = -0.1) + +# For each text individually +ggplot(df, aes(x, y)) + + geom_point() + + geom_text(aes(label = y, nudge_y = c(-0.1, 0.1, -0.1, 0.1))) } \seealso{ Other position adjustments: From e727e2bdc9407a9bbc732dd283f41aec70a3a253 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Thu, 27 Feb 2025 10:14:28 +0100 Subject: [PATCH 234/264] don't warn when fatten is absent (#6310) --- R/geom-crossbar.R | 2 +- R/geom-pointrange.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R index 8f9d8ccd74..f1db25bab9 100644 --- a/R/geom-crossbar.R +++ b/R/geom-crossbar.R @@ -60,7 +60,7 @@ geom_crossbar <- function(mapping = NULL, data = NULL, #' @export GeomCrossbar <- ggproto("GeomCrossbar", Geom, setup_params = function(data, params) { - if (lifecycle::is_present(params$fatten)) { + if (lifecycle::is_present(params$fatten %||% deprecated())) { deprecate_soft0( "3.6.0", "geom_crossbar(fatten)", "geom_crossbar(middle.linewidth)" diff --git a/R/geom-pointrange.R b/R/geom-pointrange.R index 1943bb4f4c..c13b6a813e 100644 --- a/R/geom-pointrange.R +++ b/R/geom-pointrange.R @@ -42,7 +42,7 @@ GeomPointrange <- ggproto("GeomPointrange", Geom, required_aes = c("x", "y", "ymin|xmin", "ymax|xmax"), setup_params = function(data, params) { - if (lifecycle::is_present(params$fatten)) { + if (lifecycle::is_present(params$fatten %||% deprecated())) { deprecate_soft0("3.6.0", "geom_pointrange(fatten)", I("the `size` aesthetic")) } else { # For backward compatibility reasons From 1800a9af9e2d29292b67a236f654e2bacb524bae Mon Sep 17 00:00:00 2001 From: Mathieu YECHE <99674960+MathieuYeche@users.noreply.github.com> Date: Fri, 7 Mar 2025 18:52:01 +0100 Subject: [PATCH 235/264] fix_6357 (#6358) See https://github.com/tidyverse/ggplot2/issues/6357 --- R/geom-ribbon.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 746684afbe..fb0c6c9040 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -183,7 +183,7 @@ GeomRibbon <- ggproto("GeomRibbon", Geom, if ((length(aes$fill) > 1 || length(aes$alpha) > 1)) { transformed <- coord$transform(flip_data(data, flipped_aes), panel_params) if (flipped_aes) { - keep <- is.finite(tranformed$y) + keep <- is.finite(transformed$y) args <- list( colours = alpha(data$fill, data$alpha)[keep], stops = rescale(transformed$y)[keep], From a641f5dee53a4e4a975f255f386de06dbcf15015 Mon Sep 17 00:00:00 2001 From: laurabrianna Date: Tue, 25 Mar 2025 04:33:58 -0400 Subject: [PATCH 236/264] Fixes #3533 - Swap date(time) types in opposite scale (#6042) * Fixes #3533 - helpful error msg on date vs datetime scale * Apply suggestions from code review Co-authored-by: Thomas Lin Pedersen * Apply suggestions from code review Co-authored-by: Thomas Lin Pedersen * add news bullet * add test * use internal data.frame --------- Co-authored-by: Thomas Lin Pedersen Co-authored-by: Teun van den Brand --- NEWS.md | 2 ++ R/scale-date.R | 6 ++++++ tests/testthat/test-scale_date.R | 15 +++++++++++++++ 3 files changed, 23 insertions(+) diff --git a/NEWS.md b/NEWS.md index ef806483df..67d35b9878 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* Date scales silently coerce to and datetime scales silently + coerce to (@laurabrianna, #3533) * New parameters for `geom_label()` (@teunbrand and @steveharoz, #5365): * The `linewidth` aesthetic is now applied and replaces the `label.size` argument. diff --git a/R/scale-date.R b/R/scale-date.R index e518c7ac11..ac0c314e18 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -394,6 +394,9 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous, i = "The value was converted to {obj_type_friendly(x)}." ), call = self$call) } + if (inherits(x, "Date")) { + x <- as.POSIXct(x) + } ggproto_parent(ScaleContinuous, self)$transform(x) }, map = function(self, x, limits = self$get_limits()) { @@ -441,6 +444,9 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous, i = "The value was converted to {obj_type_friendly(x)}." ), call = self$call) } + if (inherits(x, "POSIXct")) { + x <- as.Date(x) + } ggproto_parent(ScaleContinuous, self)$transform(x) }, get_breaks = function(self, limits = self$get_limits()) { diff --git a/tests/testthat/test-scale_date.R b/tests/testthat/test-scale_date.R index f12a35716c..b9a788bb70 100644 --- a/tests/testthat/test-scale_date.R +++ b/tests/testthat/test-scale_date.R @@ -1,4 +1,19 @@ +test_that("date(time) scales coerce data types", { + + date <- as.Date("2024-11-11") + datetime <- as.POSIXct(date) + + sc <- scale_x_datetime() + df <- sc$transform_df(data_frame0(x = date)) + expect_equal(df$x, as.numeric(datetime)) + + sc <- scale_x_date() + df <- sc$transform_df(data_frame0(x = datetime)) + expect_equal(df$x, as.numeric(date)) + +}) + # Visual tests ------------------------------------------------------------ test_that("date scale draws correctly", { From 5fe3c2a75cc5c570565c504758bfa3dbe30448bd Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 25 Mar 2025 10:22:42 +0100 Subject: [PATCH 237/264] Allow saving PDF pages (#6187) * allow saving pages * helper to deal with background * add news bullet --- NEWS.md | 2 ++ R/save.R | 20 ++++++++++++++++---- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 67d35b9878..b9b3fa8b45 100644 --- a/NEWS.md +++ b/NEWS.md @@ -310,6 +310,8 @@ (@teunbrand, #3669). * Added `scale_{x/y}_time(date_breaks, date_minor_breaks, date_labels)` (@teunbrand, #4335). +* `ggsave()` can write a multi-page pdf file when provided with a list of plots + (@teunbrand, #5093). # ggplot2 3.5.1 diff --git a/R/save.R b/R/save.R index 5e1ef5983a..523f2ef29b 100644 --- a/R/save.R +++ b/R/save.R @@ -101,17 +101,18 @@ ggsave <- function(filename, plot = get_last_plot(), dev <- validate_device(device, filename, dpi = dpi) dim <- plot_dim(c(width, height), scale = scale, units = units, limitsize = limitsize, dpi = dpi) + bg <- get_plot_background(plot, bg) - if (is_null(bg)) { - bg <- calc_element("plot.background", plot_theme(plot))$fill %||% "transparent" - } old_dev <- grDevices::dev.cur() dev(filename = filename, width = dim[1], height = dim[2], bg = bg, ...) on.exit(utils::capture.output({ grDevices::dev.off() if (old_dev > 1) grDevices::dev.set(old_dev) # restore old device unless null device })) - grid.draw(plot) + if (!is_bare_list(plot)) { + plot <- list(plot) + } + lapply(plot, grid.draw) invisible(filename) } @@ -235,6 +236,17 @@ plot_dim <- function(dim = c(NA, NA), scale = 1, units = "in", dim } +get_plot_background <- function(plot, bg = NULL, default = "transparent") { + if (!is.null(bg)) { + return(bg) + } + plot <- if (is_bare_list(plot)) plot[[1]] else plot + if (!is.ggplot(plot)) { + return(default) + } + calc_element("plot.background", plot_theme(plot))$fill %||% default +} + validate_device <- function(device, filename = NULL, dpi = 300, call = caller_env()) { force(filename) force(dpi) From 5b99d3ce68081335ad25d15f1dc4951f9f129eff Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 25 Mar 2025 10:25:23 +0100 Subject: [PATCH 238/264] Stability of layer data attributes (#6194) * prevent dropping attributes * restore attributes after layer methods * add test * add news bullet * include scale transforms * add test --- NEWS.md | 2 ++ R/geom-.R | 5 +---- R/layer.R | 25 ++++++++++++++++--------- R/scales-.R | 12 ++++++------ R/utilities.R | 8 ++++++++ tests/testthat/test-layer.R | 23 +++++++++++++++++++++++ tests/testthat/test-stats.R | 19 +++++++++++++++++++ 7 files changed, 75 insertions(+), 19 deletions(-) diff --git a/NEWS.md b/NEWS.md index b9b3fa8b45..7bcc32375c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # ggplot2 (development version) +* (internal) layer data can be attenuated with parameter attributes + (@teunbrand, #3175). * Date scales silently coerce to and datetime scales silently coerce to (@laurabrianna, #3533) * New parameters for `geom_label()` (@teunbrand and @steveharoz, #5365): diff --git a/R/geom-.R b/R/geom-.R index 843bd4c11c..c19b1f3458 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -182,10 +182,7 @@ Geom <- ggproto("Geom", ) modified_aes <- cleanup_mismatched_data(modified_aes, nrow(data), "after_scale") - - modified_aes <- data_frame0(!!!modified_aes) - - data <- data_frame0(!!!defaults(modified_aes, data)) + data[names(modified_aes)] <- modified_aes } # Override mappings with params diff --git a/R/layer.R b/R/layer.R index 6be74b5d72..2cd10c447f 100644 --- a/R/layer.R +++ b/R/layer.R @@ -347,12 +347,13 @@ Layer <- ggproto("Layer", NULL, }, compute_statistic = function(self, data, layout) { - if (empty(data)) - return(data_frame0()) + if (empty(data)) return(data_frame0()) + ptype <- vec_ptype(data) self$computed_stat_params <- self$stat$setup_params(data, self$stat_params) data <- self$stat$setup_data(data, self$computed_stat_params) - self$stat$compute_layer(data, self$computed_stat_params, layout) + data <- self$stat$compute_layer(data, self$computed_stat_params, layout) + merge_attrs(data, ptype) }, map_statistic = function(self, data, plot) { @@ -396,12 +397,13 @@ Layer <- ggproto("Layer", NULL, stat_data <- plot$scales$transform_df(stat_data) } stat_data <- cleanup_mismatched_data(stat_data, nrow(data), "after_stat") - - data_frame0(!!!defaults(stat_data, data)) + data[names(stat_data)] <- stat_data + data }, compute_geom_1 = function(self, data) { if (empty(data)) return(data_frame0()) + ptype <- vec_ptype(data) check_required_aesthetics( self$geom$required_aes, @@ -409,17 +411,18 @@ Layer <- ggproto("Layer", NULL, snake_class(self$geom) ) self$computed_geom_params <- self$geom$setup_params(data, c(self$geom_params, self$aes_params)) - self$geom$setup_data(data, self$computed_geom_params) + data <- self$geom$setup_data(data, self$computed_geom_params) + merge_attrs(data, ptype) }, compute_position = function(self, data, layout) { if (empty(data)) return(data_frame0()) - + ptype <- vec_ptype(data) data <- self$position$use_defaults(data, self$aes_params) params <- self$position$setup_params(data) data <- self$position$setup_data(data, params) - - self$position$compute_layer(data, params, layout) + data <- self$position$compute_layer(data, params, layout) + merge_attrs(data, ptype) }, compute_geom_2 = function(self, data, params = self$aes_params, theme = NULL, ...) { @@ -484,6 +487,10 @@ set_draw_key <- function(geom, draw_key = NULL) { } cleanup_mismatched_data <- function(data, n, fun) { + if (vec_duplicate_any(names(data))) { + data <- data[unique0(names(data))] + } + failed <- !lengths(data) %in% c(0, 1, n) if (!any(failed)) { return(data) diff --git a/R/scales-.R b/R/scales-.R index 87c5f6f586..6c14347f49 100644 --- a/R/scales-.R +++ b/R/scales-.R @@ -78,7 +78,8 @@ ScalesList <- ggproto("ScalesList", NULL, function(scale) scale$map_df(df = df) ), recursive = FALSE) - data_frame0(!!!mapped, df[setdiff(names(df), names(mapped))]) + df[names(mapped)] <- mapped + df }, transform_df = function(self, df) { @@ -104,7 +105,8 @@ ScalesList <- ggproto("ScalesList", NULL, function(scale) scale$transform_df(df = df) ), recursive = FALSE) - data_frame0(!!!transformed, df[setdiff(names(df), names(transformed))]) + df[names(transformed)] <- transformed + df }, backtransform_df = function(self, df) { @@ -139,10 +141,8 @@ ScalesList <- ggproto("ScalesList", NULL, } ), recursive = FALSE) - data_frame0( - !!!backtransformed, - df[setdiff(names(df), names(backtransformed))] - ) + df[names(backtransformed)] <- backtransformed + df }, # `aesthetics` is a list of aesthetic-variable mappings. The name of each diff --git a/R/utilities.R b/R/utilities.R index 3bcdaacedc..51798059c8 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -249,6 +249,14 @@ toupper <- function(x) { cli::cli_abort("Please use {.fn to_upper_ascii}, which works fine in all locales.") } +merge_attrs <- function(new, old) { + new_attr <- attributes(new) + new <- vec_restore(new, old) # copies old attributes to new + new_attr <- new_attr[setdiff(names(new_attr), names(attributes(new)))] + attributes(new) <- c(attributes(new), new_attr) + new +} + # Convert a snake_case string to camelCase camelize <- function(x, first = FALSE) { x <- gsub("_(.)", "\\U\\1", x, perl = TRUE) diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index 59970c7db5..f901d3b62f 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -154,6 +154,29 @@ test_that("layer names can be resolved", { expect_snapshot(p + l + l, error = TRUE) }) +test_that("attributes on layer data are preserved", { + # This is a good layer for testing because: + # * It needs to compute a statistic at the group level + # * It needs to setup data to reshape x/y/width/height into xmin/xmax/ymin/ymax + # * It needs to use a position adjustment + # * It has an `after_stat()` so it enters the map_statistic method + old <- stat_summary( + aes(fill = after_stat(y)), + fun = mean, geom = "col", position = "dodge" + ) + # We modify the compute aesthetics method to append a test attribute + new <- ggproto(NULL, old, compute_aesthetics = function(self, data, plot) { + data <- ggproto_parent(old, self)$compute_aesthetics(data, plot) + attr(data, "test") <- "preserve me" + data + }) + # At the end of plot building, we want to retrieve that metric + ld <- layer_data( + ggplot(mpg, aes(drv, hwy, colour = factor(year))) + new + facet_grid(~year) + + scale_y_sqrt() + ) + expect_equal(attr(ld, "test"), "preserve me") +}) # Data extraction --------------------------------------------------------- diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index 8545b485fd..f8e8b37f31 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -69,3 +69,22 @@ test_that("erroneously dropped aesthetics are found and issue a warning", { c(TRUE, FALSE, FALSE) ) }) + +test_that("stats can modify persistent attributes", { + + StatTest <- ggproto( + "StatTest", Stat, + compute_layer = function(self, data, params, layout) { + attr(data, "foo") <- "bar" + data + } + ) + + p <- ggplot(mtcars, aes(disp, mpg)) + + geom_point(stat = StatTest) + + facet_wrap(~cyl) + + ld <- layer_data(p) + expect_equal(attr(ld, "foo"), "bar") + +}) From f21a8589b10e2cbf6edb2377babe64aa89a61d86 Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 25 Mar 2025 11:50:16 +0100 Subject: [PATCH 239/264] Fallback for `validate_subclass()` (#6119) * add lookup via constructor * add tests * add news bullet * catch errors when constructor needs arguments --- NEWS.md | 2 ++ R/layer.R | 50 ++++++++++++++++++++++++++++------ tests/testthat/_snaps/layer.md | 14 +++++++--- tests/testthat/test-layer.R | 19 +++++++++++++ 4 files changed, 72 insertions(+), 13 deletions(-) diff --git a/NEWS.md b/NEWS.md index 7bcc32375c..3957042f3b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -314,6 +314,8 @@ (@teunbrand, #4335). * `ggsave()` can write a multi-page pdf file when provided with a list of plots (@teunbrand, #5093). +* (internal) When `validate_subclass()` fails to find a class directly, it tries + to retrieve the class via constructor functions (@teunbrand). # ggplot2 3.5.1 diff --git a/R/layer.R b/R/layer.R index 2cd10c447f..8ed938def6 100644 --- a/R/layer.R +++ b/R/layer.R @@ -458,18 +458,50 @@ validate_subclass <- function(x, subclass, if (inherits(x, subclass)) { return(x) - } else if (is_scalar_character(x)) { - name <- paste0(subclass, camelize(x, first = TRUE)) - obj <- find_global(name, env = env) + } + if (!is_scalar_character(x)) { + stop_input_type(x, as_cli("either a string or a {.cls {subclass}} object"), arg = x_arg) + } - if (is.null(obj) || !inherits(obj, subclass)) { - cli::cli_abort("Can't find {argname} called {.val {x}}.", call = call) - } + # Try getting class object directly + name <- paste0(subclass, camelize(x, first = TRUE)) + obj <- find_global(name, env = env) + if (inherits(obj, subclass)) { + return(obj) + } + + # Try retrieving class via constructors + name <- snakeize(name) + obj <- find_global(name, env = env, mode = "function") + if (is.function(obj)) { + obj <- try_fetch( + obj(), + error = function(cnd) { + # replace `obj()` call with name of actual constructor + cnd$call <- call(name) + cli::cli_abort( + "Failed to retrieve a {.cls {subclass}} object from {.fn {name}}.", + parent = cnd, call = call + ) + }) + } + # Position constructors return classes directly + if (inherits(obj, subclass)) { + return(obj) + } + # Try prying the class from a layer + if (inherits(obj, "Layer")) { + obj <- switch( + subclass, + Geom = obj$geom, + Stat = obj$stat, + NULL + ) + } + if (inherits(obj, subclass)) { return(obj) - } else if (is.null(x)) { - cli::cli_abort("The {.arg {x_arg}} argument cannot be empty.", call = call) } - stop_input_type(x, as_cli("either a string or a {.cls {subclass}} object")) + cli::cli_abort("Can't find {argname} called {.val {x}}.", call = call) } # helper function to adjust the draw_key slot of a geom diff --git a/tests/testthat/_snaps/layer.md b/tests/testthat/_snaps/layer.md index 79b561b17d..c796c6a530 100644 --- a/tests/testthat/_snaps/layer.md +++ b/tests/testthat/_snaps/layer.md @@ -1,14 +1,14 @@ # layer() checks its input - The `geom` argument cannot be empty. + `geom` must be either a string or a object, not `NULL`. --- - The `stat` argument cannot be empty. + `stat` must be either a string or a object, not `NULL`. --- - The `position` argument cannot be empty. + `position` must be either a string or a object, not `NULL`. --- @@ -25,7 +25,13 @@ --- - `x` must be either a string or a object, not an environment. + `environment()` must be either a string or a object, not an environment. + +--- + + Failed to retrieve a object from `geom_foo()`. + Caused by error in `geom_foo()`: + ! This function is unconstructable. # unknown params create warning diff --git a/tests/testthat/test-layer.R b/tests/testthat/test-layer.R index f901d3b62f..5e2dbf1d2b 100644 --- a/tests/testthat/test-layer.R +++ b/tests/testthat/test-layer.R @@ -10,6 +10,9 @@ test_that("layer() checks its input", { expect_snapshot_error(validate_subclass("test", "geom")) expect_snapshot_error(validate_subclass(environment(), "geom")) + + geom_foo <- function(...) stop("This function is unconstructable.") + expect_snapshot_error(layer("foo", "identity", position = "identity")) }) test_that("aesthetics go in aes_params", { @@ -154,6 +157,22 @@ test_that("layer names can be resolved", { expect_snapshot(p + l + l, error = TRUE) }) +test_that("check_subclass can resolve classes via constructors", { + + env <- new_environment(list( + geom_foobar = geom_point, + stat_foobar = stat_boxplot, + position_foobar = position_nudge, + guide_foobar = guide_axis_theta + )) + + expect_s3_class(validate_subclass("foobar", "Geom", env = env), "GeomPoint") + expect_s3_class(validate_subclass("foobar", "Stat", env = env), "StatBoxplot") + expect_s3_class(validate_subclass("foobar", "Position", env = env), "PositionNudge") + expect_s3_class(validate_subclass("foobar", "Guide", env = env), "GuideAxisTheta") + +}) + test_that("attributes on layer data are preserved", { # This is a good layer for testing because: # * It needs to compute a statistic at the group level From d2cf9db8a63562ddf744578aa838337ed4d73ceb Mon Sep 17 00:00:00 2001 From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com> Date: Tue, 25 Mar 2025 11:50:31 +0100 Subject: [PATCH 240/264] Bump deprecations (#6138) * `deprecate_stop()` for everything prior to ggplot2 3.0.0 * stuff before 3.2.0 becomes proper warning * add news bullet * document * use tidy eval idioms to replace old idioms * run revdepcheck * use dynamic deprecation strategy in `fix_bin_params()` * just treat old elements as any other misspelled element * Get more in-your-face about deprecating size in favour of linewidth * bump `qplot()` * Turn `fix_labeller()` into a check function * bump version in bullet --------- Co-authored-by: Thomas Lin Pedersen --- NEWS.md | 4 + R/aes.R | 28 +- R/annotation-custom.R | 2 +- R/bin.R | 14 +- R/facet-grid-.R | 7 +- R/facet-wrap.R | 7 +- R/fortify-map.R | 2 +- R/geom-.R | 4 +- R/geom-spoke.R | 3 +- R/labeller.R | 24 +- R/layer.R | 12 +- R/plot.R | 9 +- R/quick-plot.R | 2 +- R/theme-elements.R | 8 +- R/theme.R | 28 - man/print.ggplot.Rd | 9 +- revdep/README.md | 1185 +- revdep/cran.md | 1610 +- revdep/failures.md | 9548 +++++--- revdep/problems.md | 30024 +++++++++--------------- tests/testthat/_snaps/facet-labels.md | 5 - tests/testthat/test-facet-labels.R | 10 +- 22 files changed, 18648 insertions(+), 23897 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3957042f3b..e119ab57e3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # ggplot2 (development version) +* Deprecated functions and arguments prior to ggplot2 3.0.0 throw errors instead + of warnings. +* Functions and arguments that were soft-deprecated up to ggplot2 3.4.0 now + throw warnings. * (internal) layer data can be attenuated with parameter attributes (@teunbrand, #3175). * Date scales silently coerce to and datetime scales silently diff --git a/R/aes.R b/R/aes.R index 045d388d8a..60655a24bd 100644 --- a/R/aes.R +++ b/R/aes.R @@ -290,7 +290,7 @@ is_position_aes <- function(vars) { #' #' @export aes_ <- function(x, y, ...) { - deprecate_soft0( + deprecate_warn0( "3.0.0", "aes_()", details = "Please use tidy evaluation idioms with `aes()`" @@ -317,7 +317,7 @@ aes_ <- function(x, y, ...) { #' @rdname aes_ #' @export aes_string <- function(x, y, ...) { - deprecate_soft0( + deprecate_warn0( "3.0.0", "aes_string()", details = c( @@ -374,29 +374,7 @@ aes_all <- function(vars) { #' @keywords internal #' @export aes_auto <- function(data = NULL, ...) { - deprecate_warn0("2.0.0", "aes_auto()") - - # detect names of data - if (is.null(data)) { - cli::cli_abort("{.fn aes_auto} requires a {.cls data.frame} or names of data.frame.") - } else if (is.data.frame(data)) { - vars <- names(data) - } else { - vars <- data - } - - # automatically detected aes - vars <- intersect(ggplot_global$all_aesthetics, vars) - names(vars) <- vars - aes <- lapply(vars, function(x) parse(text = x)[[1]]) - - # explicitly defined aes - if (length(match.call()) > 2) { - args <- as.list(match.call()[-1]) - aes <- c(aes, args[names(args) != "data"]) - } - - structure(rename_aes(aes), class = "uneval") + lifecycle::deprecate_stop("2.0.0", "aes_auto()") } mapped_aesthetics <- function(x) { diff --git a/R/annotation-custom.R b/R/annotation-custom.R index 76cb26ac2c..8f060efab2 100644 --- a/R/annotation-custom.R +++ b/R/annotation-custom.R @@ -80,7 +80,7 @@ GeomCustomAnn <- ggproto("GeomCustomAnn", Geom, editGrob(grob, vp = vp, name = paste(grob$name, annotation_id())) }, - default_aes = aes_(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf) + default_aes = aes(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf) ) annotation_id <- local({ diff --git a/R/bin.R b/R/bin.R index f45fe90090..a213513b1b 100644 --- a/R/bin.R +++ b/R/bin.R @@ -240,18 +240,24 @@ bin_loc <- function(x, id) { ) } -fix_bin_params = function(params, fun, version) { +fix_bin_params <- function(params, fun, version) { + + if (package_version(version) < "3.0.0") { + deprecate <- lifecycle::deprecate_stop + } else { + deprecate <- deprecate_warn0 + } if (!is.null(params$origin)) { args <- paste0(fun, c("(origin)", "(boundary)")) - deprecate_warn0(version, args[1], args[2]) - params$boudnary <- params$origin + deprecate(version, args[1], args[2]) + params$boundary <- params$origin params$origin <- NULL } if (!is.null(params$right)) { args <- paste0(fun, c("(right)", "(closed)")) - deprecate_warn0(version, args[1], args[2]) + deprecate(version, args[1], args[2]) params$closed <- if (isTRUE(params$right)) "right" else "left" params$right <- NULL } diff --git a/R/facet-grid-.R b/R/facet-grid-.R index ff5cdf0d81..b41bbbac42 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -132,10 +132,9 @@ facet_grid <- function(rows = NULL, cols = NULL, scales = "fixed", switch = NULL, drop = TRUE, margins = FALSE, axes = "margins", axis.labels = "all", facets = deprecated()) { - # `facets` is deprecated and renamed to `rows` + # `facets` is deprecated if (lifecycle::is_present(facets)) { - deprecate_warn0("2.2.0", "facet_grid(facets)", "facet_grid(rows)") - rows <- facets + lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") } # Should become a warning in a future release @@ -177,7 +176,7 @@ facet_grid <- function(rows = NULL, cols = NULL, scales = "fixed", facets_list <- grid_as_facets_list(rows, cols) # Check for deprecated labellers - labeller <- fix_labeller(labeller) + check_labeller(labeller) ggproto(NULL, FacetGrid, shrink = shrink, diff --git a/R/facet-wrap.R b/R/facet-wrap.R index 6bc72f8af4..bbe121d37b 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -174,14 +174,15 @@ facet_wrap <- function(facets, nrow = NULL, ncol = NULL, scales = "fixed", ) # Check for deprecated labellers - labeller <- fix_labeller(labeller) + check_labeller(labeller) # Flatten all facets dimensions into a single one facets <- compact_facets(facets) if (lifecycle::is_present(switch) && !is.null(switch)) { - deprecate_warn0("2.2.0", "facet_wrap(switch)", "facet_wrap(strip.position)") - strip.position <- if (switch == "x") "bottom" else "left" + lifecycle::deprecate_stop( + "2.2.0", "facet_wrap(switch)", "facet_wrap(strip.position)" + ) } strip.position <- arg_match0(strip.position, c("top", "bottom", "left", "right")) diff --git a/R/fortify-map.R b/R/fortify-map.R index e124e57e54..19b58a04bf 100644 --- a/R/fortify-map.R +++ b/R/fortify-map.R @@ -159,6 +159,6 @@ map_data <- function(map, region = ".", exact = FALSE, ...) { borders <- function(database = "world", regions = ".", fill = NA, colour = "grey50", xlim = NULL, ylim = NULL, ...) { df <- map_data(database, regions, xlim = xlim, ylim = ylim) - geom_polygon(aes_(~long, ~lat, group = ~group), data = df, + geom_polygon(aes(.data$long, .data$lat, group = .data$group), data = df, fill = fill, colour = colour, ..., inherit.aes = FALSE) } diff --git a/R/geom-.R b/R/geom-.R index c19b1f3458..8f3705c249 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -126,7 +126,7 @@ Geom <- ggproto("Geom", # Take care of subclasses setting the wrong default when inheriting from # a geom with rename_size = TRUE if (self$rename_size && is.null(default_aes$linewidth)) { - deprecate_soft0("3.4.0", I("Using the `size` aesthetic in this geom"), I("`linewidth` in the `default_aes` field and elsewhere")) + deprecate_warn0("3.4.0", I("Using the `size` aesthetic in this geom"), I("`linewidth` in the `default_aes` field and elsewhere")) default_aes$linewidth <- default_aes$size } @@ -281,7 +281,7 @@ check_aesthetics <- function(x, n) { fix_linewidth <- function(data, name) { if (is.null(data$linewidth) && !is.null(data$size)) { - deprecate_soft0("3.4.0", I(paste0("Using the `size` aesthetic with ", name)), I("the `linewidth` aesthetic")) + deprecate_warn0("3.4.0", I(paste0("Using the `size` aesthetic with ", name)), I("the `linewidth` aesthetic")) data$linewidth <- data$size } data diff --git a/R/geom-spoke.R b/R/geom-spoke.R index 032267b765..9ffbe71144 100644 --- a/R/geom-spoke.R +++ b/R/geom-spoke.R @@ -47,8 +47,7 @@ geom_spoke <- function(mapping = NULL, data = NULL, #' @rdname geom_spoke #' @usage NULL stat_spoke <- function(...) { - deprecate_warn0("2.0.0", "stat_spoke()", "geom_spoke()") - geom_spoke(...) + lifecycle::deprecate_stop("2.0.0", "stat_spoke()", "geom_spoke()") } #' @rdname ggplot2-ggproto diff --git a/R/labeller.R b/R/labeller.R index a9ba883a79..9afd572da0 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -411,7 +411,7 @@ labeller <- function(..., .rows = NULL, .cols = NULL, keep.as.numeric = deprecated(), .multi_line = TRUE, .default = label_value) { if (lifecycle::is_present(keep.as.numeric)) { - deprecate_warn0("2.0.0", "labeller(keep.as.numeric)") + lifecycle::deprecate_stop("2.0.0", "labeller(keep.as.numeric)") } dots <- list2(...) .default <- as_labeller(.default) @@ -577,22 +577,18 @@ assemble_strips <- function(grobs, theme, horizontal = TRUE, clip) { }) } -# Repair old school labeller -fix_labeller <- function(labeller) { +# Reject old school labeller +check_labeller <- function(labeller) { + labeller <- match.fun(labeller) is_deprecated <- all(c("variable", "value") %in% names(formals(labeller))) - if (is_deprecated) { - deprecate_warn0( - "2.0.0", what = "facet_(labeller)", - details = - "Modern labellers do not take `variable` and `value` arguments anymore." - ) - old_labeller <- labeller - labeller <- function(labels) { - Map(old_labeller, names(labels), labels) - } + if (!is_deprecated) { + return(invisible()) } - labeller + lifecycle::deprecate_stop( + "2.0.0", + what = I("Providing a labeller with `variable` and `value` arguments") + ) } diff --git a/R/layer.R b/R/layer.R index 8ed938def6..4e50f7a823 100644 --- a/R/layer.R +++ b/R/layer.R @@ -104,9 +104,9 @@ layer <- function(geom = NULL, stat = NULL, # Handle show_guide/show.legend if (!is.null(params$show_guide)) { - deprecate_warn0("2.0.0", "layer(show_guide)", "layer(show.legend)", user_env = user_env) - show.legend <- params$show_guide - params$show_guide <- NULL + lifecycle::deprecate_stop( + "2.0.0", "layer(show_guide)", "layer(show.legend)" + ) } # we validate mapping before data because in geoms and stats @@ -156,7 +156,7 @@ layer <- function(geom = NULL, stat = NULL, if (geom$rename_size && "size" %in% extra_param && !"linewidth" %in% mapped_aesthetics(mapping)) { aes_params <- c(aes_params, params["size"]) extra_param <- setdiff(extra_param, "size") - deprecate_soft0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`"), user_env = user_env) + deprecate_warn0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`"), user_env = user_env) } if (check.param && length(extra_param) > 0) { cli::cli_warn("Ignoring unknown parameters: {.arg {extra_param}}", call = call_env) @@ -169,7 +169,7 @@ layer <- function(geom = NULL, stat = NULL, # Take care of size->linewidth aes renaming if (geom$rename_size && "size" %in% extra_aes && !"linewidth" %in% mapped_aesthetics(mapping)) { extra_aes <- setdiff(extra_aes, "size") - deprecate_soft0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`"), user_env = user_env) + deprecate_warn0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`"), user_env = user_env) } if (check.aes && length(extra_aes) > 0) { cli::cli_warn("Ignoring unknown aesthetics: {.field {extra_aes}}", call = call_env) @@ -273,7 +273,7 @@ Layer <- ggproto("Layer", NULL, !"linewidth" %in% names(self$computed_mapping) && "linewidth" %in% self$geom$aesthetics()) { self$computed_mapping$size <- plot$mapping$size - deprecate_soft0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`")) + deprecate_warn0("3.4.0", I("Using `size` aesthetic for lines"), I("`linewidth`")) } # defaults() strips class, but it needs to be preserved for now class(self$computed_mapping) <- "uneval" diff --git a/R/plot.R b/R/plot.R index f6a6aaeb49..c992530a0b 100644 --- a/R/plot.R +++ b/R/plot.R @@ -178,18 +178,17 @@ plot_clone <- function(plot) { #' @export #' @method print ggplot #' @examples -#' colours <- list(~class, ~drv, ~fl) +#' colours <- c("class", "drv", "fl") #' #' # Doesn't seem to do anything! #' for (colour in colours) { -#' ggplot(mpg, aes_(~ displ, ~ hwy, colour = colour)) + +#' ggplot(mpg, aes(displ, hwy, colour = .data[[colour]])) + #' geom_point() #' } #' -#' # Works when we explicitly print the plots #' for (colour in colours) { -#' print(ggplot(mpg, aes_(~ displ, ~ hwy, colour = colour)) + -#' geom_point()) +#' print(ggplot(mpg, aes(displ, hwy, colour = .data[[colour]])) + +#' geom_point()) #' } print.ggplot <- function(x, newpage = is.null(vp), vp = NULL, ...) { set_last_plot(x) diff --git a/R/quick-plot.R b/R/quick-plot.R index 38cfd895fc..64e2ab460d 100644 --- a/R/quick-plot.R +++ b/R/quick-plot.R @@ -62,7 +62,7 @@ qplot <- function(x, y, ..., data, facets = NULL, margins = FALSE, xlab = NULL, ylab = NULL, asp = NA, stat = deprecated(), position = deprecated()) { - deprecate_soft0("3.4.0", "qplot()") + deprecate_warn0("3.4.0", "qplot()") caller_env <- parent.frame() diff --git a/R/theme-elements.R b/R/theme-elements.R index c3b6ded319..4fcc4b1d25 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -94,7 +94,7 @@ element_rect <- function(fill = NULL, colour = NULL, linewidth = NULL, linetype = NULL, color = NULL, inherit.blank = FALSE, size = deprecated()) { if (lifecycle::is_present(size)) { - deprecate_soft0("3.4.0", "element_rect(size)", "element_rect(linewidth)") + deprecate_warn0("3.4.0", "element_rect(size)", "element_rect(linewidth)") linewidth <- size } @@ -115,7 +115,7 @@ element_line <- function(colour = NULL, linewidth = NULL, linetype = NULL, inherit.blank = FALSE, size = deprecated()) { if (lifecycle::is_present(size)) { - deprecate_soft0("3.4.0", "element_line(size)", "element_line(linewidth)") + deprecate_warn0("3.4.0", "element_line(size)", "element_line(linewidth)") linewidth <- size } @@ -307,7 +307,7 @@ element_grob.element_rect <- function(element, x = 0.5, y = 0.5, fill = NULL, colour = NULL, linewidth = NULL, linetype = NULL, ..., size = deprecated()) { if (lifecycle::is_present(size)) { - deprecate_soft0("3.4.0", "element_grob.element_rect(size)", "element_grob.element_rect(linewidth)") + deprecate_warn0("3.4.0", "element_grob.element_rect(size)", "element_grob.element_rect(linewidth)") linewidth <- size } @@ -357,7 +357,7 @@ element_grob.element_line <- function(element, x = 0:1, y = 0:1, default.units = "npc", id.lengths = NULL, ..., size = deprecated()) { if (lifecycle::is_present(size)) { - deprecate_soft0("3.4.0", "element_grob.element_line(size)", "element_grob.element_line(linewidth)") + deprecate_warn0("3.4.0", "element_grob.element_line(size)", "element_grob.element_line(linewidth)") linewidth <- size } diff --git a/R/theme.R b/R/theme.R index dfe986fc62..d2029cb22b 100644 --- a/R/theme.R +++ b/R/theme.R @@ -469,34 +469,6 @@ theme <- function(..., validate = TRUE) { elements <- find_args(..., complete = NULL, validate = NULL) - if (!is.null(elements$axis.ticks.margin)) { - deprecate_warn0( - "2.0.0", "theme(axis.ticks.margin)", - details = "Please set `margin` property of `axis.text` instead" - ) - elements$axis.ticks.margin <- NULL - } - if (!is.null(elements$panel.margin)) { - deprecate_warn0( - "2.2.0", "theme(panel.margin)", "theme(panel.spacing)" - ) - elements$panel.spacing <- elements$panel.margin - elements$panel.margin <- NULL - } - if (!is.null(elements$panel.margin.x)) { - deprecate_warn0( - "2.2.0", "theme(panel.margin.x)", "theme(panel.spacing.x)" - ) - elements$panel.spacing.x <- elements$panel.margin.x - elements$panel.margin.x <- NULL - } - if (!is.null(elements$panel.margin.y)) { - deprecate_warn0( - "2.2.0", "theme(panel.margin.y)", "theme(panel.spacing.y)" - ) - elements$panel.spacing.y <- elements$panel.margin.y - elements$panel.margin.y <- NULL - } if (is.unit(elements$legend.margin) && !is.margin(elements$legend.margin)) { cli::cli_warn(c( "{.var legend.margin} must be specified using {.fn margin}", diff --git a/man/print.ggplot.Rd b/man/print.ggplot.Rd index 07b2a68942..1d558a3e9e 100644 --- a/man/print.ggplot.Rd +++ b/man/print.ggplot.Rd @@ -28,18 +28,17 @@ to call \code{print()} explicitly if you want to draw a plot inside a function or for loop. } \examples{ -colours <- list(~class, ~drv, ~fl) +colours <- c("class", "drv", "fl") # Doesn't seem to do anything! for (colour in colours) { - ggplot(mpg, aes_(~ displ, ~ hwy, colour = colour)) + + ggplot(mpg, aes(displ, hwy, colour = .data[[colour]])) + geom_point() } -# Works when we explicitly print the plots for (colour in colours) { - print(ggplot(mpg, aes_(~ displ, ~ hwy, colour = colour)) + - geom_point()) + print(ggplot(mpg, aes(displ, hwy, colour = .data[[colour]])) + + geom_point()) } } \keyword{hplot} diff --git a/revdep/README.md b/revdep/README.md index 498c024ad2..ea1dc6ed4c 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,646 +1,555 @@ # Revdeps -## Failed to check (165) +## Failed to check (196) -|package |version |error |warning |note | -|:-----------------------|:-------|:------|:-------|:----| -|abctools |1.1.7 |1 | | | -|adjclust |? | | | | -|animalEKF |1.2 |1 | | | -|ANOM |0.5 |1 | | | -|atRisk |0.1.0 |1 | | | -|AutoScore |? | | | | -|baRulho |? | | | | -|bayesDP |1.3.6 |1 | | | -|BayesianFactorZoo |0.0.0.2 |1 | | | -|BayesSurvive |0.0.2 |1 | | | -|BCClong |1.0.3 |1 | | | -|BGGM |2.1.3 |1 | | | -|binsreg |1.1 |1 | | | -|bspcov |1.0.0 |1 | | | -|bsub |1.1.0 |1 | | | -|BuyseTest |3.0.4 |1 | | | -|CARBayesST |4.0 |1 | | | -|CGPfunctions |0.6.3 |1 | | | -|chemodiv |? | | | | -|cinaR |? | | | | -|cmprskcoxmsm |0.2.1 |1 | | | -|CNVScope |? | | | | -|COMMA |1.0.0 |1 | | | -|conos |? | | | | -|counterfactuals |? | | | | -|CRMetrics |? | | | | -|crosstalkr |? | | | | -|ctsem |3.10.1 |1 | | | -|DepthProc |2.1.5 |1 | | | -|DR.SC |3.4 |1 | | | -|easybgm |0.1.2 |1 | | | -|EcoEnsemble |1.1.0 |1 | | | -|ecolottery |1.0.0 |1 | | | -|EMAS |? | | | | -|EpiEstim |2.2-4 |1 | | | -|evolqg |0.3-4 |1 | | | -|EWSmethods |? | | | | -|fmx |? | | | | -|ForecastComb |1.3.1 |1 | | | -|GALLO |? | | | | -|gap |? | | | | -|gapfill |0.9.6-1 |1 | |1 | -|geneHapR |? | | | | -|GeneSelectR |? | | | | -|GeomComb |1.0 |1 | | | -|geomorph |? | | | | -|gJLS2 |0.2.0 |1 | | | -|hettx |0.1.3 |1 | | | -|Hmisc |? | | | | -|Hmsc |3.0-13 |1 | | | -|iClusterVB |0.1.2 |1 | | | +|package |version |error |warning |note | +|:----------------------|:-------|:------|:-------|:----| +|abctools |1.1.7 |1 | | | +|adjustedCurves |? | | | | +|animalEKF |1.2 |1 | | | +|ANOM |0.5 |1 | | | +|atRisk |0.2.0 |1 | | | +|autoReg |? | | | | +|AutoScore |? | | | | +|[bartMan](failures.md#bartman)|0.1.1 |__+1__ | | | +|bayesDP |1.3.7 |1 | | | +|BayesianFactorZoo |0.0.0.3 |1 | | | +|BayesSurvive |? | | | | +|BCClong |1.0.3 |1 | | | +|BGGM |2.1.5 |1 | | | +|binsreg |1.1 |1 | | | +|bspcov |1.0.1 |1 | | | +|BSTZINB |1.0.1 |1 | | | +|BuyseTest |? | | | | +|CAESAR.Suite |? | | | | +|CARBayesST |4.0 |1 | | | +|Certara.VPCResults |3.0.2 |1 | | | +|CGPfunctions |0.6.3 |1 | | | +|cia |? | | | | +|cinaR |? | | | | +|cmprskcoxmsm |0.2.1 |1 | | | +|COMMA |1.1.1 |1 | | | +|contsurvplot |? | | | | +|counterfactuals |? | | | | +|CRMetrics |0.3.2 |1 | | | +|ctsem |3.10.2 |1 | | | +|dartR.base |? | | | | +|dartR.captive |? | | | | +|dartR.popgen |? | | | | +|dartR.sexlinked |? | | | | +|dartR.sim |? | | | | +|dartR.spatial |? | | | | +|DepthProc |2.1.5 |1 | | | +|DFD |? | | | | +|dMrs |? | | | | +|DR.SC |3.4 |1 | | | +|dscoreMSM |? | | | | +|DynForest |? | | | | +|easybgm |0.2.1 |1 | | | +|EcoEnsemble |1.1.0 |1 | | | +|ecolottery |1.0.0 |1 | | | +|EpiEstim |2.2-4 |1 | | | +|evolqg |0.3-4 |1 | | | +|EWSmethods |? | | | | +|flexrsurv |? | | | | +|fmx |? | | | | +|ForecastComb |1.3.1 |1 | | | +|gap |? | | | | +|gapfill |0.9.6-1 |1 | |1 | +|genekitr |? | | | | +|GeneSelectR |? | | | | +|GeomComb |1.0 |1 | | | +|geomorph |? | | | | +|GeoTox |? | | | | +|[ggtern](failures.md#ggtern)|3.5.0 |__+1__ | |1 -1 | +|[ggThemeAssist](failures.md#ggthemeassist)|0.1.5 |__+1__ | |-1 | +|gJLS2 |0.2.0 |1 | | | +|grandR |? | | | | +|GseaVis |? | | | | +|hettx |0.1.3 |1 | | | +|Hmisc |? | | | | +|Hmsc |3.0-13 |1 | | | +|iClusterVB |0.1.4 |1 | | | +|immcp |? | | | | |[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | -|iNZightPlots |2.15.3 |1 | | | -|iNZightRegression |1.3.4 |1 | | | -|IRexamples |0.0.4 |1 | | | -|jmBIG |0.1.2 |1 | | | -|joineRML |0.4.6 |1 | | | -|kibior |? | | | | -|kmc |0.4-2 |1 | | | -|L2E |2.0 |1 | | | -|llbayesireg |1.0.0 |1 | | | -|locuszoomr |? | | | | -|LorenzRegression |2.0.0 |1 | | | -|lsirm12pl |1.3.3 |1 | | | -|MantaID |? | | | | -|MARVEL |? | | | | -|mbsts |3.0 |1 | | | -|MitoHEAR |? | | | | -|miWQS |0.4.4 |1 | | | -|mlmts |1.1.2 |1 | | | -|mlr |? | | | | -|MOCHA |? | | | | -|MRZero |0.2.0 |1 | | | -|multilevelTools |0.1.1 |1 | | | -|multinma |0.7.1 |1 | | | -|NCA |4.0.1 |1 | | | -|netcmc |1.0.2 |1 | | | -|NetworkChange |0.8 |1 | | | -|nlmeVPC |2.6 |1 | | | -|NMADiagT |0.1.2 |1 | | | -|ohun |? | | | | -|optweight |0.2.5 |1 | | | -|OVtool |1.0.3 |1 | | | -|pagoda2 |? | | | | -|PAMpal |1.2.1 |1 | | | -|PAMscapes |0.6.0 |1 | | | -|paths |0.1.1 |1 | | | -|PathwaySpace |? | | | | -|pcvr |1.0.0 |1 | | | -|PlasmaMutationDetector |? | | | | -|PlasmaMutationDetector2 |? | | | | -|PLMIX |2.1.1 |1 | | | -|polyRAD |? | | | | -|popstudy |1.0.1 |1 | | | -|pould |1.0.1 |1 | | | -|PoweREST |0.1.0 |1 | | | -|powerly |1.8.6 |1 | | | -|pre |1.0.7 |1 | | | -|ProFAST |? | | | | -|psbcSpeedUp |2.0.7 |1 | | | -|pscore |0.4.0 |1 | | | -|qPCRtools |1.0.1 |1 | | | -|qris |1.1.1 |1 | | | -|qte |1.3.1 |1 | | | -|quantilogram |3.1.1 |1 | | | -|quid |0.0.1 |1 | | | -|RcmdrPlugin.RiskDemo |3.2 |1 | | | -|rddtools |1.6.0 |1 | | | -|RGraphSpace |? | | | | -|rms |? | | | | -|RNAseqQC |? | | | | -|robmed |1.0.2 |1 | | | -|robmedExtra |0.1.0 |1 | | | -|RPPanalyzer |1.4.9 |1 | | | -|RQdeltaCT |1.3.0 |1 | | | -|RRPP |? | | | | -|rstanarm |2.32.1 |1 | | | -|RTIGER |? | | | | -|rTwig |1.1.0 |1 | | | -|RVA |? | | | | -|scCustomize |? | | | | -|SCdeconR |1.0.0 |1 | | | -|scGate |1.6.2 |1 | | | -|SCIntRuler |0.99.6 |1 | | | -|scITD |? | | | | -|scMappR |1.0.11 |1 | | | -|scpi |2.2.5 |1 | | | -|scRNAstat |0.1.1 |1 | | | -|sectorgap |0.1.0 |1 | | | -|SeedMatchR |? | | | | -|SEERaBomb |2019.2 |1 | | | -|semicmprskcoxmsm |0.2.0 |1 | | | -|SensMap |0.7 |1 | | | -|sephora |? | | | | -|Seurat |? | | | | -|shinyTempSignal |0.0.8 |1 | | | -|sievePH |1.1 |1 | | | -|sigminer |? | | | | -|Signac |? | | | | -|SimplyAgree |0.2.0 |1 | | | -|SNPassoc |? | | | | -|snplinkage |? | | | | -|SoupX |1.6.2 |1 | | | -|sparsereg |1.2 |1 | | | -|SpatialDDLS |? | | | | -|spikeSlabGAM |1.1-19 |1 | | | -|statsr |0.3.0 |1 | | | -|streamDAG |? | | | | -|survidm |1.3.2 |1 | | | -|tempted |0.1.1 |1 | | | -|TestAnaAPP |1.1.1 |1 | | | +|invivoPKfit |2.0.0 |1 | | | +|iNZightPlots |2.15.3 |1 | | | +|iNZightRegression |1.3.4 |1 | | | +|IRexamples |0.0.4 |1 | | | +|jmBIG |? | | | | +|joineRML |0.4.6 |1 | | | +|jsmodule |? | | | | +|kmc |0.4-2 |1 | | | +|KMunicate |? | | | | +|L2E |2.0 |1 | | | +|Landmarking |? | | | | +|lavaSearch2 |? | | | | +|llbayesireg |1.0.0 |1 | | | +|lnmixsurv |? | | | | +|LorenzRegression |2.1.0 |1 | | | +|lsirm12pl |1.3.3 |1 | | | +|MantaID |? | | | | +|MARVEL |? | | | | +|MaxWiK |1.0.5 |1 | | | +|mbsts |3.0 |1 | | | +|MendelianRandomization |0.10.0 |1 | | | +|miWQS |0.4.4 |1 | |1 | +|mlmts |1.1.2 |1 | | | +|mlr |? | | | | +|MRZero |0.2.0 |1 | | | +|mstate |? | | | | +|multilevelTools |0.1.1 |1 | | | +|multinma |0.7.2 |1 | | | +|multipleOutcomes |? | | | | +|MuPETFlow |? | | | | +|NCA |4.0.2 |1 | | | +|netcmc |1.0.2 |1 | | | +|NetworkChange |0.8 |1 | | | +|nlmeVPC |2.6 |1 | | | +|NMADiagT |0.1.2 |1 | | | +|[NMF](failures.md#nmf) |0.28 |__+1__ | |-1 | +|obliqueRSF |? | | | | +|OlinkAnalyze |? | | | | +|optweight |0.2.5 |1 | | | +|OVtool |1.0.3 |1 | | | +|pammtools |? | | | | +|paths |0.1.1 |1 | | | +|PathwaySpace |? | | | | +|pcvr |1.1.1.0 |1 | | | +|PLMIX |2.1.1 |1 | | | +|popstudy |1.0.1 |1 | | | +|pould |? | | | | +|PoweREST |0.1.0 |1 | | | +|powerly |1.8.6 |1 | | | +|pre |1.0.7 |1 | | | +|ProFAST |? | | | | +|psbcSpeedUp |? | | | | +|pscore |0.4.0 |1 | | | +|pubh |? | | | | +|qPCRtools |1.0.1 |1 | | | +|qris |1.1.1 |1 | | | +|qte |1.3.1 |1 | | | +|quantilogram |3.1.1 |1 | | | +|quid |0.0.1 |1 | | | +|RcmdrPlugin.RiskDemo |3.2 |1 | | | +|rddtools |1.6.0 |1 | | | +|relsurv |? | | | | +|ReporterScore |? | | | | +|RGraphSpace |? | | | | +|riskRegression |? | | | | +|rmlnomogram |? | | | | +|rms |? | | | | +|robber |? | | | | +|robmed |1.2.0 |1 | | | +|robmedExtra |0.1.1 |1 | | | +|RPPanalyzer |1.4.9 |1 | | | +|RQdeltaCT |1.3.0 |1 | | | +|RRPP |? | | | | +|rstanarm |2.32.1 |1 | | | +|rTwig |1.3.0 |1 | | | +|RVA |? | | | | +|S4DM |0.0.1 |1 | | | +|scCustomize |3.0.1 |1 | |1 | +|SCdeconR |1.0.0 |1 | | | +|scGate |1.6.2 |1 | | | +|SCIntRuler |0.99.6 |1 | | | +|scMappR |1.0.11 |1 | | | +|scpi |2.2.6 |1 | | | +|SCpubr |? | | | | +|scRNAstat |0.1.1 |1 | | | +|sectorgap |0.1.0 |1 | | | +|SEERaBomb |2019.2 |1 | | | +|semicmprskcoxmsm |0.2.0 |1 | | | +|SensMap |0.7 |1 | | | +|Seurat |5.2.1 |1 | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|SiFINeT |1.13 |1 | | | +|[sigminer](failures.md#sigminer)|2.3.1 |__+1__ | |-1 | +|Signac |1.14.0 |1 | | | +|SimplyAgree |0.2.0 |1 | | | +|smer |? | | | | +|SNPassoc |? | | | | +|snplinkage |? | | | | +|SoupX |1.6.2 |1 | | | +|SpaCCI |1.0.3 |1 | | | +|sparsereg |1.2 |1 | | | +|[spectralAnalysis](failures.md#spectralanalysis)|4.3.3 |__+1__ | |-1 | +|spikeSlabGAM |1.1-20 |1 | | | +|stabiliser |1.0.6 |1 | | | +|statsr |0.3.0 |1 | | | +|streamDAG |? | | | | +|survex |? | | | | +|survHE |? | | | | +|survidm |1.3.2 |1 | | | +|tempted |0.1.1 |1 | | | +|TestAnaAPP |? | | | | |[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | -|tidyEdSurvey |0.1.3 |1 | | | -|tidyseurat |0.8.0 |1 | | | -|tidyvpc |1.5.1 |1 | | | -|TriDimRegression |1.0.2 |1 | | | -|TSrepr |1.1.0 |1 | | | -|twang |2.6.1 |1 | | | -|updog |? | | | | -|valr |? | | | | -|vdg |1.2.3 |1 | | | -|visa |0.1.0 |1 | | | -|VisualizeSimon2Stage |? | | | | -|WRTDStidal |1.1.4 |1 | | | -|xxdi |? | | | | +|tidyEdSurvey |0.1.3 |1 | | | +|tidyseurat |0.8.0 |1 | | | +|tidyvpc |1.5.2 |1 | | | +|tinyarray |? | | | | +|treeclim |2.0.7.1 |1 | | | +|TriDimRegression |1.0.2 |1 | | | +|TSrepr |1.1.0 |1 | | | +|twang |2.6.1 |1 | | | +|vdg |1.2.3 |1 | | | +|VecDep |? | | | | +|visa |0.1.0 |1 | | | +|VisualizeSimon2Stage |? | | | | +|[wppExplorer](failures.md#wppexplorer)|2.3-4 |__+1__ | | | +|WRTDStidal |1.1.4 |1 | | | +|xxdi |? | | | | -## New problems (469) +## New problems (347) -|package |version |error |warning |note | -|:---------------------|:---------|:--------|:-------|:--------| -|[activAnalyzer](problems.md#activanalyzer)|2.1.1 |__+1__ | |1 __+1__ | -|[actxps](problems.md#actxps)|1.5.0 |__+1__ | |__+1__ | -|[adaptr](problems.md#adaptr)|1.4.0 |__+3__ | |__+1__ | -|[AeRobiology](problems.md#aerobiology)|2.0.1 |1 | |__+1__ | -|[agricolaeplotr](problems.md#agricolaeplotr)|0.5.0 |__+1__ | | | -|[alien](problems.md#alien)|1.0.2 |__+1__ | |__+1__ | -|[AlphaPart](problems.md#alphapart)|0.9.8 |1 __+1__ | | | -|[AnalysisLin](problems.md#analysislin)|0.1.2 |__+1__ | | | -|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | | -|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 | -|[AnnoProbe](problems.md#annoprobe)|0.1.7 |__+1__ | | | -|[ANOFA](problems.md#anofa)|0.1.3 |__+3__ | |__+1__ | -|[ANOPA](problems.md#anopa)|0.1.3 |__+3__ | |__+1__ | -|[AntMAN](problems.md#antman)|1.1.0 |__+2__ | |3 | -|[APCI](problems.md#apci)|1.0.8 |__+1__ | | | -|[aplot](problems.md#aplot)|0.2.3 |__+1__ | | | -|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | -|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+2__ | |1 | -|[autocogs](problems.md#autocogs)|0.1.4 |__+1__ | |1 | -|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | -|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | |__+1__ | -|[baggr](problems.md#baggr)|0.7.8 |__+3__ | |2 __+1__ | -|[banter](problems.md#banter)|0.9.6 |__+1__ | | | -|[bartMan](problems.md#bartman)|0.1.1 |__+1__ | | | -|[BasketballAnalyzeR](problems.md#basketballanalyzer)|0.5.0 |__+1__ | |2 | -|[bayefdr](problems.md#bayefdr)|0.2.1 |__+2__ | | | -|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | -|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | -|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+2__ | |__+1__ | -|[BayesMallows](problems.md#bayesmallows)|2.2.2 |__+1__ | |1 | -|[bayesplay](problems.md#bayesplay)|0.9.3 |__+2__ | |__+1__ | -|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+2__ | |1 | -|[bayestestR](problems.md#bayestestr)|0.14.0 |1 __+1__ | | | -|[BCEA](problems.md#bcea)|2.4.6 |__+3__ | |__+1__ | -|[BDgraph](problems.md#bdgraph)|2.73 |__+1__ | |1 __+1__ | -|[BEAMR](problems.md#beamr)|1.1.0 |__+1__ | | | -|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | -|[BeeGUTS](problems.md#beeguts)|1.1.3 |__+2__ | |2 __+1__ | -|[besthr](problems.md#besthr)|0.3.2 |__+2__ | |__+1__ | -|[betaclust](problems.md#betaclust)|1.0.3 |__+1__ | |__+1__ | -|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | -|[biodosetools](problems.md#biodosetools)|3.6.1 |__+1__ | | | -|[BioPred](problems.md#biopred)|1.0.1 |__+1__ | |__+1__ | -|[BlandAltmanLeh](problems.md#blandaltmanleh)|0.3.1 |__+1__ | | | -|[bmggum](problems.md#bmggum)|0.1.0 |__+1__ | |3 | -|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | | -|[braidReports](problems.md#braidreports)|0.5.4 |__+1__ | | | -|[BRcal](problems.md#brcal)|0.0.4 |__+2__ | |__+1__ | -|[breathtestcore](problems.md#breathtestcore)|0.8.7 |__+1__ | | | -|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | -|[calibrationband](problems.md#calibrationband)|0.2.1 |__+1__ | | | -|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | -|[cases](problems.md#cases)|0.1.1 |__+1__ | |__+1__ | -|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | -|[ceterisParibus](problems.md#ceterisparibus)|0.4.2 |__+1__ | |2 | -|[cfda](problems.md#cfda)|0.11.0 |__+3__ | |__+1__ | -|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | -|[chillR](problems.md#chillr)|0.75 |__+1__ | | | -|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | -|[CINNA](problems.md#cinna)|1.2.2 |__+2__ | |1 __+1__ | -|[circhelp](problems.md#circhelp)|1.1 |__+2__ | |__+1__ | -|[clifro](problems.md#clifro)|3.2-5 |__+1__ | | | -|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | -|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | -|[cloneRate](problems.md#clonerate)|0.2.3 |__+1__ | |2 __+1__ | -|[clustEff](problems.md#clusteff)|0.3.1 |__+1__ | | | -|[ClustImpute](problems.md#clustimpute)|0.2.4 |__+1__ | |1 | -|[cmstatr](problems.md#cmstatr)|0.9.3 |__+3__ | |__+1__ | -|[codaredistlm](problems.md#codaredistlm)|0.1.0 |__+1__ | | | -|[coefplot](problems.md#coefplot)|1.2.8 |__+1__ | | | -|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | -|[complmrob](problems.md#complmrob)|0.7.0 |__+1__ | | | -|[conjoint](problems.md#conjoint)|1.41 |__+1__ | | | -|[conquestr](problems.md#conquestr)|1.3.4 |__+1__ | |__+1__ | -|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | | -|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 | -|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | -|[corx](problems.md#corx)|1.0.7.2 |__+1__ | | | -|[cosinor2](problems.md#cosinor2)|0.2.1 |__+2__ | |__+1__ | -|[CoSMoS](problems.md#cosmos)|2.1.0 |__+1__ | |__+1__ | -|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | -|[coursekata](problems.md#coursekata)|0.18.0 |__+2__ | | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[Coxmos](problems.md#coxmos)|1.0.2 |1 __+1__ | |1 | -|[cpr](problems.md#cpr)|0.4.0 |1 __+1__ | |1 __+1__ | -|[cpsvote](problems.md#cpsvote)|0.1.0 |__+1__ | | | -|[crimeutils](problems.md#crimeutils)|0.5.1 |__+1__ | | | -|[crmPack](problems.md#crmpack)|1.0.6 |__+2__ | |1 | -|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | -|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | -|[cubble](problems.md#cubble)|1.0.0 |__+1__ | |1 __+1__ | -|[curtailment](problems.md#curtailment)|0.2.6 |__+1__ | | | -|[dabestr](problems.md#dabestr)|2023.9.12 |__+1__ | |__+1__ | -|[DAISIEprep](problems.md#daisieprep)|0.4.0 |__+1__ | | | -|[dbmss](problems.md#dbmss)|2.9-2 |__+2__ | |__+1__ | -|[deeptime](problems.md#deeptime)|2.0.0 |__+2__ | |1 __+1__ | -|[descriptio](problems.md#descriptio)|1.3 |__+1__ | |1 | -|[directlabels](problems.md#directlabels)|2024.1.21 |__+1__ | |__+1__ | -|[disto](problems.md#disto)|0.2.0 |__+2__ | |1 __+1__ | -|[distributional](problems.md#distributional)|0.4.0 |__+1__ | | | -|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | -|[dotwhisker](problems.md#dotwhisker)|0.8.2 |__+2__ | |__+1__ | -|[DRomics](problems.md#dromics)|2.5-2 |1 __+1__ | |1 __+1__ | -|[dtwclust](problems.md#dtwclust)|6.0.0 |__+1__ |1 |2 | -|[duke](problems.md#duke)|0.0.3 |__+1__ | | | -|[easysurv](problems.md#easysurv)|2.0.1 |__+2__ | |__+1__ | -|[EGAnet](problems.md#eganet)|2.0.7 |__+1__ | |1 | -|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | -|[emmeans](problems.md#emmeans)|1.10.4 |1 __+1__ | |2 | -|[EMMIXmfa](problems.md#emmixmfa)|2.0.14 |__+1__ | | | -|[entropart](problems.md#entropart)|1.6-15 |__+2__ | |__+1__ | -|[EnvStats](problems.md#envstats)|3.0.0 |__+1__ | |1 | -|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 | -|[epiphy](problems.md#epiphy)|0.5.0 |__+1__ | | | -|[EQUALSTATS](problems.md#equalstats)|0.4.0 |__+1__ | |1 | -|[ergm.multi](problems.md#ergmmulti)|0.2.1 |__+2__ | |__+1__ | -|[esci](problems.md#esci)|1.0.3 |__+2__ | | | -|[evalITR](problems.md#evalitr)|1.0.0 |1 | |1 __+1__ | -|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | | -|[EvoPhylo](problems.md#evophylo)|0.3.2 |1 __+1__ | |1 __+1__ | -|[expirest](problems.md#expirest)|0.1.6 |__+1__ | | | -|[explainer](problems.md#explainer)|1.0.1 |__+1__ | |1 | -|[exuber](problems.md#exuber)|1.0.2 |__+1__ | |__+1__ | -|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | | -|[ezplot](problems.md#ezplot)|0.7.13 |__+1__ | | | -|[fable.prophet](problems.md#fableprophet)|0.1.0 |__+1__ | |1 __+1__ | -|[fabletools](problems.md#fabletools)|0.4.2 |__+2__ | | | -|[factoextra](problems.md#factoextra)|1.0.7 |__+1__ | | | -|[fairmodels](problems.md#fairmodels)|1.2.1 |__+1__ | | | -|[fastR2](problems.md#fastr2)|1.2.4 |__+1__ | |1 | -|[faux](problems.md#faux)|1.2.1 |3 | |__+1__ | -|[fddm](problems.md#fddm)|1.0-2 |__+1__ | |1 | -|[feasts](problems.md#feasts)|0.3.2 |__+1__ | | | -|[fergm](problems.md#fergm)|1.1.4 |__+1__ | | | -|[ffp](problems.md#ffp)|0.2.2 |__+1__ | | | -|[fic](problems.md#fic)|1.0.0 |__+1__ | |2 | -|[fido](problems.md#fido)|1.1.1 |1 __+2__ | |2 | -|[fitdistrplus](problems.md#fitdistrplus)|1.2-1 |__+3__ | |__+1__ | -|[fitlandr](problems.md#fitlandr)|0.1.0 |__+1__ | | | -|[flexsurv](problems.md#flexsurv)|2.3.2 |__+1__ | |2 | -|[flipr](problems.md#flipr)|0.3.3 |1 | |1 __+1__ | -|[FLOPART](problems.md#flopart)|2024.6.19 |__+1__ | |__+1__ | -|[fmesher](problems.md#fmesher)|0.1.7 |__+2__ | |1 __+1__ | -|[fmf](problems.md#fmf)|1.1.1 |__+1__ | |1 | -|[forestly](problems.md#forestly)|0.1.1 |__+1__ | |__+1__ | -|[FossilSim](problems.md#fossilsim)|2.4.0 |__+1__ | | | -|[FPDclustering](problems.md#fpdclustering)|2.3.1 |__+1__ | | | -|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | -|[funcharts](problems.md#funcharts)|1.5.0 |__+1__ | | | -|[FunnelPlotR](problems.md#funnelplotr)|0.5.0 |__+2__ | |__+1__ | -|[genekitr](problems.md#genekitr)|1.2.8 |__+1__ | | | -|[geoheatmap](problems.md#geoheatmap)|0.1.0 |__+1__ | |__+1__ | -|[geomtextpath](problems.md#geomtextpath)|0.1.4 |__+2__ | | | -|[geostan](problems.md#geostan)|0.6.2 |__+1__ | |3 | -|[GGally](problems.md#ggally)|2.2.1 |__+2__ | | | -|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | -|[ggbrain](problems.md#ggbrain)|0.8.1 |__+1__ | |1 __+1__ | -|[ggbreak](problems.md#ggbreak)|0.1.2 |__+2__ | |__+1__ | -|[ggcharts](problems.md#ggcharts)|0.2.1 |__+3__ | |__+1__ | -|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | -|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | -|[ggeasy](problems.md#ggeasy)|0.1.4 |__+3__ | |__+1__ | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggESDA](problems.md#ggesda)|0.2.0 |__+2__ | |__+1__ | -|[ggExtra](problems.md#ggextra)|0.10.1 |__+1__ | |1 __+1__ | -|[ggfacto](problems.md#ggfacto)|0.3.1 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | -|[ggfocus](problems.md#ggfocus)|1.0.0 |__+1__ | |1 __+1__ | -|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 | -|[ggformula](problems.md#ggformula)|0.12.0 |__+3__ |__+1__ |1 __+1__ | -|[ggfortify](problems.md#ggfortify)|0.4.17 |__+3__ | |__+1__ | -|[gggenomes](problems.md#gggenomes)|1.0.1 |__+2__ | |__+1__ | -|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+1__ | |__+1__ | -|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ | |__+1__ | -|[ggHoriPlot](problems.md#gghoriplot)|1.0.1 |__+1__ | |__+1__ | -|[ggiraph](problems.md#ggiraph)|0.8.10 |__+2__ | |1 | -|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+2__ | |__+1__ | -|[ggmatplot](problems.md#ggmatplot)|0.1.2 |__+3__ | |__+1__ | -|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | |__+1__ | -|[ggmulti](problems.md#ggmulti)|1.0.7 |__+3__ | |__+1__ | -|[ggpackets](problems.md#ggpackets)|0.2.1 |__+3__ | |__+1__ | -|[ggparallel](problems.md#ggparallel)|0.4.0 |__+1__ | | | -|[ggparty](problems.md#ggparty)|1.0.0 |__+2__ | |2 __+1__ | -|[ggpicrust2](problems.md#ggpicrust2)|1.7.3 |__+1__ | |2 | -|[ggplotlyExtra](problems.md#ggplotlyextra)|0.0.1 |__+1__ | |1 | -|[ggPMX](problems.md#ggpmx)|1.2.11 |__+2__ | |2 __+1__ | -|[ggpol](problems.md#ggpol)|0.0.7 |__+1__ | |2 | -|[ggprism](problems.md#ggprism)|1.0.5 |__+3__ | |__+1__ | -|[ggpubr](problems.md#ggpubr)|0.6.0 |__+2__ | | | -|[ggrain](problems.md#ggrain)|0.0.4 |__+2__ | |__+1__ | -|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | |1 __+1__ | -|[ggredist](problems.md#ggredist)|0.0.2 |__+1__ | | | -|[ggRtsy](problems.md#ggrtsy)|0.1.0 |__+2__ | |1 __+1__ | -|[ggseqplot](problems.md#ggseqplot)|0.8.4 |__+3__ | |__+1__ | -|[ggside](problems.md#ggside)|0.3.1 |__+1__ |__+1__ | | -|[ggsmc](problems.md#ggsmc)|0.1.2.0 |__+1__ | |1 | -|[ggspatial](problems.md#ggspatial)|1.1.9 |__+2__ | | | -|[ggstatsplot](problems.md#ggstatsplot)|0.12.4 |1 __+1__ | | | -|[ggtern](problems.md#ggtern)|3.5.0 |__+1__ | |2 | -|[ggupset](problems.md#ggupset)|0.4.0 |__+1__ | | | -|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 __+1__ | -|[GimmeMyPlot](problems.md#gimmemyplot)|0.1.0 |__+3__ | |__+1__ | -|[giniVarCI](problems.md#ginivarci)|0.0.1-3 |__+1__ | |1 | -|[gMCPLite](problems.md#gmcplite)|0.1.5 |__+1__ | |__+1__ | -|[gMOIP](problems.md#gmoip)|1.5.2 |__+2__ | |__+1__ | -|[GofCens](problems.md#gofcens)|1.1 |__+1__ | | | -|[greatR](problems.md#greatr)|2.0.0 |__+1__ | |__+1__ | -|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | | -|[gsDesign](problems.md#gsdesign)|3.6.4 |__+3__ | |__+1__ | -|[gtExtras](problems.md#gtextras)|0.5.0 |__+1__ | | | -|[HaploCatcher](problems.md#haplocatcher)|1.0.4 |__+1__ | |__+1__ | -|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 __+1__ | -|[healthyR.ts](problems.md#healthyrts)|0.3.0 |__+2__ | |1 __+1__ | -|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |1 __+1__ | -|[hermiter](problems.md#hermiter)|2.3.1 |__+1__ | |2 __+1__ | -|[heumilkr](problems.md#heumilkr)|0.2.0 |__+1__ | |__+1__ | -|[hilldiv](problems.md#hilldiv)|1.5.1 |__+1__ | | | -|[hmclearn](problems.md#hmclearn)|0.0.5 |__+1__ | | | -|[HTLR](problems.md#htlr)|0.4-4 |__+1__ | |2 __+1__ | -|[HVT](problems.md#hvt)|24.5.2 |__+1__ | | | -|[hypsoLoop](problems.md#hypsoloop)|0.2.0 | |__+1__ | | -|[ibdsim2](problems.md#ibdsim2)|2.1.1 |__+1__ | | | -|[ICtest](problems.md#ictest)|0.3-5 |__+1__ | |1 | -|[idiogramFISH](problems.md#idiogramfish)|2.0.13 |1 | |__+1__ | -|[IDMIR](problems.md#idmir)|0.1.0 |__+2__ | |__+1__ | -|[idopNetwork](problems.md#idopnetwork)|0.1.2 |__+1__ | |__+1__ | -|[ihclust](problems.md#ihclust)|0.1.0 |__+1__ | | | -|[immunarch](problems.md#immunarch)|0.9.1 |__+1__ | |1 | -|[incidental](problems.md#incidental)|0.1 |__+1__ | |__+1__ | -|[infer](problems.md#infer)|1.0.7 |__+3__ | |__+1__ | -|[injurytools](problems.md#injurytools)|1.0.3 |__+1__ | |__+1__ | -|[inlabru](problems.md#inlabru)|2.11.1 |1 __+1__ | |1 | -|[insurancerating](problems.md#insurancerating)|0.7.4 |__+1__ | | | -|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.3 |__+2__ | |1 __+1__ | -|[IPV](problems.md#ipv)|1.0.0 |__+2__ | |1 __+1__ | -|[IRon](problems.md#iron)|0.1.4 |__+1__ | |1 | -|[irt](problems.md#irt)|0.2.9 |__+1__ | |1 | -|[isoorbi](problems.md#isoorbi)|1.3.1 |__+1__ | |1 __+1__ | -|[ivDiag](problems.md#ivdiag)|1.0.6 |__+1__ | | | -|[ivreg](problems.md#ivreg)|0.6-3 |__+1__ | |__+1__ | -|[jarbes](problems.md#jarbes)|2.2.1 |__+1__ | |__+1__ | -|[karel](problems.md#karel)|0.1.1 |__+2__ | |1 | -|[kDGLM](problems.md#kdglm)|1.2.0 |1 __+1__ | | | -|[KMEANS.KNN](problems.md#kmeansknn)|0.1.0 |__+2__ | | | -|[latentcor](problems.md#latentcor)|2.0.1 |__+1__ | | | -|[lcars](problems.md#lcars)|0.3.8 |__+2__ | | | -|[lemon](problems.md#lemon)|0.4.9 |__+3__ | |__+1__ | -|[lfproQC](problems.md#lfproqc)|0.2.0 |__+2__ | |1 __+1__ | -|[lgpr](problems.md#lgpr)|1.2.4 |__+1__ | |2 | -|[LightLogR](problems.md#lightlogr)|0.3.8 |__+1__ | | | -|[LMoFit](problems.md#lmofit)|0.1.7 |__+1__ | |1 __+1__ | -|[lnmixsurv](problems.md#lnmixsurv)|3.1.6 |__+2__ | |4 __+1__ | -|[LocalControl](problems.md#localcontrol)|1.1.4 |__+1__ | |2 | -|[LocalCop](problems.md#localcop)|0.0.1 |1 | |1 __+1__ | -|[LongDat](problems.md#longdat)|1.1.2 |__+1__ | |__+1__ | -|[longreadvqs](problems.md#longreadvqs)|0.1.3 |__+2__ | |__+1__ | -|[lpdensity](problems.md#lpdensity)|2.4 |__+1__ | | | -|[lspartition](problems.md#lspartition)|0.4 |__+1__ | |1 | -|[LSTbook](problems.md#lstbook)|0.5.0 |1 __+1__ |1 |1 __+1__ | -|[manydata](problems.md#manydata)|0.9.3 |__+1__ | |1 | -|[manymome](problems.md#manymome)|0.2.2 |__+1__ | | | -|[mapbayr](problems.md#mapbayr)|0.10.0 |__+1__ | | | -|[MBNMAdose](problems.md#mbnmadose)|0.4.3 |__+1__ | |1 __+1__ | -|[MBNMAtime](problems.md#mbnmatime)|0.2.4 |1 | |__+1__ | -|[mecoturn](problems.md#mecoturn)|0.3.0 |__+1__ | | | -|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | -|[metR](problems.md#metr)|0.15.0 |__+3__ | |1 __+1__ | -|[metrica](problems.md#metrica)|2.1.0 |__+1__ | |__+1__ | -|[miceRanger](problems.md#miceranger)|1.5.0 |__+1__ | | | -|[microbial](problems.md#microbial)|0.0.21 |__+2__ | |__+1__ | -|[MicrobiomeSurv](problems.md#microbiomesurv)|0.1.0 |__+1__ | | | -|[migraph](problems.md#migraph)|1.4.2 |__+1__ | | | -|[mikropml](problems.md#mikropml)|1.6.1 |__+1__ | | | -|[MiMIR](problems.md#mimir)|1.5 |__+1__ | | | -|[miRetrieve](problems.md#miretrieve)|1.3.4 |__+1__ | | | -|[MiscMetabar](problems.md#miscmetabar)|0.9.3 |__+2__ | | | -|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | | -|[mixpoissonreg](problems.md#mixpoissonreg)|1.0.0 |__+3__ | |__+1__ | -|[mizer](problems.md#mizer)|2.5.1 |__+1__ | |1 | -|[mlr3spatiotempcv](problems.md#mlr3spatiotempcv)|2.3.1 |1 __+1__ | |1 | -|[mlr3viz](problems.md#mlr3viz)|0.9.0 |__+2__ | | | -|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 | -|[moreparty](problems.md#moreparty)|0.4 |__+1__ | |__+1__ | -|[mosaicCalc](problems.md#mosaiccalc)|0.6.4 |__+2__ | |1 __+1__ | -|[mosaicData](problems.md#mosaicdata)|0.20.4 |__+1__ | |1 | -|[mosaicModel](problems.md#mosaicmodel)|0.3.0 |__+1__ | |1 __+1__ | -|[mppR](problems.md#mppr)|1.5.0 |__+1__ | |__+1__ | -|[MSCMT](problems.md#mscmt)|1.4.0 |__+1__ | |__+1__ | -|[mstate](problems.md#mstate)|0.3.3 |__+2__ | |1 | -|[mtb](problems.md#mtb)|0.1.8 |__+1__ | | | -|[mulgar](problems.md#mulgar)|1.0.2 |__+1__ | |1 | -|[MultivariateAnalysis](problems.md#multivariateanalysis)|0.5.0 |__+1__ | | | -|[mxfda](problems.md#mxfda)|0.2.1 | | |__+1__ | -|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | -|[neatStats](problems.md#neatstats)|1.13.3 |__+1__ | | | -|[netcom](problems.md#netcom)|2.1.7 |__+1__ | |1 __+1__ | -|[NetFACS](problems.md#netfacs)|0.5.0 |__+2__ | | | -|[neuroUp](problems.md#neuroup)|0.3.1 |__+3__ | |__+1__ | -|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 | -|[nichetools](problems.md#nichetools)|0.3.1 |__+1__ | |__+1__ | -|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 __+1__ | -|[nonmem2R](problems.md#nonmem2r)|0.2.5 |__+2__ | |__+1__ | -|[nphRCT](problems.md#nphrct)|0.1.1 |__+1__ | |__+1__ | -|[nprobust](problems.md#nprobust)|0.4.0 |__+1__ | |1 | -|[nzelect](problems.md#nzelect)|0.4.0 |__+2__ | |2 __+1__ | -|[OBIC](problems.md#obic)|3.0.3 |__+1__ | |1 __+1__ | -|[oceanic](problems.md#oceanic)|0.1.7 |__+1__ | |2 | -|[oddsratio](problems.md#oddsratio)|2.0.1 |__+2__ | |1 __+1__ | -|[ofpetrial](problems.md#ofpetrial)|0.1.1 |__+1__ | | | -|[OmicNavigator](problems.md#omicnavigator)|1.13.13 |__+1__ | |1 | -|[omu](problems.md#omu)|1.1.2 |1 __+1__ | |__+1__ | -|[OncoBayes2](problems.md#oncobayes2)|0.8-9 |__+1__ | |2 | -|[oncomsm](problems.md#oncomsm)|0.1.4 |__+2__ | |2 __+1__ | -|[OneSampleLogRankTest](problems.md#onesamplelogranktest)|0.9.2 |__+2__ | |__+1__ | -|[onpoint](problems.md#onpoint)|1.0.5 |__+1__ | | | -|[ordbetareg](problems.md#ordbetareg)|0.7.2 |__+1__ | |2 | -|[packcircles](problems.md#packcircles)|0.3.6 |__+1__ | |__+1__ | -|[pafr](problems.md#pafr)|0.0.2 |__+1__ | |1 | -|[patchwork](problems.md#patchwork)|1.2.0 |__+1__ | | | -|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | | -|[patientProfilesVis](problems.md#patientprofilesvis)|2.0.9 |1 __+1__ | |1 __+1__ | -|[PCADSC](problems.md#pcadsc)|0.8.0 |__+1__ | |3 | -|[pcutils](problems.md#pcutils)|0.2.6 |__+1__ | | | -|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 __+1__ | -|[personalized](problems.md#personalized)|0.2.7 |__+1__ | | | -|[phyloseqGraphTest](problems.md#phyloseqgraphtest)|0.1.1 |__+2__ | |__+1__ | -|[PieGlyph](problems.md#pieglyph)|1.0.0 |1 __+2__ | |__+1__ | -|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | | -|[platetools](problems.md#platetools)|0.1.7 |__+1__ | | | -|[PLNmodels](problems.md#plnmodels)|1.2.0 |__+1__ | |1 __+1__ | -|[plotBart](problems.md#plotbart)|0.1.7 |__+1__ | | | -|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 | -|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 | -|[pmartR](problems.md#pmartr)|2.4.5 |__+1__ | |1 | -|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |1 | -|[posterior](problems.md#posterior)|1.6.0 |1 | |__+1__ | -|[PPQplan](problems.md#ppqplan)|1.1.0 |1 | |2 __+1__ | -|[ppseq](problems.md#ppseq)|0.2.5 |__+1__ | |1 __+1__ | -|[PPtreeregViz](problems.md#pptreeregviz)|2.0.5 |__+2__ | |1 __+1__ | -|[precintcon](problems.md#precintcon)|2.3.0 |__+1__ | | | -|[precrec](problems.md#precrec)|0.14.4 |__+1__ | |1 __+1__ | -|[priorsense](problems.md#priorsense)|1.0.2 |__+2__ | |__+1__ | -|[probably](problems.md#probably)|1.0.3 |__+1__ | | | -|[processmapR](problems.md#processmapr)|0.5.5 |__+1__ | | | -|[projpred](problems.md#projpred)|2.8.0 |1 __+2__ | |1 | -|[psborrow](problems.md#psborrow)|0.2.1 |__+1__ | | | -|[pubh](problems.md#pubh)|1.3.7 |1 __+1__ | |__+1__ | -|[PUPMSI](problems.md#pupmsi)|0.1.0 |__+1__ | | | -|[qacBase](problems.md#qacbase)|1.0.3 |__+1__ | | | -|[qPCRhelper](problems.md#qpcrhelper)|0.1.0 |__+2__ | |__+1__ | -|[r2dii.plot](problems.md#r2diiplot)|0.4.0 |__+1__ | | | -|[r2spss](problems.md#r2spss)|0.3.2 |__+2__ | |1 | -|[radiant.basics](problems.md#radiantbasics)|1.6.6 |__+1__ | | | -|[radiant.data](problems.md#radiantdata)|1.6.6 |__+1__ | | | -|[radiant.model](problems.md#radiantmodel)|1.6.6 |__+1__ | | | -|[Radviz](problems.md#radviz)|0.9.3 |__+2__ | |__+1__ | -|[randomForestExplainer](problems.md#randomforestexplainer)|0.10.1 |__+3__ | |1 __+1__ | -|[rassta](problems.md#rassta)|1.0.6 |__+3__ | | | -|[rater](problems.md#rater)|1.3.1 |__+1__ | |2 | -|[RBesT](problems.md#rbest)|1.7-3 |__+2__ | |2 __+1__ | -|[rddensity](problems.md#rddensity)|2.5 |__+1__ | | | -|[RecordTest](problems.md#recordtest)|2.2.0 |__+2__ | |__+1__ | -|[reda](problems.md#reda)|0.5.4 |__+2__ | |2 __+1__ | -|[redist](problems.md#redist)|4.2.0 |__+1__ | |1 __+1__ | -|[registr](problems.md#registr)|2.1.0 |2 __+1__ | |2 __+1__ | -|[reliabilitydiag](problems.md#reliabilitydiag)|0.2.1 |__+1__ | | | -|[relliptical](problems.md#relliptical)|1.3.0 |__+1__ | |1 | -|[reportRmd](problems.md#reportrmd)|0.1.0 |__+2__ | |__+1__ | -|[reservr](problems.md#reservr)|0.0.3 |1 __+1__ | |2 __+1__ | -|[RestoreNet](problems.md#restorenet)|1.0.1 |__+1__ |1 | | -|[rfPermute](problems.md#rfpermute)|2.5.2 |__+1__ | | | -|[RKorAPClient](problems.md#rkorapclient)|0.8.1 |__+1__ | | | -|[roahd](problems.md#roahd)|1.4.3 |__+1__ | |1 | -|[robCompositions](problems.md#robcompositions)|2.4.1 |__+1__ | |3 | -|[romic](problems.md#romic)|1.1.3 |__+2__ | | | -|[roptions](problems.md#roptions)|1.0.3 |__+1__ | |1 | -|[rSAFE](problems.md#rsafe)|0.1.4 |__+2__ | |__+1__ | -|[santaR](problems.md#santar)|1.2.4 |1 __+1__ | | | -|[saros](problems.md#saros)|1.2.0 |__+2__ | | | -|[scatterpie](problems.md#scatterpie)|0.2.4 |__+2__ | |__+1__ | -|[scdtb](problems.md#scdtb)|0.1.0 |__+1__ | | | -|[scoringutils](problems.md#scoringutils)|1.2.2 |1 __+1__ | |__+1__ | -|[scUtils](problems.md#scutils)|0.1.0 |__+1__ | |1 | -|[SCVA](problems.md#scva)|1.3.1 |__+1__ | | | -|[sdmTMB](problems.md#sdmtmb)|0.6.0 |__+1__ | |1 | -|[SDMtune](problems.md#sdmtune)|1.3.1 |1 __+1__ | | | -|[sedproxy](problems.md#sedproxy)|0.7.5 |__+2__ | |__+1__ | -|[see](problems.md#see)|0.9.0 |__+1__ | | | -|[seedreg](problems.md#seedreg)|1.0.3 |__+1__ | | | -|[semfindr](problems.md#semfindr)|0.1.8 |__+3__ | |__+1__ | -|[sensiPhy](problems.md#sensiphy)|0.8.5 |1 __+1__ | | | -|[sglg](problems.md#sglg)|0.2.2 |__+1__ | | | -|[sgsR](problems.md#sgsr)|1.4.5 |__+1__ | | | -|[SHAPforxgboost](problems.md#shapforxgboost)|0.1.3 |__+1__ | | | -|[ShapleyOutlier](problems.md#shapleyoutlier)|0.1.1 |__+2__ | |__+1__ | -|[shinipsum](problems.md#shinipsum)|0.1.1 |__+1__ | | | -|[signatureSurvival](problems.md#signaturesurvival)|1.0.0 |__+1__ | |1 | -|[SimCorrMix](problems.md#simcorrmix)|0.1.1 |__+2__ | |3 __+1__ | -|[SimMultiCorrData](problems.md#simmulticorrdata)|0.2.2 |__+1__ | |1 __+1__ | -|[SimNPH](problems.md#simnph)|0.5.5 |__+1__ | | | -|[slendr](problems.md#slendr)|0.9.1 |1 __+1__ | |1 | -|[smallsets](problems.md#smallsets)|2.0.0 |__+2__ | |1 __+1__ | -|[spinifex](problems.md#spinifex)|0.3.7.0 |__+1__ | | | -|[sport](problems.md#sport)|0.2.1 |__+1__ | |1 | -|[spotoroo](problems.md#spotoroo)|0.1.4 |__+2__ | |1 __+1__ | -|[SqueakR](problems.md#squeakr)|1.3.0 |1 | |1 __+1__ | -|[stability](problems.md#stability)|0.5.0 |__+1__ | | | -|[statgenGWAS](problems.md#statgengwas)|1.0.9 |__+1__ | |2 | -|[statgenHTP](problems.md#statgenhtp)|1.0.6.1 |__+3__ | |2 __+1__ | -|[sugrrants](problems.md#sugrrants)|0.2.9 |__+2__ | |__+1__ | -|[superb](problems.md#superb)|0.95.15 |__+3__ | |__+1__ | -|[surveyexplorer](problems.md#surveyexplorer)|0.2.0 |__+1__ | | | -|[survivalAnalysis](problems.md#survivalanalysis)|0.3.0 |1 __+1__ | |__+1__ | -|[survminer](problems.md#survminer)|0.4.9 |__+3__ | |1 __+1__ | -|[survParamSim](problems.md#survparamsim)|0.1.6 |__+1__ | |__+1__ | -|[survstan](problems.md#survstan)|0.0.7.1 |__+1__ | |3 __+1__ | 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|__+1__ | |1 | +|[robomit](problems.md#robomit)|1.0.6 |__+1__ |__+1__ |__+1__ | +|[romic](problems.md#romic)|1.1.3 |__+1__ | | | +|[roptions](problems.md#roptions)|1.0.3 |__+1__ | |1 | +|[rsimsum](problems.md#rsimsum)|0.13.0 | |__+1__ |1 | +|[rSRD](problems.md#rsrd)|0.1.8 |__+1__ |__+1__ |__+1__ | +|[saeRobust](problems.md#saerobust)|0.5.0 |__+2__ |__+1__ |__+1__ | +|[scUtils](problems.md#scutils)|0.1.0 |__+1__ | |1 | +|[SCVA](problems.md#scva)|1.3.1 |__+1__ | | | +|[SDMtune](problems.md#sdmtune)|1.3.2 |1 __+1__ | |__+1__ | +|[seAMLess](problems.md#seamless)|0.1.1 |__+1__ | |1 | +|[seedreg](problems.md#seedreg)|1.0.3 |__+1__ | | | +|[segen](problems.md#segen)|1.1.0 | |__+1__ | | +|[sensitivity](problems.md#sensitivity)|1.30.1 |__+1__ |__+1__ |1 __+1__ | +|[sglg](problems.md#sglg)|0.2.2 |__+1__ | | | +|[sgsR](problems.md#sgsr)|1.4.5 |__+1__ | | | +|[SHAPforxgboost](problems.md#shapforxgboost)|0.1.3 |__+1__ | | | +|[SHELF](problems.md#shelf)|1.11.0 | |__+1__ |__+1__ | 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+|[surveyexplorer](problems.md#surveyexplorer)|0.2.0 |__+1__ | | | +|[tabledown](problems.md#tabledown)|1.0.0 |__+1__ | |1 | +|[TCIU](problems.md#tciu)|1.2.7 |__+2__ | |1 __+1__ | +|[tcplfit2](problems.md#tcplfit2)|0.1.7 |__+1__ | |1 __+1__ | +|[tetragon](problems.md#tetragon)|1.3.0 | |__+1__ | | +|[thematic](problems.md#thematic)|0.1.6 |__+2__ | | | +|[tidybayes](problems.md#tidybayes)|3.0.7 |2 __+1__ | | | +|[tidycat](problems.md#tidycat)|0.1.2 |__+2__ | |1 __+1__ | +|[tidyCDISC](problems.md#tidycdisc)|0.2.1 |__+1__ | |1 | +|[tidyplots](problems.md#tidyplots)|0.2.1 |__+3__ | |__+1__ | +|[tidytreatment](problems.md#tidytreatment)|0.3.1 |__+1__ | |1 __+1__ | +|[timetk](problems.md#timetk)|2.9.0 |__+1__ | |1 | +|[TOSTER](problems.md#toster)|0.8.3 |__+3__ | |__+1__ | +|[TransProR](problems.md#transpror)|0.0.6 |__+1__ | | | +|[TreatmentPatterns](problems.md#treatmentpatterns)|2.7.0 |__+1__ | | | +|[TreatmentSelection](problems.md#treatmentselection)|2.1.1 |__+1__ |__+1__ |__+1__ | +|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 |__+1__ | | | +|[tricolore](problems.md#tricolore)|1.2.4 |__+2__ | |1 __+1__ | +|[tsnet](problems.md#tsnet)|0.1.0 |__+1__ | |2 | +|[UCSCXenaShiny](problems.md#ucscxenashiny)|2.1.0 |__+1__ | |1 __+1__ | +|[umiAnalyzer](problems.md#umianalyzer)|1.0.0 |__+1__ | | | +|[usmap](problems.md#usmap)|0.7.1 |__+3__ | |1 __+1__ | +|[vaccineff](problems.md#vaccineff)|1.0.0 |__+1__ | | | +|[valr](problems.md#valr)|0.8.3 |__+1__ | |1 | +|[visOmopResults](problems.md#visomopresults)|1.0.0 |__+1__ | | | +|[visvow](problems.md#visvow)|1.3.11 |__+1__ |__+1__ |__+1__ | +|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 __+1__ | +|[voluModel](problems.md#volumodel)|0.2.2 |1 __+1__ | |__+1__ | +|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | | +|[VWPre](problems.md#vwpre)|1.2.4 |__+1__ | |__+1__ | +|[WebAnalytics](problems.md#webanalytics)|0.9.12 |__+2__ |1 __+1__ |__+1__ | +|[WhatsR](problems.md#whatsr)|1.0.4 |__+2__ |__+1__ |__+1__ | +|[wilson](problems.md#wilson)|2.4.2 |__+1__ | | | +|[wordmap](problems.md#wordmap)|0.9.2 |__+1__ | |1 | +|[xpose](problems.md#xpose)|0.4.19 |__+3__ | |__+1__ | +|[xpose.xtras](problems.md#xposextras)|0.0.2 |__+2__ | |3 __+1__ | +|[yamlet](problems.md#yamlet)|1.2.0 |__+2__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 4a1365f7a5..d521f55150 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,16 +1,16 @@ ## revdepcheck results -We checked 5209 reverse dependencies (5199 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 5478 reverse dependencies (5461 from CRAN + 17 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 469 new problems - * We failed to check 155 packages + * We saw 347 new problems + * We failed to check 179 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* activAnalyzer +* ABHgenotypeR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -18,24 +18,31 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* adaptr +* adklakedata + checking examples ... ERROR + +* adobeanalyticsr + checking whether package ‘adobeanalyticsr’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* adw checking examples ... ERROR - checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * AeRobiology + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * agricolaeplotr checking tests ... ERROR - -* alien checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* AlphaPart +* agridat checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * AnalysisLin checking examples ... ERROR @@ -46,37 +53,29 @@ Issues with CRAN packages are summarised below. * ANN2 checking tests ... ERROR -* AnnoProbe - checking examples ... ERROR - -* ANOFA - checking examples ... ERROR +* APCI checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE -* ANOPA +* APCtools checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* AntMAN - checking examples ... ERROR - checking tests ... ERROR - -* APCI +* applicable checking tests ... ERROR -* aplot +* ARPALData checking examples ... ERROR + checking whether package ‘ARPALData’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* applicable - checking tests ... ERROR +* arulesViz + checking whether package ‘arulesViz’ can be installed ... WARNING -* ASRgenomics - checking examples ... ERROR - checking tests ... ERROR +* asremlPlus + checking whether package ‘asremlPlus’ can be installed ... WARNING + checking R code for possible problems ... NOTE * autocogs checking tests ... ERROR @@ -85,88 +84,66 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* autoReg - checking examples ... ERROR - checking running R code from vignettes ... ERROR +* autoTS checking re-building of vignette outputs ... NOTE -* baggr +* backShift checking examples ... ERROR - checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘backShift’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* banter - checking examples ... ERROR - -* bartMan - checking examples ... ERROR - -* BasketballAnalyzeR - checking examples ... ERROR - -* bayefdr - checking examples ... ERROR - checking tests ... ERROR - * bayesAB checking tests ... ERROR +* bayesforecast + checking running R code from vignettes ... ERROR + checking whether package ‘bayesforecast’ can be installed ... WARNING + checking R code for possible problems ... NOTE + checking re-building of vignette outputs ... NOTE + * BayesGrowth checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* BayesianReasoning +* BayesianMCPMod + checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* BayesMallows +* BayesianReasoning checking tests ... ERROR -* bayesplay - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* BayesMallows + checking tests ... ERROR * bayesplot - checking examples ... ERROR checking tests ... ERROR -* bayestestR - checking examples ... ERROR - * BCEA checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* BDgraph - checking running R code from vignettes ... ERROR + checking whether package ‘BCEA’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE * BEAMR checking examples ... ERROR + checking whether package ‘BEAMR’ can be installed ... WARNING + checking R code for possible problems ... NOTE * beastt checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* BeeGUTS - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* besthr +* biclust checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* betaclust - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘biclust’ can be installed ... WARNING + checking R code for possible problems ... NOTE * biclustermd checking tests ... ERROR @@ -174,125 +151,114 @@ Issues with CRAN packages are summarised below. * biodosetools checking tests ... ERROR -* BioPred - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* BlandAltmanLeh - checking running R code from vignettes ... ERROR - -* bmggum - checking examples ... ERROR - * boxly checking tests ... ERROR -* braidReports - checking examples ... ERROR - -* BRcal - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* breathtestcore - checking tests ... ERROR - * brolgar checking examples ... ERROR -* calibrationband +* cartograflow checking examples ... ERROR -* cartograflow +* cats checking examples ... ERROR -* cases +* CausalImpact + checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘CausalImpact’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* cats - checking examples ... ERROR +* celltrackR + checking re-building of vignette outputs ... NOTE -* ceterisParibus - checking tests ... ERROR +* cellularautomata + checking running R code from vignettes ... ERROR + +* CensMFM + checking whether package ‘CensMFM’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* cfda +* CFO checking examples ... ERROR + checking whether package ‘CFO’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* changepoint.geo checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * cheem checking tests ... ERROR * chillR checking examples ... ERROR + checking whether package ‘chillR’ can be installed ... WARNING + checking R code for possible problems ... NOTE * chronicle checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* CINNA - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* circhelp +* cjoint checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* clifro checking tests ... ERROR + checking whether package ‘cjoint’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* clickstream + checking whether package ‘clickstream’ can be installed ... WARNING * clinDataReview checking examples ... ERROR checking tests ... ERROR checking re-building of vignette outputs ... NOTE +* clinDR + checking examples ... ERROR + * clinUtils checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* cloneRate - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* CLONETv2 + checking whether package ‘CLONETv2’ can be installed ... WARNING -* clustEff +* ClusROC checking examples ... ERROR + checking tests ... ERROR + checking whether package ‘ClusROC’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* ClustImpute +* clustcurv checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* clustMD + checking whether package ‘clustMD’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* cmstatr +* cnmap checking examples ... ERROR - checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * codaredistlm checking examples ... ERROR -* coefplot - checking examples ... ERROR +* codez + checking whether package ‘codez’ can be installed ... WARNING * CohortPlat checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* complmrob +* colorrepel checking examples ... ERROR -* conjoint - checking examples ... ERROR - -* conquestr - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * CoreMicrobiomeR checking examples ... ERROR @@ -304,14 +270,6 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* corx - checking tests ... ERROR - -* cosinor2 - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * CoSMoS checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -319,35 +277,29 @@ Issues with CRAN packages are summarised below. * countfitteR checking tests ... ERROR -* coursekata - checking examples ... ERROR - checking tests ... ERROR - * covidcast checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* Coxmos +* creditmodel checking examples ... ERROR - -* cpr checking running R code from vignettes ... ERROR + checking whether package ‘creditmodel’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* cpsvote - checking running R code from vignettes ... ERROR - -* crimeutils - checking examples ... ERROR - -* crmPack - checking examples ... ERROR - checking running R code from vignettes ... ERROR +* cricketr + checking whether package ‘cricketr’ can be installed ... WARNING + checking R code for possible problems ... NOTE * crosshap checking examples ... ERROR +* CRTgeeDR + checking whether package ‘CRTgeeDR’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * ctrialsgov checking tests ... ERROR @@ -355,34 +307,49 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* curtailment +* DAISIE checking examples ... ERROR -* dabestr - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * DAISIEprep checking tests ... ERROR -* dbmss +* daltoolbox checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘daltoolbox’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* dawaR + checking examples ... ERROR + +* DDPNA + checking examples ... ERROR + checking whether package ‘DDPNA’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* Deducer + checking examples ... ERROR + checking whether package ‘Deducer’ can be installed ... WARNING + checking R code for possible problems ... NOTE * deeptime + checking examples ... ERROR + checking tests ... ERROR + +* desplot + checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘desplot’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* descriptio +* diceR checking examples ... ERROR - -* directlabels + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* disto +* directlabels checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -394,46 +361,66 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* dotwhisker +* divent + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* doBy + checking whether package ‘doBy’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* DoseFinding + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking whether package ‘DoseFinding’ can be installed ... WARNING + checking R code for possible problems ... NOTE + checking re-building of vignette outputs ... NOTE + +* dotsViolin + checking examples ... ERROR + +* dr4pl checking examples ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘dr4pl’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE * DRomics checking examples ... ERROR + checking whether package ‘DRomics’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* dtwclust - checking tests ... ERROR +* drpop + checking whether package ‘drpop’ can be installed ... WARNING + checking R code for possible problems ... NOTE * duke checking tests ... ERROR +* dymo + checking whether package ‘dymo’ can be installed ... WARNING + +* dynr + checking whether package ‘dynr’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * easysurv checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* EGAnet - checking examples ... ERROR - * EGM checking tests ... ERROR -* emmeans - checking examples ... ERROR - -* EMMIXmfa - checking examples ... ERROR - * entropart checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* EnvStats - checking examples ... ERROR - * epiCleanr checking examples ... ERROR @@ -443,11 +430,6 @@ Issues with CRAN packages are summarised below. * EQUALSTATS checking examples ... ERROR -* ergm.multi - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * esci checking examples ... ERROR checking tests ... ERROR @@ -458,26 +440,15 @@ Issues with CRAN packages are summarised below. * eventstudyr checking tests ... ERROR -* EvoPhylo - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE - * expirest checking tests ... ERROR * explainer checking examples ... ERROR -* exuber - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ezEDA checking tests ... ERROR -* ezplot - checking examples ... ERROR - * fable.prophet checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -486,17 +457,16 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* factoextra - checking examples ... ERROR - * fairmodels checking tests ... ERROR -* fastR2 +* FCPS checking examples ... ERROR + checking whether package ‘FCPS’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* faux - checking re-building of vignette outputs ... NOTE +* fdANOVA + checking examples ... ERROR * fddm checking running R code from vignettes ... ERROR @@ -504,70 +474,48 @@ Issues with CRAN packages are summarised below. * feasts checking tests ... ERROR -* fergm - checking examples ... ERROR - * ffp checking examples ... ERROR -* fic - checking running R code from vignettes ... ERROR - * fido checking examples ... ERROR checking tests ... ERROR -* fitdistrplus - checking examples ... ERROR - checking tests ... ERROR +* FielDHub checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* fitlandr +* figuRes2 checking examples ... ERROR + checking running R code from vignettes ... ERROR * flexsurv + checking tests ... ERROR checking running R code from vignettes ... ERROR * flipr checking re-building of vignette outputs ... NOTE -* FLOPART - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* fmesher - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* fmf - checking examples ... ERROR - -* forestly - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* FossilSim - checking examples ... ERROR - -* FPDclustering +* forestmodel checking examples ... ERROR + checking whether package ‘forestmodel’ can be installed ... WARNING + checking R code for possible problems ... NOTE * frailtyEM checking examples ... ERROR -* funcharts - checking examples ... ERROR - -* FunnelPlotR +* gapmap checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* genekitr +* gapminder checking examples ... ERROR +* GEInter + checking whether package ‘GEInter’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * geoheatmap checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -576,11 +524,10 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* geostan - checking examples ... ERROR +* ggalign + checking for code/documentation mismatches ... WARNING * GGally - checking examples ... ERROR checking tests ... ERROR * gganimate @@ -588,34 +535,19 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggbrain - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggbreak - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggcharts +* ggblanket checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * ggdark checking examples ... ERROR checking tests ... ERROR -* ggdist - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... NOTE +* ggdemetra + checking whether package ‘ggdemetra’ can be installed ... WARNING -* ggeasy +* ggdist checking examples ... ERROR checking tests ... ERROR - checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * ggedit @@ -623,46 +555,23 @@ Issues with CRAN packages are summarised below. * ggESDA checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggExtra - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggfacto - checking examples ... ERROR * ggfixest checking tests ... ERROR -* ggfocus - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggforce checking examples ... ERROR * ggformula - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR checking for code/documentation mismatches ... WARNING - checking re-building of vignette outputs ... NOTE * ggfortify - checking examples ... ERROR checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* gggenomes - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * ggh4x + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * gghighlight @@ -671,24 +580,15 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggHoriPlot - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggiraph checking examples ... ERROR checking tests ... ERROR -* ggiraphExtra - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* ggmap + checking whether package ‘ggmap’ can be installed ... WARNING -* ggmatplot +* ggmcmc checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * ggmice checking running R code from vignettes ... ERROR @@ -700,49 +600,18 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggpackets - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggparallel checking tests ... ERROR -* ggparty - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggpicrust2 - checking examples ... ERROR - * ggplotlyExtra checking examples ... ERROR -* ggPMX - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggpol checking examples ... ERROR -* ggprism - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggpubr - checking examples ... ERROR checking tests ... ERROR -* ggrain - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * ggraph checking examples ... ERROR checking re-building of vignette outputs ... NOTE @@ -762,8 +631,13 @@ Issues with CRAN packages are summarised below. checking re-building of vignette outputs ... NOTE * ggside + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking whether package ‘ggside’ can be installed ... WARNING checking for code/documentation mismatches ... WARNING + checking R code for possible problems ... NOTE + checking re-building of vignette outputs ... NOTE * ggsmc checking running R code from vignettes ... ERROR @@ -775,8 +649,9 @@ Issues with CRAN packages are summarised below. * ggstatsplot checking examples ... ERROR -* ggtern - checking examples ... ERROR +* ggswissmaps + checking whether package ‘ggswissmaps’ can be installed ... WARNING + checking whether the namespace can be loaded with stated dependencies ... NOTE * ggupset checking examples ... ERROR @@ -785,46 +660,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* GimmeMyPlot - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* giniVarCI +* Greymodels checking examples ... ERROR -* gMCPLite - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* GWASinspector + checking whether package ‘GWASinspector’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* gMOIP +* GWlasso checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE -* GofCens +* harbinger checking examples ... ERROR + checking whether package ‘harbinger’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* greatR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* Greymodels - checking examples ... ERROR - -* gsDesign +* HCmodelSets checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* gtExtras - checking tests ... ERROR - -* HaploCatcher - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘HCmodelSets’ can be installed ... WARNING + checking R code for possible problems ... NOTE * healthyR checking running R code from vignettes ... ERROR @@ -840,79 +694,59 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* hermiter - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* heumilkr +* heemod checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE -* hilldiv - checking examples ... ERROR - -* hmclearn - checking examples ... ERROR +* hesim + checking tests ... ERROR -* HTLR +* hmsidwR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * HVT checking examples ... ERROR + checking whether package ‘HVT’ can be installed ... WARNING + checking R code for possible problems ... NOTE * hypsoLoop checking whether package ‘hypsoLoop’ can be installed ... WARNING -* ibdsim2 - checking examples ... ERROR - -* ICtest - checking examples ... ERROR +* iCARH + checking whether package ‘iCARH’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* idiogramFISH - checking installed package size ... NOTE - -* IDMIR - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* ICSsmoothing + checking tests ... ERROR -* idopNetwork +* incidental checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ihclust +* industRial checking examples ... ERROR -* immunarch +* infer checking examples ... ERROR - -* incidental checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* infer +* inferCSN checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * injurytools checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* inlabru - checking examples ... ERROR - -* insurancerating - checking examples ... ERROR - * inTextSummaryTable checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* inti + checking whether package ‘inti’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * IPV checking examples ... ERROR checking running R code from vignettes ... ERROR @@ -921,23 +755,12 @@ Issues with CRAN packages are summarised below. * IRon checking examples ... ERROR -* irt - checking examples ... ERROR - * isoorbi checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ivDiag - checking examples ... ERROR - -* ivreg - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* jarbes - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* jenga + checking whether package ‘jenga’ can be installed ... WARNING * karel checking examples ... ERROR @@ -946,9 +769,10 @@ Issues with CRAN packages are summarised below. * kDGLM checking examples ... ERROR -* KMEANS.KNN +* Keyboard checking examples ... ERROR - checking tests ... ERROR + checking whether package ‘Keyboard’ can be installed ... WARNING + checking R code for possible problems ... NOTE * latentcor checking examples ... ERROR @@ -968,66 +792,39 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* lgpr - checking tests ... ERROR - -* LightLogR - checking examples ... ERROR +* lilikoi + checking whether package ‘lilikoi’ can be installed ... WARNING + checking R code for possible problems ... NOTE * LMoFit checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* lnmixsurv - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* LocalControl - checking running R code from vignettes ... ERROR - * LocalCop checking re-building of vignette outputs ... NOTE -* LongDat +* lognorm checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* longreadvqs - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* lpdensity +* lsl checking examples ... ERROR -* lspartition +* MAINT.Data checking examples ... ERROR - -* LSTbook - checking tests ... ERROR - checking re-building of vignette outputs ... NOTE - -* manydata checking tests ... ERROR + checking whether package ‘MAINT.Data’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* manymome - checking examples ... ERROR - -* mapbayr - checking examples ... ERROR - -* MBNMAdose - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* MBNMAtime - checking re-building of vignette outputs ... NOTE +* MarketMatching + checking re-building of vignette outputs ... ERROR -* mecoturn +* metacart checking examples ... ERROR + checking whether package ‘metacart’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* MetaNet +* MetAlyzer checking examples ... ERROR * metR @@ -1036,21 +833,10 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* metrica - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* miceRanger - checking running R code from vignettes ... ERROR - -* microbial - checking examples ... ERROR +* mgcViz checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* MicrobiomeSurv - checking examples ... ERROR - * migraph checking tests ... ERROR @@ -1070,21 +856,13 @@ Issues with CRAN packages are summarised below. * misspi checking examples ... ERROR -* mixpoissonreg - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * mizer checking tests ... ERROR -* mlr3spatiotempcv - checking examples ... ERROR - -* mlr3viz +* MLEce checking examples ... ERROR - checking tests ... ERROR + checking whether package ‘MLEce’ can be installed ... WARNING + checking R code for possible problems ... NOTE * modeltime.resample checking tests ... ERROR @@ -1093,60 +871,55 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* mosaicCalc - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* mosaicData - checking examples ... ERROR - -* mosaicModel - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * mppR checking running R code from vignettes ... ERROR + checking whether package ‘mppR’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* MSCMT - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* mstate +* MPTmultiverse checking examples ... ERROR checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * mtb checking tests ... ERROR +* mudfold + checking whether package ‘mudfold’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * mulgar checking examples ... ERROR -* MultivariateAnalysis +* MultiTraits checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* mxfda - checking installed package size ... NOTE +* mvSLOUCH + checking re-building of vignette outputs ... NOTE -* neatmaps - checking examples ... ERROR +* naive + checking whether package ‘naive’ can be installed ... WARNING -* neatStats - checking examples ... ERROR +* ncappc + checking whether package ‘ncappc’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* netcom - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* neatmaps + checking examples ... ERROR * NetFACS checking examples ... ERROR checking running R code from vignettes ... ERROR -* neuroUp +* NetworkInference checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘NetworkInference’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE * NHSRplotthedots @@ -1162,131 +935,72 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* nonmem2R - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* nphRCT - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* nprobust - checking examples ... ERROR - * nzelect checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* OBIC - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* oceanic - checking examples ... ERROR * oddsratio checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ofpetrial - checking examples ... ERROR - * OmicNavigator checking tests ... ERROR -* omu - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE - -* OncoBayes2 - checking examples ... ERROR - -* oncomsm - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* OneSampleLogRankTest - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* onpoint - checking examples ... ERROR - * ordbetareg checking examples ... ERROR -* packcircles - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * pafr checking tests ... ERROR -* patchwork - checking examples ... ERROR - * pathviewr checking tests ... ERROR -* patientProfilesVis +* pdxTrees checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* PCADSC +* PeakError checking examples ... ERROR -* pcutils +* PeakSegJoint checking examples ... ERROR -* pdxTrees - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* PeakSegOptimal + checking examples ... ERROR * personalized checking tests ... ERROR -* phyloseqGraphTest +* Plasmidprofiler checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE -* PieGlyph - checking examples ... ERROR +* plotDK checking tests ... ERROR - checking re-building of vignette outputs ... NOTE -* Plasmidprofiler +* PlotFTIR checking examples ... ERROR - -* platetools checking tests ... ERROR - -* PLNmodels checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* plotBart - checking tests ... ERROR - -* plotDK - checking tests ... ERROR * plotly checking examples ... ERROR checking tests ... ERROR +* plotthis + checking examples ... ERROR + * pmartR checking tests ... ERROR * pmxTools checking tests ... ERROR +* pogit + checking whether package ‘pogit’ can be installed ... WARNING + checking R code for possible problems ... NOTE + * posterior + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * PPQplan @@ -1296,16 +1010,22 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* PPtreeregViz - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * precintcon checking examples ... ERROR -* precrec +* pRecipe + checking whether package ‘pRecipe’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* PReMiuM + checking whether package ‘PReMiuM’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* prevR + checking examples ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘prevR’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE * priorsense @@ -1319,149 +1039,111 @@ Issues with CRAN packages are summarised below. * processmapR checking tests ... ERROR -* projpred - checking examples ... ERROR - checking running R code from vignettes ... ERROR - * psborrow checking tests ... ERROR -* pubh +* PupilPre checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* PUPMSI - checking examples ... ERROR - -* qacBase - checking examples ... ERROR - -* qPCRhelper +* qgcomp checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘qgcomp’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* r2dii.plot +* qpNCA checking tests ... ERROR - -* r2spss - checking examples ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘qpNCA’ can be installed ... WARNING + checking R code for possible problems ... NOTE + checking re-building of vignette outputs ... NOTE -* radiant.basics - checking examples ... ERROR +* r2dii.plot + checking tests ... ERROR -* radiant.data - checking examples ... ERROR +* r4ss + checking whether package ‘r4ss’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* radiant.model +* r6qualitytools checking examples ... ERROR + checking whether package ‘r6qualitytools’ can be installed ... WARNING + checking R code for possible problems ... NOTE * Radviz checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* randomForestExplainer - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * rassta checking examples ... ERROR checking tests ... ERROR - checking running R code from vignettes ... ERROR * rater checking tests ... ERROR -* RBesT - checking examples ... ERROR - checking running R code from vignettes ... ERROR +* ratlas + checking tests ... ERROR checking re-building of vignette outputs ... NOTE -* rddensity +* RclusTool checking examples ... ERROR + checking whether package ‘RclusTool’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* RecordTest +* RDS checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘RDS’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* reda - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* redist - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* regtomean + checking whether package ‘regtomean’ can be installed ... WARNING -* registr - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* reliabilitydiag - checking examples ... ERROR +* RKorAPClient + checking tests ... ERROR -* relliptical - checking examples ... ERROR +* rmcfs + checking whether package ‘rmcfs’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* reportRmd +* rnmamod checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘rnmamod’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE -* reservr - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE - -* RestoreNet - checking examples ... ERROR - -* rfPermute - checking examples ... ERROR - -* RKorAPClient - checking tests ... ERROR - * roahd checking examples ... ERROR -* robCompositions +* robomit checking examples ... ERROR + checking whether package ‘robomit’ can be installed ... WARNING + checking R code for possible problems ... NOTE * romic - checking examples ... ERROR checking tests ... ERROR * roptions checking examples ... ERROR -* rSAFE - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* santaR - checking tests ... ERROR +* rsimsum + checking whether package ‘rsimsum’ can be installed ... WARNING -* saros +* rSRD checking examples ... ERROR - checking tests ... ERROR + checking whether package ‘rSRD’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* scatterpie +* saeRobust checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* scdtb checking tests ... ERROR - -* scoringutils - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘saeRobust’ can be installed ... WARNING + checking R code for possible problems ... NOTE * scUtils checking tests ... ERROR @@ -1469,31 +1151,23 @@ Issues with CRAN packages are summarised below. * SCVA checking examples ... ERROR -* sdmTMB - checking examples ... ERROR - * SDMtune checking tests ... ERROR + checking installed package size ... NOTE -* sedproxy - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* see +* seAMLess checking examples ... ERROR * seedreg checking examples ... ERROR -* semfindr - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* segen + checking whether package ‘segen’ can be installed ... WARNING -* sensiPhy +* sensitivity checking examples ... ERROR + checking whether package ‘sensitivity’ can be installed ... WARNING + checking R code for possible problems ... NOTE * sglg checking examples ... ERROR @@ -1504,127 +1178,92 @@ Issues with CRAN packages are summarised below. * SHAPforxgboost checking examples ... ERROR -* ShapleyOutlier +* SHELF + checking whether package ‘SHELF’ can be installed ... WARNING + checking R code for possible problems ... NOTE + +* signatureSurvival checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘signatureSurvival’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* shinipsum +* SimNPH checking tests ... ERROR -* signatureSurvival - checking examples ... ERROR +* simRestore + checking tests ... ERROR -* SimCorrMix +* singleCellHaystack checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘singleCellHaystack’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* SimMultiCorrData - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* SNPannotator + checking whether package ‘SNPannotator’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* SimNPH - checking tests ... ERROR - -* slendr +* soc.ca checking examples ... ERROR + checking whether package ‘soc.ca’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* smallsets +* SOMbrero checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking tests ... ERROR + checking whether package ‘SOMbrero’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* spinifex +* spectralR checking tests ... ERROR -* sport +* spinifex checking tests ... ERROR -* spotoroo +* spooky + checking whether package ‘spooky’ can be installed ... WARNING + +* sport checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * SqueakR checking re-building of vignette outputs ... NOTE -* stability - checking examples ... ERROR - * statgenGWAS checking tests ... ERROR * statgenHTP - checking examples ... ERROR checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* sugrrants - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE -* superb +* Superpower checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR + checking whether package ‘Superpower’ can be installed ... WARNING + checking R code for possible problems ... NOTE checking re-building of vignette outputs ... NOTE * surveyexplorer checking examples ... ERROR -* survivalAnalysis - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE - -* survminer - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* survParamSim - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* survstan - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* SVMMaj - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* Sysrecon - checking examples ... ERROR - * tabledown checking examples ... ERROR -* tcgaViz - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * TCIU checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* tcpl - checking tests ... ERROR +* tcplfit2 + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* tern - checking examples ... ERROR +* tetragon + checking whether package ‘tetragon’ can be installed ... WARNING * thematic checking examples ... ERROR checking tests ... ERROR -* Thermistor - checking examples ... ERROR - * tidybayes checking examples ... ERROR @@ -1636,11 +1275,7 @@ Issues with CRAN packages are summarised below. * tidyCDISC checking tests ... ERROR -* tidysdm - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* tidySEM +* tidyplots checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR @@ -1650,48 +1285,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* timeplyr - checking examples ... ERROR - * timetk checking tests ... ERROR -* tinyarray - checking examples ... ERROR - -* tipmap - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* tornado +* TOSTER checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* TOSTER +* TransProR checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * TreatmentPatterns checking tests ... ERROR * TreatmentSelection checking examples ... ERROR - -* TreeDep - checking examples ... ERROR - -* TreeDist - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* treeheatr - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking whether package ‘TreatmentSelection’ can be installed ... WARNING + checking R code for possible problems ... NOTE * trelliscopejs checking tests ... ERROR @@ -1701,59 +1313,35 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* triptych - checking examples ... ERROR - * tsnet checking tests ... ERROR -* UBayFS +* UCSCXenaShiny checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* Umatrix - checking examples ... ERROR - * umiAnalyzer checking examples ... ERROR -* UnalR - checking examples ... ERROR - checking tests ... ERROR - -* unmconf - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * usmap checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* vannstats - checking examples ... ERROR - -* vDiveR - checking examples ... ERROR - -* venn - checking examples ... ERROR - -* vimpclust - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* vaccineff + checking tests ... ERROR -* vip - checking examples ... ERROR +* valr checking tests ... ERROR -* VirtualPop - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* visOmopResults + checking tests ... ERROR -* viscomp - checking examples ... ERROR +* visvow + checking tests ... ERROR + checking whether package ‘visvow’ can be installed ... WARNING + checking R code for possible problems ... NOTE * vivaldi checking examples ... ERROR @@ -1761,37 +1349,45 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* voiceR +* voluModel checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* vvshiny checking tests ... ERROR -* volcano3D - checking examples ... ERROR +* VWPre checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* voluModel +* WebAnalytics checking examples ... ERROR - checking re-building of vignette outputs ... NOTE + checking tests ... ERROR + checking whether package ‘WebAnalytics’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* vsd +* WhatsR checking examples ... ERROR + checking tests ... ERROR + checking whether package ‘WhatsR’ can be installed ... WARNING + checking R code for possible problems ... NOTE -* vvshiny +* wilson checking tests ... ERROR -* walker - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE +* wordmap + checking tests ... ERROR -* WVPlots +* xpose checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* xaringanthemer - checking tests ... ERROR +* xpose.xtras + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * yamlet checking examples ... ERROR @@ -1799,158 +1395,182 @@ Issues with CRAN packages are summarised below. ### Failed to check -* abctools (NA) -* adjclust (NA) -* animalEKF (NA) -* ANOM (NA) -* atRisk (NA) -* AutoScore (NA) -* baRulho (NA) -* bayesDP (NA) -* BayesianFactorZoo (NA) -* BayesSurvive (NA) -* BCClong (NA) -* BGGM (NA) -* binsreg (NA) -* bspcov (NA) -* bsub (NA) -* BuyseTest (NA) -* CARBayesST (NA) -* CGPfunctions (NA) -* chemodiv (NA) -* cinaR (NA) -* cmprskcoxmsm (NA) -* CNVScope (NA) -* COMMA (NA) -* conos (NA) -* counterfactuals (NA) -* CRMetrics (NA) -* crosstalkr (NA) -* ctsem (NA) -* DepthProc (NA) -* DR.SC (NA) -* easybgm (NA) -* EcoEnsemble (NA) -* ecolottery (NA) -* EMAS (NA) -* EpiEstim (NA) -* evolqg (NA) -* ForecastComb (NA) -* GALLO (NA) -* gap (NA) -* gapfill (NA) -* geneHapR (NA) -* GeneSelectR (NA) -* GeomComb (NA) -* gJLS2 (NA) -* hettx (NA) -* Hmisc (NA) -* Hmsc (NA) -* iClusterVB (NA) -* inventorize (NA) -* iNZightPlots (NA) -* iNZightRegression (NA) -* IRexamples (NA) -* jmBIG (NA) -* joineRML (NA) -* kibior (NA) -* kmc (NA) -* L2E (NA) -* llbayesireg (NA) -* locuszoomr (NA) -* LorenzRegression (NA) -* lsirm12pl (NA) -* MARVEL (NA) -* mbsts (NA) -* MitoHEAR (NA) -* miWQS (NA) -* mlmts (NA) -* mlr (NA) -* MOCHA (NA) -* MRZero (NA) -* multilevelTools (NA) -* multinma (NA) -* NCA (NA) -* netcmc (NA) -* NetworkChange (NA) -* nlmeVPC (NA) -* NMADiagT (NA) -* ohun (NA) -* optweight (NA) -* OVtool (NA) -* pagoda2 (NA) -* PAMpal (NA) -* PAMscapes (NA) -* paths (NA) -* pcvr (NA) -* PlasmaMutationDetector (NA) -* PlasmaMutationDetector2 (NA) -* PLMIX (NA) -* polyRAD (NA) -* popstudy (NA) -* pould (NA) -* PoweREST (NA) -* powerly (NA) -* pre (NA) -* ProFAST (NA) -* psbcSpeedUp (NA) -* pscore (NA) -* qPCRtools (NA) -* qris (NA) -* qte (NA) -* quantilogram (NA) -* quid (NA) -* RcmdrPlugin.RiskDemo (NA) -* rddtools (NA) -* RNAseqQC (NA) -* robmed (NA) -* robmedExtra (NA) -* RPPanalyzer (NA) -* RQdeltaCT (NA) -* rstanarm (NA) -* RTIGER (NA) -* rTwig (NA) -* RVA (NA) -* scCustomize (NA) -* SCdeconR (NA) -* scGate (NA) -* SCIntRuler (NA) -* scITD (NA) -* scMappR (NA) -* scpi (NA) -* scRNAstat (NA) -* sectorgap (NA) -* SeedMatchR (NA) -* SEERaBomb (NA) -* semicmprskcoxmsm (NA) -* SensMap (NA) -* sephora (NA) -* Seurat (NA) -* shinyTempSignal (NA) -* sievePH (NA) -* sigminer (NA) -* Signac (NA) -* SimplyAgree (NA) -* SNPassoc (NA) -* snplinkage (NA) -* SoupX (NA) -* sparsereg (NA) -* SpatialDDLS (NA) -* spikeSlabGAM (NA) -* statsr (NA) -* streamDAG (NA) -* survidm (NA) -* tempted (NA) -* TestAnaAPP (NA) -* tidydr (NA) -* tidyEdSurvey (NA) -* tidyseurat (NA) -* tidyvpc (NA) -* TriDimRegression (NA) -* TSrepr (NA) -* twang (NA) -* updog (NA) -* valr (NA) -* vdg (NA) -* visa (NA) -* WRTDStidal (NA) +* abctools (NA) +* adjustedCurves (NA) +* animalEKF (NA) +* ANOM (NA) +* atRisk (NA) +* autoReg (NA) +* AutoScore (NA) +* bartMan (NA) +* bayesDP (NA) +* BayesianFactorZoo (NA) +* BayesSurvive (NA) +* BCClong (NA) +* BGGM (NA) +* binsreg (NA) +* bspcov (NA) +* BSTZINB (NA) +* BuyseTest (NA) +* CAESAR.Suite (NA) +* CARBayesST (NA) +* Certara.VPCResults (NA) +* CGPfunctions (NA) +* cinaR (NA) +* cmprskcoxmsm (NA) +* COMMA (NA) +* contsurvplot (NA) +* counterfactuals (NA) +* CRMetrics (NA) +* ctsem (NA) +* dartR.base (NA) +* dartR.captive (NA) +* dartR.popgen (NA) +* dartR.sexlinked (NA) +* dartR.sim (NA) +* dartR.spatial (NA) +* DepthProc (NA) +* DFD (NA) +* dMrs (NA) +* DR.SC (NA) +* dscoreMSM (NA) +* easybgm (NA) +* EcoEnsemble (NA) +* ecolottery (NA) +* EpiEstim (NA) +* evolqg (NA) +* flexrsurv (NA) +* ForecastComb (NA) +* gap (NA) +* gapfill (NA) +* genekitr (NA) +* GeneSelectR (NA) +* GeomComb (NA) +* ggtern (NA) +* ggThemeAssist (NA) +* gJLS2 (NA) +* grandR (NA) +* GseaVis (NA) +* hettx (NA) +* Hmisc (NA) +* Hmsc (NA) +* iClusterVB (NA) +* immcp (NA) +* inventorize (NA) +* invivoPKfit (NA) +* iNZightPlots (NA) +* iNZightRegression (NA) +* IRexamples (NA) +* jmBIG (NA) +* joineRML (NA) +* jsmodule (NA) +* kmc (NA) +* KMunicate (NA) +* L2E (NA) +* Landmarking (NA) +* lavaSearch2 (NA) +* llbayesireg (NA) +* lnmixsurv (NA) +* LorenzRegression (NA) +* lsirm12pl (NA) +* MARVEL (NA) +* MaxWiK (NA) +* mbsts (NA) +* MendelianRandomization (NA) +* miWQS (NA) +* mlmts (NA) +* mlr (NA) +* MRZero (NA) +* mstate (NA) +* multilevelTools (NA) +* multinma (NA) +* multipleOutcomes (NA) +* MuPETFlow (NA) +* NCA (NA) +* netcmc (NA) +* NetworkChange (NA) +* nlmeVPC (NA) +* NMADiagT (NA) +* NMF (NA) +* obliqueRSF (NA) +* OlinkAnalyze (NA) +* optweight (NA) +* OVtool (NA) +* pammtools (NA) +* paths (NA) +* pcvr (NA) +* PLMIX (NA) +* popstudy (NA) +* pould (NA) +* PoweREST (NA) +* powerly (NA) +* pre (NA) +* ProFAST (NA) +* psbcSpeedUp (NA) +* pscore (NA) +* qPCRtools (NA) +* qris (NA) +* qte (NA) +* quantilogram (NA) +* quid (NA) +* RcmdrPlugin.RiskDemo (NA) +* rddtools (NA) +* relsurv (NA) +* ReporterScore (NA) +* riskRegression (NA) +* robber (NA) +* robmed (NA) +* robmedExtra (NA) +* RPPanalyzer (NA) +* RQdeltaCT (NA) +* rstanarm (NA) +* rTwig (NA) +* RVA (NA) +* S4DM (NA) +* scCustomize (NA) +* SCdeconR (NA) +* scGate (NA) +* SCIntRuler (NA) +* scMappR (NA) +* scpi (NA) +* SCpubr (NA) +* scRNAstat (NA) +* sectorgap (NA) +* SEERaBomb (NA) +* semicmprskcoxmsm (NA) +* SensMap (NA) +* Seurat (NA) +* shinyTempSignal (NA) +* sievePH (NA) +* SiFINeT (NA) +* sigminer (NA) +* Signac (NA) +* SimplyAgree (NA) +* SNPassoc (NA) +* snplinkage (NA) +* SoupX (NA) +* SpaCCI (NA) +* sparsereg (NA) +* spectralAnalysis (NA) +* spikeSlabGAM (NA) +* stabiliser (NA) +* statsr (NA) +* streamDAG (NA) +* survex (NA) +* survHE (NA) +* survidm (NA) +* tempted (NA) +* TestAnaAPP (NA) +* tidydr (NA) +* tidyEdSurvey (NA) +* tidyseurat (NA) +* tidyvpc (NA) +* tinyarray (NA) +* treeclim (NA) +* TriDimRegression (NA) +* TSrepr (NA) +* twang (NA) +* vdg (NA) +* visa (NA) +* wppExplorer (NA) +* WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 444f4e174b..16b90a9326 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -29,7 +29,7 @@ Run `revdepcheck::cloud_details(, "abctools")` for more info ** package ‘abctools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c abctools.c -o abctools.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o abctools.so abctools.o init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -53,7 +53,7 @@ ERROR: lazy loading failed for package ‘abctools’ ** package ‘abctools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c abctools.c -o abctools.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o abctools.so abctools.o init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -70,17 +70,17 @@ ERROR: lazy loading failed for package ‘abctools’ ``` -# adjclust +# adjustedCurves
-* Version: 0.6.9 -* GitHub: https://github.com/pneuvial/adjclust -* Source code: https://github.com/cran/adjclust -* Date/Publication: 2024-02-08 08:50:05 UTC -* Number of recursive dependencies: 119 +* Version: 0.11.2 +* GitHub: https://github.com/RobinDenz1/adjustedCurves +* Source code: https://github.com/cran/adjustedCurves +* Date/Publication: 2024-07-29 14:30:02 UTC +* Number of recursive dependencies: 177 -Run `revdepcheck::cloud_details(, "adjclust")` for more info +Run `revdepcheck::cloud_details(, "adjustedCurves")` for more info
@@ -89,27 +89,27 @@ Run `revdepcheck::cloud_details(, "adjclust")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/adjclust/new/adjclust.Rcheck’ +* using log directory ‘/tmp/workdir/adjustedCurves/new/adjustedCurves.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘adjclust/DESCRIPTION’ ... OK +* checking for file ‘adjustedCurves/DESCRIPTION’ ... OK ... - When sourcing ‘hicClust.R’: -Error: there is no package called ‘HiTC’ +--- finished re-building ‘plot_customization.rmd’ + +SUMMARY: processing the following file failed: + ‘introduction.Rmd’ + +Error: Vignette re-building failed. Execution halted - ‘hicClust.Rmd’ using ‘UTF-8’... failed - ‘notesCHAC.Rmd’ using ‘UTF-8’... OK - ‘snpClust.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK * DONE -Status: 1 WARNING, 2 NOTEs +Status: 2 ERRORs, 1 WARNING, 3 NOTEs @@ -119,27 +119,27 @@ Status: 1 WARNING, 2 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/adjclust/old/adjclust.Rcheck’ +* using log directory ‘/tmp/workdir/adjustedCurves/old/adjustedCurves.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘adjclust/DESCRIPTION’ ... OK +* checking for file ‘adjustedCurves/DESCRIPTION’ ... OK ... - When sourcing ‘hicClust.R’: -Error: there is no package called ‘HiTC’ +--- finished re-building ‘plot_customization.rmd’ + +SUMMARY: processing the following file failed: + ‘introduction.Rmd’ + +Error: Vignette re-building failed. Execution halted - ‘hicClust.Rmd’ using ‘UTF-8’... failed - ‘notesCHAC.Rmd’ using ‘UTF-8’... OK - ‘snpClust.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK * DONE -Status: 1 WARNING, 2 NOTEs +Status: 2 ERRORs, 1 WARNING, 3 NOTEs @@ -216,7 +216,7 @@ ERROR: lazy loading failed for package ‘animalEKF’ * GitHub: https://github.com/PhilipPallmann/ANOM * Source code: https://github.com/cran/ANOM * Date/Publication: 2017-04-12 13:32:33 UTC -* Number of recursive dependencies: 60 +* Number of recursive dependencies: 63 Run `revdepcheck::cloud_details(, "ANOM")` for more info @@ -276,10 +276,10 @@ ERROR: lazy loading failed for package ‘ANOM’
-* Version: 0.1.0 +* Version: 0.2.0 * GitHub: NA * Source code: https://github.com/cran/atRisk -* Date/Publication: 2023-08-08 14:50:05 UTC +* Date/Publication: 2025-01-14 18:50:01 UTC * Number of recursive dependencies: 37 Run `revdepcheck::cloud_details(, "atRisk")` for more info @@ -334,17 +334,17 @@ ERROR: lazy loading failed for package ‘atRisk’ ``` -# AutoScore +# autoReg
-* Version: 1.0.0 -* GitHub: https://github.com/nliulab/AutoScore -* Source code: https://github.com/cran/AutoScore -* Date/Publication: 2022-10-15 22:15:26 UTC -* Number of recursive dependencies: 170 +* Version: 0.3.3 +* GitHub: https://github.com/cardiomoon/autoReg +* Source code: https://github.com/cran/autoReg +* Date/Publication: 2023-11-14 05:53:27 UTC +* Number of recursive dependencies: 215 -Run `revdepcheck::cloud_details(, "AutoScore")` for more info +Run `revdepcheck::cloud_details(, "autoReg")` for more info
@@ -353,27 +353,27 @@ Run `revdepcheck::cloud_details(, "AutoScore")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck’ +* using log directory ‘/tmp/workdir/autoReg/new/autoReg.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘AutoScore/DESCRIPTION’ ... OK +* checking for file ‘autoReg/DESCRIPTION’ ... OK ... -* this is package ‘AutoScore’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘survAUC’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... OK + ‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK + ‘Getting_started.Rmd’ using ‘UTF-8’... OK + ‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK + ‘Survival.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK @@ -383,44 +383,44 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck’ +* using log directory ‘/tmp/workdir/autoReg/old/autoReg.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘AutoScore/DESCRIPTION’ ... OK +* checking for file ‘autoReg/DESCRIPTION’ ... OK ... -* this is package ‘AutoScore’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘survAUC’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... OK + ‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK + ‘Getting_started.Rmd’ using ‘UTF-8’... OK + ‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK + ‘Survival.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK ``` -# baRulho +# AutoScore
-* Version: 2.1.2 -* GitHub: https://github.com/ropensci/baRulho -* Source code: https://github.com/cran/baRulho -* Date/Publication: 2024-08-31 13:10:07 UTC -* Number of recursive dependencies: 115 +* Version: 1.0.0 +* GitHub: https://github.com/nliulab/AutoScore +* Source code: https://github.com/cran/AutoScore +* Date/Publication: 2022-10-15 22:15:26 UTC +* Number of recursive dependencies: 173 -Run `revdepcheck::cloud_details(, "baRulho")` for more info +Run `revdepcheck::cloud_details(, "AutoScore")` for more info
@@ -429,22 +429,22 @@ Run `revdepcheck::cloud_details(, "baRulho")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/baRulho/new/baRulho.Rcheck’ +* using log directory ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘baRulho/DESCRIPTION’ ... OK +* checking for file ‘AutoScore/DESCRIPTION’ ... OK ... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: 'warbleR', 'ohun' - -Package suggested but not available for checking: ‘Rraven’ +Package required but not available: ‘survAUC’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -459,22 +459,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/baRulho/old/baRulho.Rcheck’ +* using log directory ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘baRulho/DESCRIPTION’ ... OK +* checking for file ‘AutoScore/DESCRIPTION’ ... OK ... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: 'warbleR', 'ohun' - -Package suggested but not available for checking: ‘Rraven’ +Package required but not available: ‘survAUC’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -485,16 +485,78 @@ Status: 1 ERROR +``` +# bartMan + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/bartMan +* Date/Publication: 2024-07-24 12:10:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "bartMan")` for more info + +
+ +## Newly broken + +* checking whether package ‘bartMan’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘bartMan’ ... +** package ‘bartMan’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in eval(exprs[i], envir) : object 'justify_grobs' not found +Error: unable to load R code in package ‘bartMan’ +Execution halted +ERROR: lazy loading failed for package ‘bartMan’ +* removing ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/bartMan’ + + +``` +### CRAN + +``` +* installing *source* package ‘bartMan’ ... +** package ‘bartMan’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (bartMan) + + ``` # bayesDP
-* Version: 1.3.6 +* Version: 1.3.7 * GitHub: https://github.com/graemeleehickey/bayesDP * Source code: https://github.com/cran/bayesDP -* Date/Publication: 2022-01-30 22:20:02 UTC -* Number of recursive dependencies: 80 +* Date/Publication: 2025-01-12 11:40:10 UTC +* Number of recursive dependencies: 79 Run `revdepcheck::cloud_details(, "bayesDP")` for more info @@ -517,10 +579,10 @@ Run `revdepcheck::cloud_details(, "bayesDP")` for more info ** package ‘bayesDP’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o bayesDP.so RcppExports.o bdplm.o ppexp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/bayesDP/new/bayesDP.Rcheck/00LOCK-bayesDP/00new/bayesDP/libs ** R @@ -542,10 +604,10 @@ ERROR: lazy loading failed for package ‘bayesDP’ ** package ‘bayesDP’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c bdplm.cpp -o bdplm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c ppexp.cpp -o ppexp.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o bayesDP.so RcppExports.o bdplm.o ppexp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/bayesDP/old/bayesDP.Rcheck/00LOCK-bayesDP/00new/bayesDP/libs ** R @@ -564,11 +626,11 @@ ERROR: lazy loading failed for package ‘bayesDP’
-* Version: 0.0.0.2 +* Version: 0.0.0.3 * GitHub: NA * Source code: https://github.com/cran/BayesianFactorZoo -* Date/Publication: 2023-11-14 12:43:44 UTC -* Number of recursive dependencies: 75 +* Date/Publication: 2024-10-04 09:30:08 UTC +* Number of recursive dependencies: 74 Run `revdepcheck::cloud_details(, "BayesianFactorZoo")` for more info @@ -632,73 +694,71 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’ * GitHub: https://github.com/ocbe-uio/BayesSurvive * Source code: https://github.com/cran/BayesSurvive * Date/Publication: 2024-06-04 13:20:12 UTC -* Number of recursive dependencies: 129 +* Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info
-## In both - -* checking whether package ‘BayesSurvive’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘BayesSurvive’ ... -** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked -** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether the compiler supports GNU C++... yes -checking whether g++ -std=gnu++17 accepts -g... yes +* using log directory ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘BayesSurvive/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘BayesSurvive’ -* removing ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/BayesSurvive’ +* this is package ‘BayesSurvive’ version ‘0.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘BayesSurvive’ ... -** package ‘BayesSurvive’ successfully unpacked and MD5 sums checked -** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether the compiler supports GNU C++... yes -checking whether g++ -std=gnu++17 accepts -g... yes +* using log directory ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘BayesSurvive/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘BayesSurvive’ -* removing ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck/BayesSurvive’ +* this is package ‘BayesSurvive’ version ‘0.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -710,7 +770,7 @@ ERROR: lazy loading failed for package ‘BayesSurvive’ * GitHub: NA * Source code: https://github.com/cran/BCClong * Date/Publication: 2024-06-24 00:00:02 UTC -* Number of recursive dependencies: 145 +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "BCClong")` for more info @@ -733,11 +793,11 @@ Run `revdepcheck::cloud_details(, "BCClong")` for more info ** package ‘BCClong’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... ** R @@ -760,11 +820,11 @@ ERROR: lazy loading failed for package ‘BCClong’ ** package ‘BCClong’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BCC.cpp -o BCC.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Likelihood.cpp -o Likelihood.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c c_which.cpp -o c_which.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BCClong.so BCC.o Likelihood.o RcppExports.o c_which.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR ... ** R @@ -784,11 +844,11 @@ ERROR: lazy loading failed for package ‘BCClong’
-* Version: 2.1.3 +* Version: 2.1.5 * GitHub: https://github.com/donaldRwilliams/BGGM * Source code: https://github.com/cran/BGGM -* Date/Publication: 2024-07-05 20:30:02 UTC -* Number of recursive dependencies: 209 +* Date/Publication: 2024-12-22 21:40:02 UTC +* Number of recursive dependencies: 211 Run `revdepcheck::cloud_details(, "BGGM")` for more info @@ -810,13 +870,13 @@ Run `revdepcheck::cloud_details(, "BGGM")` for more info * installing *source* package ‘BGGM’ ... ** package ‘BGGM’ successfully unpacked and MD5 sums checked ** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether we are using the GNU C++ compiler... yes -checking whether g++ -std=gnu++17 accepts -g... yes +configure: creating ./config.status +config.status: creating src/Makevars +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppDist/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppDist/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c bggm_fast.cpp -o bggm_fast.o ... ** data *** moving datasets to lazyload DB @@ -837,13 +897,13 @@ ERROR: lazy loading failed for package ‘BGGM’ * installing *source* package ‘BGGM’ ... ** package ‘BGGM’ successfully unpacked and MD5 sums checked ** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether we are using the GNU C++ compiler... yes -checking whether g++ -std=gnu++17 accepts -g... yes +configure: creating ./config.status +config.status: creating src/Makevars +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppDist/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppDist/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c bggm_fast.cpp -o bggm_fast.o ... ** data *** moving datasets to lazyload DB @@ -920,11 +980,11 @@ ERROR: lazy loading failed for package ‘binsreg’
-* Version: 1.0.0 +* Version: 1.0.1 * GitHub: https://github.com/statjs/bspcov * Source code: https://github.com/cran/bspcov -* Date/Publication: 2024-02-06 16:50:08 UTC -* Number of recursive dependencies: 122 +* Date/Publication: 2024-11-13 20:10:02 UTC +* Number of recursive dependencies: 111 Run `revdepcheck::cloud_details(, "bspcov")` for more info @@ -978,26 +1038,26 @@ ERROR: lazy loading failed for package ‘bspcov’ ``` -# bsub +# BSTZINB
-* Version: 1.1.0 -* GitHub: https://github.com/jokergoo/bsub -* Source code: https://github.com/cran/bsub -* Date/Publication: 2021-07-01 15:50:10 UTC -* Number of recursive dependencies: 79 +* Version: 1.0.1 +* GitHub: https://github.com/SumanM47/BSTZINB +* Source code: https://github.com/cran/BSTZINB +* Date/Publication: 2024-10-31 22:50:02 UTC +* Number of recursive dependencies: 110 -Run `revdepcheck::cloud_details(, "bsub")` for more info +Run `revdepcheck::cloud_details(, "BSTZINB")` for more info
## In both -* checking whether package ‘bsub’ can be installed ... ERROR +* checking whether package ‘BSTZINB’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bsub/new/bsub.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/BSTZINB/new/BSTZINB.Rcheck/00install.out’ for details. ``` ## Installation @@ -1005,36 +1065,40 @@ Run `revdepcheck::cloud_details(, "bsub")` for more info ### Devel ``` -* installing *source* package ‘bsub’ ... -** package ‘bsub’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BSTZINB’ ... +** package ‘BSTZINB’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bsub’ -* removing ‘/tmp/workdir/bsub/new/bsub.Rcheck/bsub’ +ERROR: lazy loading failed for package ‘BSTZINB’ +* removing ‘/tmp/workdir/BSTZINB/new/BSTZINB.Rcheck/BSTZINB’ ``` ### CRAN ``` -* installing *source* package ‘bsub’ ... -** package ‘bsub’ successfully unpacked and MD5 sums checked +* installing *source* package ‘BSTZINB’ ... +** package ‘BSTZINB’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bsub’ -* removing ‘/tmp/workdir/bsub/old/bsub.Rcheck/bsub’ +ERROR: lazy loading failed for package ‘BSTZINB’ +* removing ‘/tmp/workdir/BSTZINB/old/BSTZINB.Rcheck/BSTZINB’ ``` @@ -1042,89 +1106,163 @@ ERROR: lazy loading failed for package ‘bsub’
-* Version: 3.0.4 +* Version: 3.0.5 * GitHub: https://github.com/bozenne/BuyseTest * Source code: https://github.com/cran/BuyseTest -* Date/Publication: 2024-07-01 09:20:02 UTC -* Number of recursive dependencies: 133 +* Date/Publication: 2024-10-13 21:40:02 UTC +* Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "BuyseTest")` for more info
-## In both - -* checking whether package ‘BuyseTest’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘BuyseTest’ ... -** package ‘BuyseTest’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +* using log directory ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘BuyseTest/DESCRIPTION’ ... OK ... -installing to /tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Error: unable to load R code in package ‘BuyseTest’ -Execution halted -ERROR: lazy loading failed for package ‘BuyseTest’ -* removing ‘/tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/BuyseTest’ +* this is package ‘BuyseTest’ version ‘3.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘BuyseTest’ ... -** package ‘BuyseTest’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_buyseTest.cpp -o FCT_buyseTest.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c FCT_precompute.cpp -o FCT_precompute.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c utils-from-riskRegression.cpp -o utils-from-riskRegression.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o BuyseTest.so FCT_buyseTest.o FCT_precompute.o RcppExports.o utils-from-riskRegression.o -L/opt/R/4.3.1/lib/R/lib -lR +* using log directory ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘BuyseTest/DESCRIPTION’ ... OK ... -installing to /tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/00LOCK-BuyseTest/00new/BuyseTest/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Error: unable to load R code in package ‘BuyseTest’ -Execution halted -ERROR: lazy loading failed for package ‘BuyseTest’ -* removing ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/BuyseTest’ +* this is package ‘BuyseTest’ version ‘3.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -``` -# CARBayesST -
-* Version: 4.0 + + +``` +# CAESAR.Suite + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/XiaoZhangryy/CAESAR.Suite +* Source code: https://github.com/cran/CAESAR.Suite +* Date/Publication: 2024-09-16 14:20:06 UTC +* Number of recursive dependencies: 269 + +Run `revdepcheck::cloud_details(, "CAESAR.Suite")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/CAESAR.Suite/new/CAESAR.Suite.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK +... +* this is package ‘CAESAR.Suite’ version ‘0.1.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ProFAST’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CAESAR.Suite/old/CAESAR.Suite.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK +... +* this is package ‘CAESAR.Suite’ version ‘0.1.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ProFAST’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# CARBayesST + +
+ +* Version: 4.0 * GitHub: https://github.com/duncanplee/CARBayesST * Source code: https://github.com/cran/CARBayesST * Date/Publication: 2023-10-30 16:40:02 UTC -* Number of recursive dependencies: 118 +* Number of recursive dependencies: 106 Run `revdepcheck::cloud_details(, "CARBayesST")` for more info @@ -1147,9 +1285,9 @@ Run `revdepcheck::cloud_details(, "CARBayesST")` for more info ** package ‘CARBayesST’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayesST.so CARBayesST.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/CARBayesST/new/CARBayesST.Rcheck/00LOCK-CARBayesST/00new/CARBayesST/libs ** R @@ -1171,9 +1309,9 @@ ERROR: lazy loading failed for package ‘CARBayesST’ ** package ‘CARBayesST’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayesST.cpp -o CARBayesST.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayesST.so CARBayesST.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/00LOCK-CARBayesST/00new/CARBayesST/libs ** R @@ -1187,6 +1325,66 @@ ERROR: lazy loading failed for package ‘CARBayesST’ * removing ‘/tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/CARBayesST’ +``` +# Certara.VPCResults + +
+ +* Version: 3.0.2 +* GitHub: NA +* Source code: https://github.com/cran/Certara.VPCResults +* Date/Publication: 2024-12-02 15:30:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "Certara.VPCResults")` for more info + +
+ +## In both + +* checking whether package ‘Certara.VPCResults’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Certara.VPCResults/new/Certara.VPCResults.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Certara.VPCResults’ ... +** package ‘Certara.VPCResults’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Certara.VPCResults’ +* removing ‘/tmp/workdir/Certara.VPCResults/new/Certara.VPCResults.Rcheck/Certara.VPCResults’ + + +``` +### CRAN + +``` +* installing *source* package ‘Certara.VPCResults’ ... +** package ‘Certara.VPCResults’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Certara.VPCResults’ +* removing ‘/tmp/workdir/Certara.VPCResults/old/Certara.VPCResults.Rcheck/Certara.VPCResults’ + + ``` # CGPfunctions @@ -1196,7 +1394,7 @@ ERROR: lazy loading failed for package ‘CARBayesST’ * GitHub: https://github.com/ibecav/CGPfunctions * Source code: https://github.com/cran/CGPfunctions * Date/Publication: 2020-11-12 14:50:09 UTC -* Number of recursive dependencies: 148 +* Number of recursive dependencies: 155 Run `revdepcheck::cloud_details(, "CGPfunctions")` for more info @@ -1252,17 +1450,16 @@ ERROR: lazy loading failed for package ‘CGPfunctions’ ``` -# chemodiv +# cia
-* Version: 0.3.0 -* GitHub: https://github.com/hpetren/chemodiv -* Source code: https://github.com/cran/chemodiv -* Date/Publication: 2023-08-17 17:52:33 UTC -* Number of recursive dependencies: 170 +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/cia +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "chemodiv")` for more info +Run `revdepcheck::cloud_details(, "cia")` for more info
@@ -1271,27 +1468,7 @@ Run `revdepcheck::cloud_details(, "chemodiv")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/chemodiv/new/chemodiv.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘chemodiv/DESCRIPTION’ ... OK -... -* this is package ‘chemodiv’ version ‘0.3.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'fmcsR', 'ChemmineR' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR @@ -1301,27 +1478,7 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/chemodiv/old/chemodiv.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘chemodiv/DESCRIPTION’ ... OK -... -* this is package ‘chemodiv’ version ‘0.3.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'fmcsR', 'ChemmineR' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR @@ -1336,7 +1493,7 @@ Status: 1 ERROR * GitHub: https://github.com/eonurk/cinaR * Source code: https://github.com/cran/cinaR * Date/Publication: 2022-05-18 14:00:09 UTC -* Number of recursive dependencies: 177 +* Number of recursive dependencies: 171 Run `revdepcheck::cloud_details(, "cinaR")` for more info @@ -1351,18 +1508,18 @@ Run `revdepcheck::cloud_details(, "cinaR")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘cinaR/DESCRIPTION’ ... OK ... +* this is package ‘cinaR’ version ‘0.2.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: - 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', - 'TxDb.Hsapiens.UCSC.hg19.knownGene', - 'TxDb.Mmusculus.UCSC.mm10.knownGene' +Packages required but not available: 'ChIPseeker', 'fgsea' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -1381,18 +1538,18 @@ Status: 1 ERROR * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘cinaR/DESCRIPTION’ ... OK ... +* this is package ‘cinaR’ version ‘0.2.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: - 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', - 'TxDb.Hsapiens.UCSC.hg19.knownGene', - 'TxDb.Mmusculus.UCSC.mm10.knownGene' +Packages required but not available: 'ChIPseeker', 'fgsea' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -1465,91 +1622,15 @@ ERROR: lazy loading failed for package ‘cmprskcoxmsm’ * removing ‘/tmp/workdir/cmprskcoxmsm/old/cmprskcoxmsm.Rcheck/cmprskcoxmsm’ -``` -# CNVScope - -
- -* Version: 3.7.2 -* GitHub: https://github.com/jamesdalg/CNVScope -* Source code: https://github.com/cran/CNVScope -* Date/Publication: 2022-03-30 23:40:08 UTC -* Number of recursive dependencies: 206 - -Run `revdepcheck::cloud_details(, "CNVScope")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/CNVScope/new/CNVScope.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CNVScope/DESCRIPTION’ ... OK -... -Packages required but not available: 'GenomicInteractions', 'rtracklayer' - -Packages suggested but not available for checking: - 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', - 'BSgenome.Hsapiens.UCSC.hg19' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/CNVScope/old/CNVScope.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CNVScope/DESCRIPTION’ ... OK -... -Packages required but not available: 'GenomicInteractions', 'rtracklayer' - -Packages suggested but not available for checking: - 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', - 'BSgenome.Hsapiens.UCSC.hg19' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # COMMA
-* Version: 1.0.0 +* Version: 1.1.1 * GitHub: NA * Source code: https://github.com/cran/COMMA -* Date/Publication: 2024-07-21 10:10:05 UTC +* Date/Publication: 2024-12-13 21:10:02 UTC * Number of recursive dependencies: 72 Run `revdepcheck::cloud_details(, "COMMA")` for more info @@ -1573,6 +1654,8 @@ Run `revdepcheck::cloud_details(, "COMMA")` for more info ** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -1591,6 +1674,8 @@ ERROR: lazy loading failed for package ‘COMMA’ ** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : @@ -1602,17 +1687,17 @@ ERROR: lazy loading failed for package ‘COMMA’ ``` -# conos +# contsurvplot
-* Version: 1.5.2 -* GitHub: https://github.com/kharchenkolab/conos -* Source code: https://github.com/cran/conos -* Date/Publication: 2024-02-26 19:30:05 UTC -* Number of recursive dependencies: 240 +* Version: 0.2.1 +* GitHub: https://github.com/RobinDenz1/contsurvplot +* Source code: https://github.com/cran/contsurvplot +* Date/Publication: 2023-08-15 08:00:03 UTC +* Number of recursive dependencies: 156 -Run `revdepcheck::cloud_details(, "conos")` for more info +Run `revdepcheck::cloud_details(, "contsurvplot")` for more info
@@ -1621,22 +1706,22 @@ Run `revdepcheck::cloud_details(, "conos")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ +* using log directory ‘/tmp/workdir/contsurvplot/new/contsurvplot.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK +* checking for file ‘contsurvplot/DESCRIPTION’ ... OK ... +* this is package ‘contsurvplot’ version ‘0.2.1’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Package suggested but not available for checking: ‘pagoda2’ +Package required but not available: ‘riskRegression’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -1651,22 +1736,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ +* using log directory ‘/tmp/workdir/contsurvplot/old/contsurvplot.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘conos/DESCRIPTION’ ... OK +* checking for file ‘contsurvplot/DESCRIPTION’ ... OK ... +* this is package ‘contsurvplot’ version ‘0.2.1’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Package suggested but not available for checking: ‘pagoda2’ +Package required but not available: ‘riskRegression’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -1682,11 +1767,11 @@ Status: 1 ERROR
-* Version: 0.1.4 +* Version: 0.1.6 * GitHub: https://github.com/dandls/counterfactuals * Source code: https://github.com/cran/counterfactuals -* Date/Publication: 2024-05-14 19:00:02 UTC -* Number of recursive dependencies: 227 +* Date/Publication: 2024-10-17 12:00:06 UTC +* Number of recursive dependencies: 217 Run `revdepcheck::cloud_details(, "counterfactuals")` for more info @@ -1701,9 +1786,9 @@ Run `revdepcheck::cloud_details(, "counterfactuals")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘counterfactuals/DESCRIPTION’ ... OK @@ -1731,9 +1816,9 @@ Status: 1 NOTE * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘counterfactuals/DESCRIPTION’ ... OK @@ -1758,151 +1843,59 @@ Status: 1 NOTE
-* Version: 0.3.0 +* Version: 0.3.2 * GitHub: https://github.com/khodosevichlab/CRMetrics * Source code: https://github.com/cran/CRMetrics -* Date/Publication: 2023-09-01 09:00:06 UTC -* Number of recursive dependencies: 239 +* Date/Publication: 2024-11-08 00:20:06 UTC +* Number of recursive dependencies: 242 Run `revdepcheck::cloud_details(, "CRMetrics")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK -... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘CRMetrics’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE +* checking whether package ‘CRMetrics’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/CRMetrics’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘CRMetrics/DESCRIPTION’ ... OK -... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘CRMetrics’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE - - - - - -``` -# crosstalkr - -
- -* Version: 1.0.5 -* GitHub: NA -* Source code: https://github.com/cran/crosstalkr -* Date/Publication: 2024-05-17 11:40:09 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "crosstalkr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/crosstalkr/new/crosstalkr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘crosstalkr/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ensembldb’ - -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/crosstalkr/old/crosstalkr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘crosstalkr/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘ensembldb’ - -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘CRMetrics’ ... +** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘CRMetrics’ +* removing ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/CRMetrics’ ``` @@ -1910,11 +1903,11 @@ Status: 1 ERROR
-* Version: 3.10.1 +* Version: 3.10.2 * GitHub: https://github.com/cdriveraus/ctsem * Source code: https://github.com/cran/ctsem -* Date/Publication: 2024-08-19 14:40:06 UTC -* Number of recursive dependencies: 158 +* Date/Publication: 2025-01-13 11:00:08 UTC +* Number of recursive dependencies: 160 Run `revdepcheck::cloud_details(, "ctsem")` for more info @@ -1937,16 +1930,16 @@ Run `revdepcheck::cloud_details(, "ctsem")` for more info ** package ‘ctsem’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus @@ -1964,16 +1957,16 @@ ERROR: compilation failed for package ‘ctsem’ ** package ‘ctsem’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus @@ -1984,369 +1977,397 @@ ERROR: compilation failed for package ‘ctsem’ ``` -# DepthProc +# dartR.base
-* Version: 2.1.5 -* GitHub: https://github.com/zzawadz/DepthProc -* Source code: https://github.com/cran/DepthProc -* Date/Publication: 2022-02-03 20:30:02 UTC -* Number of recursive dependencies: 134 +* Version: 0.98 +* GitHub: NA +* Source code: https://github.com/cran/dartR.base +* Date/Publication: 2024-09-19 13:20:02 UTC +* Number of recursive dependencies: 288 -Run `revdepcheck::cloud_details(, "DepthProc")` for more info +Run `revdepcheck::cloud_details(, "dartR.base")` for more info
-## In both - -* checking whether package ‘DepthProc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +* using log directory ‘/tmp/workdir/dartR.base/new/dartR.base.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.base/DESCRIPTION’ ... OK ... -installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ +* this is package ‘dartR.base’ version ‘0.98’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SNPassoc’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +* using log directory ‘/tmp/workdir/dartR.base/old/dartR.base.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.base/DESCRIPTION’ ... OK ... -installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘DepthProc’ -* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ +* this is package ‘dartR.base’ version ‘0.98’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SNPassoc’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# DR.SC +# dartR.captive
-* Version: 3.4 -* GitHub: https://github.com/feiyoung/DR.SC -* Source code: https://github.com/cran/DR.SC -* Date/Publication: 2024-03-19 08:40:02 UTC -* Number of recursive dependencies: 151 +* Version: 0.75 +* GitHub: NA +* Source code: https://github.com/cran/dartR.captive +* Date/Publication: 2023-11-27 17:10:09 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "DR.SC")` for more info +Run `revdepcheck::cloud_details(, "dartR.captive")` for more info
-## In both - -* checking whether package ‘DR.SC’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘DR.SC’ ... -** package ‘DR.SC’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o +* using log directory ‘/tmp/workdir/dartR.captive/new/dartR.captive.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.captive/DESCRIPTION’ ... OK ... -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘DR.SC’ -* removing ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/DR.SC’ +* this is package ‘dartR.captive’ version ‘0.75’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘DR.SC’ ... -** package ‘DR.SC’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o +* using log directory ‘/tmp/workdir/dartR.captive/old/dartR.captive.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.captive/DESCRIPTION’ ... OK ... -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘DR.SC’ -* removing ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck/DR.SC’ +* this is package ‘dartR.captive’ version ‘0.75’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# easybgm +# dartR.popgen
-* Version: 0.1.2 -* GitHub: https://github.com/KarolineHuth/easybgm -* Source code: https://github.com/cran/easybgm -* Date/Publication: 2024-03-13 13:40:02 UTC +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/dartR.popgen +* Date/Publication: 2024-06-27 23:20:04 UTC * Number of recursive dependencies: 175 -Run `revdepcheck::cloud_details(, "easybgm")` for more info +Run `revdepcheck::cloud_details(, "dartR.popgen")` for more info
-## In both - -* checking whether package ‘easybgm’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ +* using log directory ‘/tmp/workdir/dartR.popgen/new/dartR.popgen.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.popgen/DESCRIPTION’ ... OK +... +* this is package ‘dartR.popgen’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ +* using log directory ‘/tmp/workdir/dartR.popgen/old/dartR.popgen.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.popgen/DESCRIPTION’ ... OK +... +* this is package ‘dartR.popgen’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# EcoEnsemble +# dartR.sexlinked
-* Version: 1.1.0 -* GitHub: https://github.com/CefasRepRes/EcoEnsemble -* Source code: https://github.com/cran/EcoEnsemble -* Date/Publication: 2024-08-19 17:20:06 UTC -* Number of recursive dependencies: 91 +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/dartR.sexlinked +* Date/Publication: 2024-06-24 15:40:02 UTC +* Number of recursive dependencies: 120 -Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info +Run `revdepcheck::cloud_details(, "dartR.sexlinked")` for more info
-## In both - -* checking whether package ‘EcoEnsemble’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/dartR.sexlinked/new/dartR.sexlinked.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.sexlinked/DESCRIPTION’ ... OK +... +* this is package ‘dartR.sexlinked’ version ‘1.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ ``` ### CRAN ``` -* installing *source* package ‘EcoEnsemble’ ... -** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/dartR.sexlinked/old/dartR.sexlinked.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.sexlinked/DESCRIPTION’ ... OK +... +* this is package ‘dartR.sexlinked’ version ‘1.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 -ERROR: compilation failed for package ‘EcoEnsemble’ -* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ ``` -# ecolottery +# dartR.sim
-* Version: 1.0.0 -* GitHub: https://github.com/frmunoz/ecolottery -* Source code: https://github.com/cran/ecolottery -* Date/Publication: 2017-07-03 11:01:29 UTC -* Number of recursive dependencies: 88 +* Version: 0.70 +* GitHub: https://github.com/green-striped-gecko/dartR.sim +* Source code: https://github.com/cran/dartR.sim +* Date/Publication: 2023-11-20 19:30:02 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "ecolottery")` for more info +Run `revdepcheck::cloud_details(, "dartR.sim")` for more info
-## In both - -* checking whether package ‘ecolottery’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ +* using log directory ‘/tmp/workdir/dartR.sim/new/dartR.sim.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.sim/DESCRIPTION’ ... OK +... +* this is package ‘dartR.sim’ version ‘0.70’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘ecolottery’ ... -** package ‘ecolottery’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ecolottery’ -* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ +* using log directory ‘/tmp/workdir/dartR.sim/old/dartR.sim.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dartR.sim/DESCRIPTION’ ... OK +... +* this is package ‘dartR.sim’ version ‘0.70’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘dartR.base’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# EMAS +# dartR.spatial
-* Version: 0.2.2 +* Version: 0.78 * GitHub: NA -* Source code: https://github.com/cran/EMAS -* Date/Publication: 2022-08-11 13:50:07 UTC -* Number of recursive dependencies: 186 +* Source code: https://github.com/cran/dartR.spatial +* Date/Publication: 2023-11-15 00:50:02 UTC +* Number of recursive dependencies: 168 -Run `revdepcheck::cloud_details(, "EMAS")` for more info +Run `revdepcheck::cloud_details(, "dartR.spatial")` for more info
@@ -2355,22 +2376,22 @@ Run `revdepcheck::cloud_details(, "EMAS")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/EMAS/new/EMAS.Rcheck’ +* using log directory ‘/tmp/workdir/dartR.spatial/new/dartR.spatial.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘EMAS/DESCRIPTION’ ... OK +* checking for file ‘dartR.spatial/DESCRIPTION’ ... OK ... +* this is package ‘dartR.spatial’ version ‘0.78’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: - 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', - 'IlluminaHumanMethylation450kanno.ilmn12.hg19' +Package required but not available: ‘dartR.base’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -2385,22 +2406,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/EMAS/old/EMAS.Rcheck’ +* using log directory ‘/tmp/workdir/dartR.spatial/old/dartR.spatial.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘EMAS/DESCRIPTION’ ... OK +* checking for file ‘dartR.spatial/DESCRIPTION’ ... OK ... +* this is package ‘dartR.spatial’ version ‘0.78’ +* package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: - 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', - 'IlluminaHumanMethylation450kanno.ilmn12.hg19' +Package required but not available: ‘dartR.base’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -2412,26 +2433,26 @@ Status: 1 ERROR ``` -# EpiEstim +# DepthProc
-* Version: 2.2-4 -* GitHub: https://github.com/mrc-ide/EpiEstim -* Source code: https://github.com/cran/EpiEstim -* Date/Publication: 2021-01-07 16:20:10 UTC -* Number of recursive dependencies: 91 +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "EpiEstim")` for more info +Run `revdepcheck::cloud_details(, "DepthProc")` for more info
## In both -* checking whether package ‘EpiEstim’ can be installed ... ERROR +* checking whether package ‘DepthProc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. ``` ## Installation @@ -2439,125 +2460,68 @@ Run `revdepcheck::cloud_details(, "EpiEstim")` for more info ### Devel ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/DepthProc’ ``` ### CRAN ``` -* installing *source* package ‘EpiEstim’ ... -** package ‘EpiEstim’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/old/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘EpiEstim’ -* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ - - -``` -# evolqg - -
- -* Version: 0.3-4 -* GitHub: https://github.com/lem-usp/evolqg -* Source code: https://github.com/cran/evolqg -* Date/Publication: 2023-12-05 15:20:12 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "evolqg")` for more info - -
- -## In both - -* checking whether package ‘evolqg’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ - - -``` -### CRAN - -``` -* installing *source* package ‘evolqg’ ... -** package ‘evolqg’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘evolqg’ -* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ +ERROR: lazy loading failed for package ‘DepthProc’ +* removing ‘/tmp/workdir/DepthProc/old/DepthProc.Rcheck/DepthProc’ ``` -# EWSmethods +# DFD
-* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/EWSmethods -* Number of recursive dependencies: 140 +* Version: 0.2.0 +* GitHub: https://github.com/MohmedSoudy/DFD +* Source code: https://github.com/cran/DFD +* Date/Publication: 2024-08-28 18:20:02 UTC +* Number of recursive dependencies: 207 -Run `revdepcheck::cloud_details(, "EWSmethods")` for more info +Run `revdepcheck::cloud_details(, "DFD")` for more info
@@ -2566,7 +2530,27 @@ Run `revdepcheck::cloud_details(, "EWSmethods")` for more info ### Devel ``` +* using log directory ‘/tmp/workdir/DFD/new/DFD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DFD/DESCRIPTION’ ... OK +... +* this is package ‘DFD’ version ‘0.2.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘signatureSearch’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR @@ -2576,23 +2560,44 @@ Run `revdepcheck::cloud_details(, "EWSmethods")` for more info ### CRAN ``` +* using log directory ‘/tmp/workdir/DFD/old/DFD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DFD/DESCRIPTION’ ... OK +... +* this is package ‘DFD’ version ‘0.2.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘signatureSearch’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR ``` -# fmx +# dMrs
-* Version: NA +* Version: 1.0.0 * GitHub: NA -* Source code: https://github.com/cran/fmx -* Number of recursive dependencies: 93 +* Source code: https://github.com/cran/dMrs +* Date/Publication: 2025-01-21 15:40:05 UTC +* Number of recursive dependencies: 137 -Run `revdepcheck::cloud_details(, "fmx")` for more info +Run `revdepcheck::cloud_details(, "dMrs")` for more info
@@ -2601,7 +2606,27 @@ Run `revdepcheck::cloud_details(, "fmx")` for more info ### Devel ``` - +* using log directory ‘/tmp/workdir/dMrs/new/dMrs.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dMrs/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... NONE +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘dMrs.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK @@ -2611,33 +2636,53 @@ Run `revdepcheck::cloud_details(, "fmx")` for more info ### CRAN ``` - +* using log directory ‘/tmp/workdir/dMrs/old/dMrs.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘dMrs/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... NONE +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘dMrs.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK ``` -# ForecastComb +# DR.SC
-* Version: 1.3.1 -* GitHub: https://github.com/ceweiss/ForecastComb -* Source code: https://github.com/cran/ForecastComb -* Date/Publication: 2018-08-07 13:50:08 UTC -* Number of recursive dependencies: 74 +* Version: 3.4 +* GitHub: https://github.com/feiyoung/DR.SC +* Source code: https://github.com/cran/DR.SC +* Date/Publication: 2024-03-19 08:40:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "ForecastComb")` for more info +Run `revdepcheck::cloud_details(, "DR.SC")` for more info
## In both -* checking whether package ‘ForecastComb’ can be installed ... ERROR +* checking whether package ‘DR.SC’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/00install.out’ for details. ``` ## Installation @@ -2645,52 +2690,68 @@ Run `revdepcheck::cloud_details(, "ForecastComb")` for more info ### Devel ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o +... ** R ** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/new/DR.SC.Rcheck/DR.SC’ ``` ### CRAN ``` -* installing *source* package ‘ForecastComb’ ... -** package ‘ForecastComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DR.SC’ ... +** package ‘DR.SC’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c getNB_fast.cpp -o getNB_fast.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job.cpp -o mt_paral_job.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -fpic -g -O2 -c mt_paral_job2.cpp -o mt_paral_job2.o +... ** R ** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘ForecastComb’ -* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ +ERROR: lazy loading failed for package ‘DR.SC’ +* removing ‘/tmp/workdir/DR.SC/old/DR.SC.Rcheck/DR.SC’ ``` -# GALLO +# dscoreMSM
-* Version: 1.5 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/GALLO -* Date/Publication: 2024-06-04 15:30:20 UTC -* Number of recursive dependencies: 142 +* Source code: https://github.com/cran/dscoreMSM +* Date/Publication: 2024-12-13 16:40:02 UTC +* Number of recursive dependencies: 121 -Run `revdepcheck::cloud_details(, "GALLO")` for more info +Run `revdepcheck::cloud_details(, "dscoreMSM")` for more info
@@ -2699,27 +2760,27 @@ Run `revdepcheck::cloud_details(, "GALLO")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/GALLO/new/GALLO.Rcheck’ +* using log directory ‘/tmp/workdir/dscoreMSM/new/dscoreMSM.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘GALLO/DESCRIPTION’ ... OK +* checking for file ‘dscoreMSM/DESCRIPTION’ ... OK ... -* this is package ‘GALLO’ version ‘1.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘dscoreMSM.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK @@ -2729,44 +2790,43 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/GALLO/old/GALLO.Rcheck’ +* using log directory ‘/tmp/workdir/dscoreMSM/old/dscoreMSM.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘GALLO/DESCRIPTION’ ... OK +* checking for file ‘dscoreMSM/DESCRIPTION’ ... OK ... -* this is package ‘GALLO’ version ‘1.5’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘dscoreMSM.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK ``` -# gap +# DynForest
-* Version: 1.6 -* GitHub: https://github.com/jinghuazhao/R -* Source code: https://github.com/cran/gap -* Date/Publication: 2024-08-27 04:40:06 UTC -* Number of recursive dependencies: 199 +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/DynForest +* Number of recursive dependencies: 143 -Run `revdepcheck::cloud_details(, "gap")` for more info +Run `revdepcheck::cloud_details(, "DynForest")` for more info
@@ -2775,27 +2835,7 @@ Run `revdepcheck::cloud_details(, "gap")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/gap/new/gap.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘gap/DESCRIPTION’ ... OK -... ---- failed re-building ‘jss.Rnw’ - -SUMMARY: processing the following file failed: - ‘jss.Rnw’ - -Error: Vignette re-building failed. -Execution halted -* DONE -Status: 4 NOTEs @@ -2805,59 +2845,33 @@ Status: 4 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/gap/old/gap.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘gap/DESCRIPTION’ ... OK -... ---- failed re-building ‘jss.Rnw’ -SUMMARY: processing the following file failed: - ‘jss.Rnw’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 4 NOTEs ``` -# gapfill +# easybgm
-* Version: 0.9.6-1 -* GitHub: https://github.com/florafauna/gapfill -* Source code: https://github.com/cran/gapfill -* Date/Publication: 2021-02-12 10:10:05 UTC -* Number of recursive dependencies: 71 +* Version: 0.2.1 +* GitHub: https://github.com/KarolineHuth/easybgm +* Source code: https://github.com/cran/easybgm +* Date/Publication: 2024-10-17 08:30:02 UTC +* Number of recursive dependencies: 180 -Run `revdepcheck::cloud_details(, "gapfill")` for more info +Run `revdepcheck::cloud_details(, "easybgm")` for more info
## In both -* checking whether package ‘gapfill’ can be installed ... ERROR +* checking whether package ‘easybgm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages which this enhances but not available for checking: - 'raster', 'doParallel', 'doMPI' + See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. ``` ## Installation @@ -2865,229 +2879,195 @@ Run `revdepcheck::cloud_details(, "gapfill")` for more info ### Devel ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ ``` ### CRAN ``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs ** R -... -** data -*** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ ``` -# geneHapR +# EcoEnsemble
-* Version: 1.2.4 -* GitHub: NA -* Source code: https://github.com/cran/geneHapR -* Date/Publication: 2024-03-01 14:32:40 UTC -* Number of recursive dependencies: 180 +* Version: 1.1.0 +* GitHub: https://github.com/CefasRepRes/EcoEnsemble +* Source code: https://github.com/cran/EcoEnsemble +* Date/Publication: 2024-08-19 17:20:06 UTC +* Number of recursive dependencies: 90 -Run `revdepcheck::cloud_details(, "geneHapR")` for more info +Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info
-## Error before installation +## In both -### Devel +* checking whether package ‘EcoEnsemble’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. + ``` -``` -* using log directory ‘/tmp/workdir/geneHapR/new/geneHapR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘geneHapR/DESCRIPTION’ ... OK -... -* this is package ‘geneHapR’ version ‘1.2.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ +## Installation -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +### Devel +``` +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/geneHapR/old/geneHapR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘geneHapR/DESCRIPTION’ ... OK -... -* this is package ‘geneHapR’ version ‘1.2.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ ``` -# GeneSelectR +# ecolottery
-* Version: 1.0.1 -* GitHub: https://github.com/dzhakparov/GeneSelectR -* Source code: https://github.com/cran/GeneSelectR -* Date/Publication: 2024-02-03 14:00:05 UTC -* Number of recursive dependencies: 191 +* Version: 1.0.0 +* GitHub: https://github.com/frmunoz/ecolottery +* Source code: https://github.com/cran/ecolottery +* Date/Publication: 2017-07-03 11:01:29 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "GeneSelectR")` for more info +Run `revdepcheck::cloud_details(, "ecolottery")` for more info
-## Error before installation +## In both + +* checking whether package ‘ecolottery’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/GeneSelectR/new/GeneSelectR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK -... -+ build_vignettes = FALSE) - - When sourcing ‘example.R’: -Error: there is no package called ‘devtools’ +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - - ‘example.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/new/ecolottery.Rcheck/ecolottery’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/GeneSelectR/old/GeneSelectR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK -... -+ build_vignettes = FALSE) - - When sourcing ‘example.R’: -Error: there is no package called ‘devtools’ +* installing *source* package ‘ecolottery’ ... +** package ‘ecolottery’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted - - ‘example.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 WARNING, 1 NOTE - - - +ERROR: lazy loading failed for package ‘ecolottery’ +* removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ ``` -# GeomComb +# EpiEstim
-* Version: 1.0 -* GitHub: https://github.com/ceweiss/GeomComb -* Source code: https://github.com/cran/GeomComb -* Date/Publication: 2016-11-27 16:02:26 -* Number of recursive dependencies: 75 +* Version: 2.2-4 +* GitHub: https://github.com/mrc-ide/EpiEstim +* Source code: https://github.com/cran/EpiEstim +* Date/Publication: 2021-01-07 16:20:10 UTC +* Number of recursive dependencies: 90 -Run `revdepcheck::cloud_details(, "GeomComb")` for more info +Run `revdepcheck::cloud_details(, "EpiEstim")` for more info
## In both -* checking whether package ‘GeomComb’ can be installed ... ERROR +* checking whether package ‘EpiEstim’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/00install.out’ for details. ``` ## Installation @@ -3095,92 +3075,61 @@ Run `revdepcheck::cloud_details(, "GeomComb")` for more info ### Devel ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/new/EpiEstim.Rcheck/EpiEstim’ ``` ### CRAN ``` -* installing *source* package ‘GeomComb’ ... -** package ‘GeomComb’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EpiEstim’ ... +** package ‘EpiEstim’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘GeomComb’ -* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ - - -``` -# geomorph - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/geomorph -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "geomorph")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - +ERROR: lazy loading failed for package ‘EpiEstim’ +* removing ‘/tmp/workdir/EpiEstim/old/EpiEstim.Rcheck/EpiEstim’ ``` -# gJLS2 +# evolqg
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/gJLS2 -* Date/Publication: 2021-09-30 09:00:05 UTC -* Number of recursive dependencies: 45 +* Version: 0.3-4 +* GitHub: https://github.com/lem-usp/evolqg +* Source code: https://github.com/cran/evolqg +* Date/Publication: 2023-12-05 15:20:12 UTC +* Number of recursive dependencies: 110 -Run `revdepcheck::cloud_details(, "gJLS2")` for more info +Run `revdepcheck::cloud_details(, "evolqg")` for more info
## In both -* checking whether package ‘gJLS2’ can be installed ... ERROR +* checking whether package ‘evolqg’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details. ``` ## Installation @@ -3188,118 +3137,99 @@ Run `revdepcheck::cloud_details(, "gJLS2")` for more info ### Devel ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’ ``` ### CRAN ``` -* installing *source* package ‘gJLS2’ ... -** package ‘gJLS2’ successfully unpacked and MD5 sums checked +* installing *source* package ‘evolqg’ ... +** package ‘evolqg’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘gJLS2’ -* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ +ERROR: lazy loading failed for package ‘evolqg’ +* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ ``` -# hettx +# EWSmethods
-* Version: 0.1.3 -* GitHub: https://github.com/bfifield/hettx -* Source code: https://github.com/cran/hettx -* Date/Publication: 2023-08-19 22:22:34 UTC -* Number of recursive dependencies: 85 +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/EWSmethods +* Number of recursive dependencies: 139 -Run `revdepcheck::cloud_details(, "hettx")` for more info +Run `revdepcheck::cloud_details(, "EWSmethods")` for more info
-## In both - -* checking whether package ‘hettx’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ + + + + ``` ### CRAN ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ + + + + ``` -# Hmisc +# flexrsurv
-* Version: 5.1-3 +* Version: 2.0.18 * GitHub: NA -* Source code: https://github.com/cran/Hmisc -* Date/Publication: 2024-05-28 07:10:02 UTC -* Number of recursive dependencies: 170 +* Source code: https://github.com/cran/flexrsurv +* Date/Publication: 2024-02-09 16:10:02 UTC +* Number of recursive dependencies: 129 -Run `revdepcheck::cloud_details(, "Hmisc")` for more info +Run `revdepcheck::cloud_details(, "flexrsurv")` for more info
@@ -3308,16 +3238,16 @@ Run `revdepcheck::cloud_details(, "Hmisc")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/Hmisc/new/Hmisc.Rcheck’ +* using log directory ‘/tmp/workdir/flexrsurv/new/flexrsurv.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘Hmisc/DESCRIPTION’ ... OK +* checking for file ‘flexrsurv/DESCRIPTION’ ... OK ... * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK @@ -3328,7 +3258,7 @@ Run `revdepcheck::cloud_details(, "Hmisc")` for more info * checking compiled code ... OK * checking examples ... OK * DONE -Status: 4 NOTEs +Status: OK @@ -3338,16 +3268,16 @@ Status: 4 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/Hmisc/old/Hmisc.Rcheck’ +* using log directory ‘/tmp/workdir/flexrsurv/old/flexrsurv.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘Hmisc/DESCRIPTION’ ... OK +* checking for file ‘flexrsurv/DESCRIPTION’ ... OK ... * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK @@ -3358,97 +3288,68 @@ Status: 4 NOTEs * checking compiled code ... OK * checking examples ... OK * DONE -Status: 4 NOTEs +Status: OK ``` -# Hmsc +# fmx
-* Version: 3.0-13 -* GitHub: https://github.com/hmsc-r/HMSC -* Source code: https://github.com/cran/Hmsc -* Date/Publication: 2022-08-11 14:10:14 UTC -* Number of recursive dependencies: 76 +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/fmx +* Number of recursive dependencies: 93 -Run `revdepcheck::cloud_details(, "Hmsc")` for more info +Run `revdepcheck::cloud_details(, "fmx")` for more info
-## In both - -* checking whether package ‘Hmsc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ + + + + ``` ### CRAN ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ + + + + ``` -# iClusterVB +# ForecastComb
-* Version: 0.1.2 -* GitHub: https://github.com/AbdalkarimA/iClusterVB -* Source code: https://github.com/cran/iClusterVB -* Date/Publication: 2024-08-20 19:10:02 UTC -* Number of recursive dependencies: 127 +* Version: 1.3.1 +* GitHub: https://github.com/ceweiss/ForecastComb +* Source code: https://github.com/cran/ForecastComb +* Date/Publication: 2018-08-07 13:50:08 UTC +* Number of recursive dependencies: 73 -Run `revdepcheck::cloud_details(, "iClusterVB")` for more info +Run `revdepcheck::cloud_details(, "ForecastComb")` for more info
## In both -* checking whether package ‘iClusterVB’ can be installed ... ERROR +* checking whether package ‘ForecastComb’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/00install.out’ for details. ``` ## Installation @@ -3456,66 +3357,1211 @@ Run `revdepcheck::cloud_details(, "iClusterVB")` for more info ### Devel ``` -* installing *source* package ‘iClusterVB’ ... -** package ‘iClusterVB’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R -... ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘iClusterVB’ -* removing ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/iClusterVB’ +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/new/ForecastComb.Rcheck/ForecastComb’ ``` ### CRAN ``` -* installing *source* package ‘iClusterVB’ ... -** package ‘iClusterVB’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ForecastComb’ ... +** package ‘ForecastComb’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R -... ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘iClusterVB’ -* removing ‘/tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/iClusterVB’ +ERROR: lazy loading failed for package ‘ForecastComb’ +* removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ ``` -# inventorize +# gap
-* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/inventorize -* Date/Publication: 2022-05-31 22:20:09 UTC -* Number of recursive dependencies: 71 +* Version: 1.6 +* GitHub: https://github.com/jinghuazhao/R +* Source code: https://github.com/cran/gap +* Date/Publication: 2024-08-27 04:40:06 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "gap")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/gap/new/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/gap/old/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + +``` +# gapfill + +
+ +* Version: 0.9.6-1 +* GitHub: https://github.com/florafauna/gapfill +* Source code: https://github.com/cran/gapfill +* Date/Publication: 2021-02-12 10:10:05 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "gapfill")` for more info + +
+ +## In both + +* checking whether package ‘gapfill’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'raster', 'doParallel', 'doMPI' + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/new/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ + + +``` +### CRAN + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ + + +``` +# genekitr + +
+ +* Version: 1.2.8 +* GitHub: https://github.com/GangLiLab/genekitr +* Source code: https://github.com/cran/genekitr +* Date/Publication: 2024-09-06 13:00:06 UTC +* Number of recursive dependencies: 199 + +Run `revdepcheck::cloud_details(, "genekitr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘genekitr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +Package suggested but not available for checking: ‘fgsea’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘genekitr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +Package suggested but not available for checking: ‘fgsea’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# GeneSelectR + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/dzhakparov/GeneSelectR +* Source code: https://github.com/cran/GeneSelectR +* Date/Publication: 2024-02-03 14:00:05 UTC +* Number of recursive dependencies: 183 + +Run `revdepcheck::cloud_details(, "GeneSelectR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/new/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/old/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + + + +``` +# GeomComb + +
+ +* Version: 1.0 +* GitHub: https://github.com/ceweiss/GeomComb +* Source code: https://github.com/cran/GeomComb +* Date/Publication: 2016-11-27 16:02:26 +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "GeomComb")` for more info + +
+ +## In both + +* checking whether package ‘GeomComb’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/new/GeomComb.Rcheck/GeomComb’ + + +``` +### CRAN + +``` +* installing *source* package ‘GeomComb’ ... +** package ‘GeomComb’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘GeomComb’ +* removing ‘/tmp/workdir/GeomComb/old/GeomComb.Rcheck/GeomComb’ + + +``` +# geomorph + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/geomorph +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "geomorph")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# GeoTox + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/GeoTox +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "GeoTox")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# ggtern + +
+ +* Version: 3.5.0 +* GitHub: NA +* Source code: https://github.com/cran/ggtern +* Date/Publication: 2024-03-24 21:50:02 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "ggtern")` for more info + +
+ +## Newly broken + +* checking whether package ‘ggtern’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘chemometrics’ + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘sp’ + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ggtern’ ... +** package ‘ggtern’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** demo +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'update_guides' not found +Error: unable to load R code in package ‘ggtern’ +Execution halted +ERROR: lazy loading failed for package ‘ggtern’ +* removing ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/ggtern’ + + +``` +### CRAN + +``` +* installing *source* package ‘ggtern’ ... +** package ‘ggtern’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** demo +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (ggtern) + + +``` +# ggThemeAssist + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/calligross/ggthemeassist +* Source code: https://github.com/cran/ggThemeAssist +* Date/Publication: 2016-08-13 16:50:55 +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "ggThemeAssist")` for more info + +
+ +## Newly broken + +* checking whether package ‘ggThemeAssist’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ggThemeAssist/new/ggThemeAssist.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ggThemeAssist’ ... +** package ‘ggThemeAssist’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in is.element("extrafont", installed.packages()[, 1]) : + unused argument (installed.packages()[, 1]) +Error: unable to load R code in package ‘ggThemeAssist’ +Execution halted +ERROR: lazy loading failed for package ‘ggThemeAssist’ +* removing ‘/tmp/workdir/ggThemeAssist/new/ggThemeAssist.Rcheck/ggThemeAssist’ + + +``` +### CRAN + +``` +* installing *source* package ‘ggThemeAssist’ ... +** package ‘ggThemeAssist’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (ggThemeAssist) + + +``` +# gJLS2 + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/gJLS2 +* Date/Publication: 2021-09-30 09:00:05 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "gJLS2")` for more info + +
+ +## In both + +* checking whether package ‘gJLS2’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/new/gJLS2.Rcheck/gJLS2’ + + +``` +### CRAN + +``` +* installing *source* package ‘gJLS2’ ... +** package ‘gJLS2’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gJLS2’ +* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’ + + +``` +# grandR + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/erhard-lab/grandR +* Source code: https://github.com/cran/grandR +* Date/Publication: 2025-01-22 22:10:02 UTC +* Number of recursive dependencies: 265 + +Run `revdepcheck::cloud_details(, "grandR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘grandR/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘getting-started.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘grandR/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘getting-started.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# GseaVis + +
+ +* Version: 0.0.5 +* GitHub: https://github.com/junjunlab/GseaVis +* Source code: https://github.com/cran/GseaVis +* Date/Publication: 2022-12-20 19:40:07 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "GseaVis")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GseaVis/new/GseaVis.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GseaVis/DESCRIPTION’ ... OK +... +* this is package ‘GseaVis’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘DOSE’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GseaVis/old/GseaVis.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GseaVis/DESCRIPTION’ ... OK +... +* this is package ‘GseaVis’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘DOSE’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# hettx + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "hettx")` for more info + +
+ +## In both + +* checking whether package ‘hettx’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ + + +``` +### CRAN + +``` +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ + + +``` +# Hmisc + +
+ +* Version: 5.2-2 +* GitHub: NA +* Source code: https://github.com/cran/Hmisc +* Date/Publication: 2025-01-10 23:30:03 UTC +* Number of recursive dependencies: 173 + +Run `revdepcheck::cloud_details(, "Hmisc")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/Hmisc/new/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/Hmisc/old/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs + + + + + +``` +# Hmsc + +
+ +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "Hmsc")` for more info + +
+ +## In both + +* checking whether package ‘Hmsc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ + + +``` +### CRAN + +``` +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ + + +``` +# iClusterVB + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/AbdalkarimA/iClusterVB +* Source code: https://github.com/cran/iClusterVB +* Date/Publication: 2024-12-09 19:50:06 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "iClusterVB")` for more info + +
+ +## In both + +* checking whether package ‘iClusterVB’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/iClusterVB’ + + +``` +### CRAN + +``` +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/iClusterVB’ + + +``` +# immcp + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/YuanlongHu/immcp +* Source code: https://github.com/cran/immcp +* Date/Publication: 2022-05-12 05:50:02 UTC +* Number of recursive dependencies: 187 + +Run `revdepcheck::cloud_details(, "immcp")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘immcp/DESCRIPTION’ ... OK +... +* this is package ‘immcp’ version ‘1.0.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'clusterProfiler', 'DOSE' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘immcp/DESCRIPTION’ ... OK +... +* this is package ‘immcp’ version ‘1.0.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'clusterProfiler', 'DOSE' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# inventorize + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 Run `revdepcheck::cloud_details(, "inventorize")` for more info @@ -3556,6 +4602,7 @@ ERROR: lazy loading failed for package ‘inventorize’ ** R ** byte-compile and prepare package for lazy loading Warning in qgamma(service_level, alpha, beta) : NaNs produced +Warning in qgamma(service_level, alpha, beta) : NaNs produced ** help *** installing help indices ** building package indices @@ -3565,6 +4612,66 @@ Warning in qgamma(service_level, alpha, beta) : NaNs produced * DONE (inventorize) +``` +# invivoPKfit + +
+ +* Version: 2.0.0 +* GitHub: NA +* Source code: https://github.com/cran/invivoPKfit +* Date/Publication: 2025-01-09 14:30:02 UTC +* Number of recursive dependencies: 172 + +Run `revdepcheck::cloud_details(, "invivoPKfit")` for more info + +
+ +## In both + +* checking whether package ‘invivoPKfit’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/invivoPKfit/new/invivoPKfit.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘invivoPKfit’ ... +** package ‘invivoPKfit’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘expand1’ is not exported by 'namespace:Matrix' +Execution halted +ERROR: lazy loading failed for package ‘invivoPKfit’ +* removing ‘/tmp/workdir/invivoPKfit/new/invivoPKfit.Rcheck/invivoPKfit’ + + +``` +### CRAN + +``` +* installing *source* package ‘invivoPKfit’ ... +** package ‘invivoPKfit’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘expand1’ is not exported by 'namespace:Matrix' +Execution halted +ERROR: lazy loading failed for package ‘invivoPKfit’ +* removing ‘/tmp/workdir/invivoPKfit/old/invivoPKfit.Rcheck/invivoPKfit’ + + ``` # iNZightPlots @@ -3574,7 +4681,7 @@ Warning in qgamma(service_level, alpha, beta) : NaNs produced * GitHub: https://github.com/iNZightVIT/iNZightPlots * Source code: https://github.com/cran/iNZightPlots * Date/Publication: 2023-10-14 05:00:02 UTC -* Number of recursive dependencies: 162 +* Number of recursive dependencies: 161 Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info @@ -3634,7 +4741,7 @@ ERROR: lazy loading failed for package ‘iNZightPlots’ * GitHub: https://github.com/iNZightVIT/iNZightRegression * Source code: https://github.com/cran/iNZightRegression * Date/Publication: 2024-04-05 02:32:59 UTC -* Number of recursive dependencies: 159 +* Number of recursive dependencies: 162 Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info @@ -3694,18 +4801,168 @@ ERROR: lazy loading failed for package ‘iNZightRegression’ * GitHub: https://github.com/vinhdizzo/IRexamples * Source code: https://github.com/cran/IRexamples * Date/Publication: 2023-10-06 06:40:02 UTC -* Number of recursive dependencies: 177 +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "IRexamples")` for more info + +
+ +## In both + +* checking whether package ‘IRexamples’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ + + +``` +### CRAN + +``` +* installing *source* package ‘IRexamples’ ... +** package ‘IRexamples’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘IRexamples’ +* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ + + +``` +# jmBIG + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/jmBIG +* Date/Publication: 2025-01-19 21:00:02 UTC +* Number of recursive dependencies: 187 + +Run `revdepcheck::cloud_details(, "jmBIG")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘jmBIG/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘jmBIG’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/jmBIG/old/jmBIG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘jmBIG/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘jmBIG’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/jmBIG/old/jmBIG.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR + + + + + +``` +# joineRML + +
-Run `revdepcheck::cloud_details(, "IRexamples")` for more info +* Version: 0.4.6 +* GitHub: https://github.com/graemeleehickey/joineRML +* Source code: https://github.com/cran/joineRML +* Date/Publication: 2023-01-20 04:50:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "joineRML")` for more info
## In both -* checking whether package ‘IRexamples’ can be installed ... ERROR +* checking whether package ‘joineRML’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. ``` ## Installation @@ -3713,73 +4970,153 @@ Run `revdepcheck::cloud_details(, "IRexamples")` for more info ### Devel ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/new/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ ``` ### CRAN ``` -* installing *source* package ‘IRexamples’ ... -** package ‘IRexamples’ successfully unpacked and MD5 sums checked +* installing *source* package ‘joineRML’ ... +** package ‘joineRML’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o +... ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘IRexamples’ -* removing ‘/tmp/workdir/IRexamples/old/IRexamples.Rcheck/IRexamples’ +ERROR: lazy loading failed for package ‘joineRML’ +* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ ``` -# jmBIG +# jsmodule
-* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/jmBIG -* Date/Publication: 2024-03-20 23:40:02 UTC -* Number of recursive dependencies: 184 +* Version: 1.6.1 +* GitHub: https://github.com/jinseob2kim/jsmodule +* Source code: https://github.com/cran/jsmodule +* Date/Publication: 2025-01-08 13:10:02 UTC +* Number of recursive dependencies: 241 -Run `revdepcheck::cloud_details(, "jmBIG")` for more info +Run `revdepcheck::cloud_details(, "jsmodule")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/jsmodule/new/jsmodule.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘jsmodule/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘jsmodule.Rmd’ using ‘UTF-8’... OK + ‘jsmodule_subgroup_cmprsk.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/jsmodule/old/jsmodule.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘jsmodule/DESCRIPTION’ ... OK +... +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘jsmodule.Rmd’ using ‘UTF-8’... OK + ‘jsmodule_subgroup_cmprsk.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +# kmc + +
+ +* Version: 0.4-2 +* GitHub: https://github.com/yfyang86/kmc +* Source code: https://github.com/cran/kmc +* Date/Publication: 2022-11-22 08:30:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "kmc")` for more info
## In both -* checking whether package ‘jmBIG’ can be installed ... ERROR +* checking whether package ‘kmc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. ``` ## Installation @@ -3787,61 +5124,149 @@ Run `revdepcheck::cloud_details(, "jmBIG")` for more info ### Devel ``` -* installing *source* package ‘jmBIG’ ... -** package ‘jmBIG’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘jmBIG’ -* removing ‘/tmp/workdir/jmBIG/new/jmBIG.Rcheck/jmBIG’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ ``` ### CRAN ``` -* installing *source* package ‘jmBIG’ ... -** package ‘jmBIG’ successfully unpacked and MD5 sums checked +* installing *source* package ‘kmc’ ... +** package ‘kmc’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs ** R -** data -*** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘jmBIG’ -* removing ‘/tmp/workdir/jmBIG/old/jmBIG.Rcheck/jmBIG’ +ERROR: lazy loading failed for package ‘kmc’ +* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ ``` -# joineRML +# KMunicate
-* Version: 0.4.6 -* GitHub: https://github.com/graemeleehickey/joineRML -* Source code: https://github.com/cran/joineRML -* Date/Publication: 2023-01-20 04:50:02 UTC -* Number of recursive dependencies: 91 +* Version: 0.2.5 +* GitHub: https://github.com/ellessenne/KMunicate-package +* Source code: https://github.com/cran/KMunicate +* Date/Publication: 2024-05-16 11:50:08 UTC +* Number of recursive dependencies: 171 -Run `revdepcheck::cloud_details(, "joineRML")` for more info +Run `revdepcheck::cloud_details(, "KMunicate")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/KMunicate/new/KMunicate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘KMunicate/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘KMunicate.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/KMunicate/old/KMunicate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘KMunicate/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘KMunicate.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +# L2E + +
+ +* Version: 2.0 +* GitHub: NA +* Source code: https://github.com/cran/L2E +* Date/Publication: 2022-09-08 21:13:00 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "L2E")` for more info
## In both -* checking whether package ‘joineRML’ can be installed ... ERROR +* checking whether package ‘L2E’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. ``` ## Installation @@ -3849,68 +5274,52 @@ Run `revdepcheck::cloud_details(, "joineRML")` for more info ### Devel ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o -... +** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/new/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ ``` ### CRAN ``` -* installing *source* package ‘joineRML’ ... -** package ‘joineRML’ successfully unpacked and MD5 sums checked +* installing *source* package ‘L2E’ ... +** package ‘L2E’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c expW.cpp -o expW.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c gammaUpdate.cpp -o gammaUpdate.o -... +** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required Execution halted -ERROR: lazy loading failed for package ‘joineRML’ -* removing ‘/tmp/workdir/joineRML/old/joineRML.Rcheck/joineRML’ +ERROR: lazy loading failed for package ‘L2E’ +* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ ``` -# kibior +# Landmarking
-* Version: 0.1.1 -* GitHub: https://github.com/regisoc/kibior -* Source code: https://github.com/cran/kibior -* Date/Publication: 2021-01-28 15:20:02 UTC -* Number of recursive dependencies: 140 +* Version: 1.0.0 +* GitHub: https://github.com/isobelbarrott/Landmarking +* Source code: https://github.com/cran/Landmarking +* Date/Publication: 2022-02-15 20:00:07 UTC +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "kibior")` for more info +Run `revdepcheck::cloud_details(, "Landmarking")` for more info
@@ -3919,22 +5328,22 @@ Run `revdepcheck::cloud_details(, "kibior")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/kibior/new/kibior.Rcheck’ +* using log directory ‘/tmp/workdir/Landmarking/new/Landmarking.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘kibior/DESCRIPTION’ ... OK +* checking for file ‘Landmarking/DESCRIPTION’ ... OK ... -* this is package ‘kibior’ version ‘0.1.1’ +* this is package ‘Landmarking’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ +Package required but not available: ‘riskRegression’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -3949,22 +5358,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/kibior/old/kibior.Rcheck’ +* using log directory ‘/tmp/workdir/Landmarking/old/Landmarking.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘kibior/DESCRIPTION’ ... OK +* checking for file ‘Landmarking/DESCRIPTION’ ... OK ... -* this is package ‘kibior’ version ‘0.1.1’ +* this is package ‘Landmarking’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ +Package required but not available: ‘riskRegression’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -3976,139 +5385,79 @@ Status: 1 ERROR ``` -# kmc +# lavaSearch2
-* Version: 0.4-2 -* GitHub: https://github.com/yfyang86/kmc -* Source code: https://github.com/cran/kmc -* Date/Publication: 2022-11-22 08:30:02 UTC -* Number of recursive dependencies: 61 +* Version: 2.0.3 +* GitHub: https://github.com/bozenne/lavaSearch2 +* Source code: https://github.com/cran/lavaSearch2 +* Date/Publication: 2024-02-23 09:10:02 UTC +* Number of recursive dependencies: 149 -Run `revdepcheck::cloud_details(, "kmc")` for more info +Run `revdepcheck::cloud_details(, "lavaSearch2")` for more info
-## In both - -* checking whether package ‘kmc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/kmc/new/kmc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/new/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs -** R -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/new/kmc.Rcheck/kmc’ +* using log directory ‘/tmp/workdir/lavaSearch2/new/lavaSearch2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘lavaSearch2/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 266 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘overview.pdf.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE -``` -### CRAN -``` -* installing *source* package ‘kmc’ ... -** package ‘kmc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExport.cpp -o RcppExport.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc.cpp -o kmc.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c kmc_init.c -o kmc_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c surv2.c -o surv2.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o kmc.so RcppExport.o kmc.o kmc_init.o surv2.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/kmc/old/kmc.Rcheck/00LOCK-kmc/00new/kmc/libs -** R -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘emplik’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘kmc’ -* removing ‘/tmp/workdir/kmc/old/kmc.Rcheck/kmc’ ``` -# L2E - -
- -* Version: 2.0 -* GitHub: NA -* Source code: https://github.com/cran/L2E -* Date/Publication: 2022-09-08 21:13:00 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "L2E")` for more info - -
- -## In both - -* checking whether package ‘L2E’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/L2E/new/L2E.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel +### CRAN ``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required -Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/new/L2E.Rcheck/L2E’ +* using log directory ‘/tmp/workdir/lavaSearch2/old/lavaSearch2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘lavaSearch2/DESCRIPTION’ ... OK +... + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 266 ] + Error: Test failures + Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘overview.pdf.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 1 NOTE -``` -### CRAN -``` -* installing *source* package ‘L2E’ ... -** package ‘L2E’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘osqp’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.1 is required -Execution halted -ERROR: lazy loading failed for package ‘L2E’ -* removing ‘/tmp/workdir/L2E/old/L2E.Rcheck/L2E’ ``` @@ -4174,17 +5523,17 @@ ERROR: lazy loading failed for package ‘llbayesireg’ ``` -# locuszoomr +# lnmixsurv
-* Version: 0.3.4 -* GitHub: https://github.com/myles-lewis/locuszoomr -* Source code: https://github.com/cran/locuszoomr -* Date/Publication: 2024-09-06 10:10:02 UTC -* Number of recursive dependencies: 132 +* Version: 3.1.6 +* GitHub: NA +* Source code: https://github.com/cran/lnmixsurv +* Date/Publication: 2024-09-03 15:20:08 UTC +* Number of recursive dependencies: 195 -Run `revdepcheck::cloud_details(, "locuszoomr")` for more info +Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info
@@ -4193,27 +5542,27 @@ Run `revdepcheck::cloud_details(, "locuszoomr")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/locuszoomr/new/locuszoomr.Rcheck’ +* using log directory ‘/tmp/workdir/lnmixsurv/new/lnmixsurv.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +* checking for file ‘lnmixsurv/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ensembldb', 'rtracklayer' +--- finished re-building ‘parallel_computation.Rmd’ -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ +SUMMARY: processing the following file failed: + ‘expectation_maximization.Rmd’ + +Error: Vignette re-building failed. +Execution halted -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. * DONE -Status: 1 ERROR +Status: 2 ERRORs, 5 NOTEs @@ -4223,27 +5572,27 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/locuszoomr/old/locuszoomr.Rcheck’ +* using log directory ‘/tmp/workdir/lnmixsurv/old/lnmixsurv.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +* checking for file ‘lnmixsurv/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ensembldb', 'rtracklayer' - -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘compare.Rmd’ using ‘UTF-8’... OK + ‘expectation_maximization.Rmd’ using ‘UTF-8’... OK + ‘intercept_only.Rmd’ using ‘UTF-8’... OK + ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK + ‘parallel_computation.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: 4 NOTEs @@ -4254,10 +5603,10 @@ Status: 1 ERROR
-* Version: 2.0.0 +* Version: 2.1.0 * GitHub: https://github.com/AlJacq/LorenzRegression * Source code: https://github.com/cran/LorenzRegression -* Date/Publication: 2024-09-09 11:20:33 UTC +* Date/Publication: 2024-10-11 16:50:02 UTC * Number of recursive dependencies: 83 Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info @@ -4281,12 +5630,12 @@ Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info ** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4308,12 +5657,12 @@ ERROR: lazy loading failed for package ‘LorenzRegression’ ** package ‘LorenzRegression’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_fitness.cpp -o GA_fitness.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c GA_meanrank.cpp -o GA_meanrank.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_derivative.cpp -o PLR_derivative.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c PLR_loss.cpp -o PLR_loss.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o ... ** data *** moving datasets to lazyload DB @@ -4336,7 +5685,7 @@ ERROR: lazy loading failed for package ‘LorenzRegression’ * GitHub: NA * Source code: https://github.com/cran/lsirm12pl * Date/Publication: 2024-08-28 23:00:02 UTC -* Number of recursive dependencies: 124 +* Number of recursive dependencies: 123 Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info @@ -4359,12 +5708,12 @@ Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info ** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o ... ** R ** data @@ -4386,12 +5735,12 @@ ERROR: lazy loading failed for package ‘lsirm12pl’ ** package ‘lsirm12pl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o ... ** R ** data @@ -4449,7 +5798,7 @@ Run `revdepcheck::cloud_details(, "MantaID")` for more info * GitHub: NA * Source code: https://github.com/cran/MARVEL * Date/Publication: 2022-10-31 10:22:50 UTC -* Number of recursive dependencies: 231 +* Number of recursive dependencies: 229 Run `revdepcheck::cloud_details(, "MARVEL")` for more info @@ -4464,9 +5813,9 @@ Run `revdepcheck::cloud_details(, "MARVEL")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘MARVEL/DESCRIPTION’ ... OK @@ -4494,9 +5843,9 @@ Status: 1 NOTE * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘MARVEL/DESCRIPTION’ ... OK @@ -4516,6 +5865,70 @@ Status: 1 NOTE +``` +# MaxWiK + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/MaxWiK +* Date/Publication: 2024-11-25 11:40:13 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "MaxWiK")` for more info + +
+ +## In both + +* checking whether package ‘MaxWiK’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/MaxWiK/new/MaxWiK.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘MaxWiK’ ... +** package ‘MaxWiK’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MaxWiK’ +* removing ‘/tmp/workdir/MaxWiK/new/MaxWiK.Rcheck/MaxWiK’ + + +``` +### CRAN + +``` +* installing *source* package ‘MaxWiK’ ... +** package ‘MaxWiK’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MaxWiK’ +* removing ‘/tmp/workdir/MaxWiK/old/MaxWiK.Rcheck/MaxWiK’ + + ``` # mbsts @@ -4525,7 +5938,7 @@ Status: 1 NOTE * GitHub: NA * Source code: https://github.com/cran/mbsts * Date/Publication: 2023-01-07 01:10:02 UTC -* Number of recursive dependencies: 82 +* Number of recursive dependencies: 81 Run `revdepcheck::cloud_details(, "mbsts")` for more info @@ -4577,79 +5990,75 @@ ERROR: lazy loading failed for package ‘mbsts’ ``` -# MitoHEAR +# MendelianRandomization
-* Version: 0.1.0 +* Version: 0.10.0 * GitHub: NA -* Source code: https://github.com/cran/MitoHEAR -* Date/Publication: 2022-03-01 21:20:02 UTC -* Number of recursive dependencies: 183 +* Source code: https://github.com/cran/MendelianRandomization +* Date/Publication: 2024-04-12 10:10:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "MitoHEAR")` for more info +Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info
-## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/MitoHEAR/new/MitoHEAR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK -... -* checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Packages suggested but not available for checking: - 'karyoploteR', 'regioneR' +## In both -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking whether package ‘MendelianRandomization’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/MitoHEAR/old/MitoHEAR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK -... -* checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Packages suggested but not available for checking: - 'karyoploteR', 'regioneR' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘MendelianRandomization’ ... +** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ ``` @@ -4661,7 +6070,7 @@ Status: 1 ERROR * GitHub: https://github.com/phargarten2/miWQS * Source code: https://github.com/cran/miWQS * Date/Publication: 2021-04-02 21:50:02 UTC -* Number of recursive dependencies: 152 +* Number of recursive dependencies: 151 Run `revdepcheck::cloud_details(, "miWQS")` for more info @@ -4675,6 +6084,11 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. ``` +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘wqs’ + ``` + ## Installation ### Devel @@ -4725,7 +6139,7 @@ ERROR: lazy loading failed for package ‘miWQS’ * GitHub: NA * Source code: https://github.com/cran/mlmts * Date/Publication: 2024-08-18 08:40:06 UTC -* Number of recursive dependencies: 242 +* Number of recursive dependencies: 244 Run `revdepcheck::cloud_details(, "mlmts")` for more info @@ -4789,7 +6203,7 @@ ERROR: lazy loading failed for package ‘mlmts’ * GitHub: https://github.com/mlr-org/mlr * Source code: https://github.com/cran/mlr * Date/Publication: 2024-06-12 10:50:02 UTC -* Number of recursive dependencies: 362 +* Number of recursive dependencies: 365 Run `revdepcheck::cloud_details(, "mlr")` for more info @@ -4804,9 +6218,9 @@ Run `revdepcheck::cloud_details(, "mlr")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘mlr/DESCRIPTION’ ... OK @@ -4820,7 +6234,7 @@ Run `revdepcheck::cloud_details(, "mlr")` for more info ‘mlr.Rmd’ using ‘UTF-8’... OK * checking re-building of vignette outputs ... OK * DONE -Status: 2 NOTEs +Status: 1 WARNING, 3 NOTEs @@ -4834,9 +6248,9 @@ Status: 2 NOTEs * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘mlr/DESCRIPTION’ ... OK @@ -4856,82 +6270,6 @@ Status: 2 NOTEs -``` -# MOCHA - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/MOCHA -* Date/Publication: 2024-01-25 12:20:12 UTC -* Number of recursive dependencies: 249 - -Run `revdepcheck::cloud_details(, "MOCHA")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/MOCHA/new/MOCHA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MOCHA/DESCRIPTION’ ... OK -... - -Packages suggested but not available for checking: - 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', - 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', - 'chromVAR', 'rtracklayer' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/MOCHA/old/MOCHA.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MOCHA/DESCRIPTION’ ... OK -... - -Packages suggested but not available for checking: - 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', - 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', - 'chromVAR', 'rtracklayer' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # MRZero @@ -4990,6 +6328,82 @@ ERROR: lazy loading failed for package ‘MRZero’ * removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ +``` +# mstate + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/hputter/mstate +* Source code: https://github.com/cran/mstate +* Date/Publication: 2024-07-11 21:30:06 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "mstate")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/mstate/new/mstate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mstate/DESCRIPTION’ ... OK +... +--- failed re-building ‘Tutorial.Rnw’ + +SUMMARY: processing the following file failed: + ‘Tutorial.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/mstate/old/mstate.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mstate/DESCRIPTION’ ... OK +... +--- failed re-building ‘Tutorial.Rnw’ + +SUMMARY: processing the following file failed: + ‘Tutorial.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 NOTE + + + + + ``` # multilevelTools @@ -4999,7 +6413,7 @@ ERROR: lazy loading failed for package ‘MRZero’ * GitHub: https://github.com/JWiley/multilevelTools * Source code: https://github.com/cran/multilevelTools * Date/Publication: 2020-03-04 09:50:02 UTC -* Number of recursive dependencies: 168 +* Number of recursive dependencies: 170 Run `revdepcheck::cloud_details(, "multilevelTools")` for more info @@ -5065,11 +6479,11 @@ ERROR: lazy loading failed for package ‘multilevelTools’
-* Version: 0.7.1 +* Version: 0.7.2 * GitHub: https://github.com/dmphillippo/multinma * Source code: https://github.com/cran/multinma -* Date/Publication: 2024-06-11 12:20:06 UTC -* Number of recursive dependencies: 152 +* Date/Publication: 2024-09-16 12:20:02 UTC +* Number of recursive dependencies: 151 Run `revdepcheck::cloud_details(, "multinma")` for more info @@ -5087,55 +6501,207 @@ Run `revdepcheck::cloud_details(, "multinma")` for more info ### Devel -``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +``` +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ + + +``` +### CRAN + +``` +* installing *source* package ‘multinma’ ... +** package ‘multinma’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/usr/local/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:0: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/usr/local/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 +ERROR: compilation failed for package ‘multinma’ +* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ + + +``` +# multipleOutcomes + +
+ +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/multipleOutcomes +* Date/Publication: 2024-05-30 15:00:03 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "multipleOutcomes")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/multipleOutcomes/new/multipleOutcomes.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘multipleOutcomes/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘test.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/multipleOutcomes/old/multipleOutcomes.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘multipleOutcomes/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘test.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: OK + + + + + +``` +# MuPETFlow + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/MuPETFlow +* Date/Publication: 2025-01-15 19:40:19 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "MuPETFlow")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/MuPETFlow/new/MuPETFlow.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MuPETFlow/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MuPETFlow.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ ``` ### CRAN ``` -* installing *source* package ‘multinma’ ... -** package ‘multinma’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/MuPETFlow/old/MuPETFlow.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MuPETFlow/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MuPETFlow.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 -ERROR: compilation failed for package ‘multinma’ -* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ ``` @@ -5143,11 +6709,11 @@ ERROR: compilation failed for package ‘multinma’
-* Version: 4.0.1 +* Version: 4.0.2 * GitHub: NA * Source code: https://github.com/cran/NCA -* Date/Publication: 2024-02-23 09:30:15 UTC -* Number of recursive dependencies: 99 +* Date/Publication: 2024-11-09 18:10:02 UTC +* Number of recursive dependencies: 98 Run `revdepcheck::cloud_details(, "NCA")` for more info @@ -5207,7 +6773,7 @@ ERROR: lazy loading failed for package ‘NCA’ * GitHub: NA * Source code: https://github.com/cran/netcmc * Date/Publication: 2022-11-08 22:30:15 UTC -* Number of recursive dependencies: 61 +* Number of recursive dependencies: 60 Run `revdepcheck::cloud_details(, "netcmc")` for more info @@ -5230,14 +6796,14 @@ Run `revdepcheck::cloud_details(, "netcmc")` for more info ** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o ... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R @@ -5257,14 +6823,14 @@ ERROR: lazy loading failed for package ‘netcmc’ ** package ‘netcmc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o ... -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs ** R @@ -5285,7 +6851,7 @@ ERROR: lazy loading failed for package ‘netcmc’ * GitHub: https://github.com/jongheepark/NetworkChange * Source code: https://github.com/cran/NetworkChange * Date/Publication: 2022-03-04 07:30:02 UTC -* Number of recursive dependencies: 133 +* Number of recursive dependencies: 122 Run `revdepcheck::cloud_details(, "NetworkChange")` for more info @@ -5366,10 +6932,10 @@ Run `revdepcheck::cloud_details(, "nlmeVPC")` for more info ** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/nlmeVPC/new/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R @@ -5391,10 +6957,10 @@ ERROR: lazy loading failed for package ‘nlmeVPC’ ** package ‘nlmeVPC’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Misc.cpp -o Misc.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o nlmeVPC.so Misc.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/nlmeVPC/old/nlmeVPC.Rcheck/00LOCK-nlmeVPC/00new/nlmeVPC/libs ** R @@ -5417,7 +6983,7 @@ ERROR: lazy loading failed for package ‘nlmeVPC’ * GitHub: NA * Source code: https://github.com/cran/NMADiagT * Date/Publication: 2020-02-26 07:00:02 UTC -* Number of recursive dependencies: 79 +* Number of recursive dependencies: 78 Run `revdepcheck::cloud_details(, "NMADiagT")` for more info @@ -5469,102 +7035,53 @@ ERROR: lazy loading failed for package ‘NMADiagT’ ``` -# ohun - -
- -* Version: 1.0.2 -* GitHub: https://github.com/ropensci/ohun -* Source code: https://github.com/cran/ohun -* Date/Publication: 2024-08-19 18:40:02 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "ohun")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/ohun/new/ohun.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ohun/DESCRIPTION’ ... OK -... -* this is package ‘ohun’ version ‘1.0.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘warbleR’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/ohun/old/ohun.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘ohun/DESCRIPTION’ ... OK -... -* this is package ‘ohun’ version ‘1.0.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘warbleR’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# optweight +# NMF
-* Version: 0.2.5 +* Version: 0.28 * GitHub: NA -* Source code: https://github.com/cran/optweight -* Date/Publication: 2019-09-16 15:40:02 UTC -* Number of recursive dependencies: 55 +* Source code: https://github.com/cran/NMF +* Date/Publication: 2024-08-22 16:20:01 UTC +* Number of recursive dependencies: 132 -Run `revdepcheck::cloud_details(, "optweight")` for more info +Run `revdepcheck::cloud_details(, "NMF")` for more info
-## In both +## Newly broken -* checking whether package ‘optweight’ can be installed ... ERROR +* checking whether package ‘NMF’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/NMF/new/NMF.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘NMF-vignette.Rnw’ using knitr + Error in citation(x) : there is no package called 'doMC' + Converted 9 of 10 package citations to BibTeX + Writing 11 Bibtex entries ... OK + Results written to file 'Rpackages.bib' + Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'NMF-vignette.tex' failed. + LaTeX errors: + ! LaTeX Error: File `a4wide.sty' not found. + ... + l.62 \usepackage + {xspace}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘heatmaps.Rnw’ + + SUMMARY: processing the following files failed: + ‘NMF-vignette.Rnw’ ‘heatmaps.Rnw’ + + Error: Vignette re-building failed. + Execution halted ``` ## Installation @@ -5572,110 +7089,68 @@ Run `revdepcheck::cloud_details(, "optweight")` for more info ### Devel ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMF’ ... +** package ‘NMF’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c distance.cpp -o distance.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c divergence.cpp -o divergence.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c euclidean.cpp -o euclidean.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +... +Creating meta registry in package 'NMF' ... OK +Creating registry 'extra_handler' in package 'NMF' ... OK +Creating registry 'extra_action' in package 'NMF' ... OK +Registering extra handler 'install.packages' [function] ... OK +Creating registry 'algorithm' in package 'NMF' ... OK +Error in is.element("...", n.update) : unused argument (n.update) +Error: unable to load R code in package ‘NMF’ Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘NMF’ +* removing ‘/tmp/workdir/NMF/new/NMF.Rcheck/NMF’ ``` ### CRAN ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘NMF’ ... +** package ‘NMF’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c distance.cpp -o distance.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c divergence.cpp -o divergence.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c euclidean.cpp -o euclidean.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +... +Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (NMF) ``` -# OVtool +# obliqueRSF
-* Version: 1.0.3 +* Version: 0.1.2 * GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "OVtool")` for more info - -
- -## In both - -* checking whether package ‘OVtool’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ - - -``` -### CRAN - -``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ - - -``` -# pagoda2 - -
- -* Version: 1.0.12 -* GitHub: https://github.com/kharchenkolab/pagoda2 -* Source code: https://github.com/cran/pagoda2 -* Date/Publication: 2024-02-27 00:50:02 UTC -* Number of recursive dependencies: 162 +* Source code: https://github.com/cran/obliqueRSF +* Date/Publication: 2022-08-28 20:50:02 UTC +* Number of recursive dependencies: 117 -Run `revdepcheck::cloud_details(, "pagoda2")` for more info +Run `revdepcheck::cloud_details(, "obliqueRSF")` for more info
@@ -5684,27 +7159,27 @@ Run `revdepcheck::cloud_details(, "pagoda2")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/pagoda2/new/pagoda2.Rcheck’ +* using log directory ‘/tmp/workdir/obliqueRSF/new/obliqueRSF.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘pagoda2/DESCRIPTION’ ... OK +* checking for file ‘obliqueRSF/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rjson’ - -Package suggested but not available for checking: ‘scde’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK * DONE -Status: 1 ERROR +Status: OK @@ -5714,117 +7189,129 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/pagoda2/old/pagoda2.Rcheck’ +* using log directory ‘/tmp/workdir/obliqueRSF/old/obliqueRSF.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘pagoda2/DESCRIPTION’ ... OK +* checking for file ‘obliqueRSF/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rjson’ +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: OK + -Package suggested but not available for checking: ‘scde’ -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +``` +# OlinkAnalyze + +
+ +* Version: 4.0.2 +* GitHub: https://github.com/Olink-Proteomics/OlinkRPackage +* Source code: https://github.com/cran/OlinkAnalyze +* Date/Publication: 2024-11-22 16:20:02 UTC +* Number of recursive dependencies: 210 + +Run `revdepcheck::cloud_details(, "OlinkAnalyze")` for more info + +
+ +## Error before installation + +### Devel +``` +* using log directory ‘/tmp/workdir/OlinkAnalyze/new/OlinkAnalyze.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK +... +--- finished re-building ‘plate_randomizer.Rmd’ +SUMMARY: processing the following file failed: + ‘Vignett.Rmd’ -``` -# PAMpal +Error: Vignette re-building failed. +Execution halted -
+* DONE +Status: 1 ERROR, 2 NOTEs -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/PAMpal -* Date/Publication: 2024-07-11 22:50:02 UTC -* Number of recursive dependencies: 118 -Run `revdepcheck::cloud_details(, "PAMpal")` for more info -
-## In both -* checking whether package ‘PAMpal’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/00install.out’ for details. - ``` +``` +### CRAN -## Installation +``` +* using log directory ‘/tmp/workdir/OlinkAnalyze/old/OlinkAnalyze.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK +... +--- finished re-building ‘plate_randomizer.Rmd’ -### Devel +SUMMARY: processing the following file failed: + ‘Vignett.Rmd’ -``` -* installing *source* package ‘PAMpal’ ... -** package ‘PAMpal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Error: Vignette re-building failed. Execution halted -ERROR: lazy loading failed for package ‘PAMpal’ -* removing ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/PAMpal’ + +* DONE +Status: 1 ERROR, 2 NOTEs -``` -### CRAN -``` -* installing *source* package ‘PAMpal’ ... -** package ‘PAMpal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘PAMpal’ -* removing ‘/tmp/workdir/PAMpal/old/PAMpal.Rcheck/PAMpal’ ``` -# PAMscapes +# optweight
-* Version: 0.6.0 +* Version: 0.2.5 * GitHub: NA -* Source code: https://github.com/cran/PAMscapes -* Date/Publication: 2024-07-09 22:50:02 UTC -* Number of recursive dependencies: 110 +* Source code: https://github.com/cran/optweight +* Date/Publication: 2019-09-16 15:40:02 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "PAMscapes")` for more info +Run `revdepcheck::cloud_details(, "optweight")` for more info
## In both -* checking whether package ‘PAMscapes’ can be installed ... ERROR +* checking whether package ‘optweight’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. ``` ## Installation @@ -5832,59 +7319,57 @@ Run `revdepcheck::cloud_details(, "PAMscapes")` for more info ### Devel ``` -* installing *source* package ‘PAMscapes’ ... -** package ‘PAMscapes’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PAMscapes’ -* removing ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/PAMscapes’ +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ ``` ### CRAN ``` -* installing *source* package ‘PAMscapes’ ... -** package ‘PAMscapes’ successfully unpacked and MD5 sums checked +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rjson’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘PAMscapes’ -* removing ‘/tmp/workdir/PAMscapes/old/PAMscapes.Rcheck/PAMscapes’ +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ ``` -# paths +# OVtool
-* Version: 0.1.1 +* Version: 1.0.3 * GitHub: NA -* Source code: https://github.com/cran/paths -* Date/Publication: 2021-06-18 08:40:02 UTC -* Number of recursive dependencies: 102 +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 156 -Run `revdepcheck::cloud_details(, "paths")` for more info +Run `revdepcheck::cloud_details(, "OVtool")` for more info
## In both -* checking whether package ‘paths’ can be installed ... ERROR +* checking whether package ‘OVtool’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. ``` ## Installation @@ -5892,53 +7377,52 @@ Run `revdepcheck::cloud_details(, "paths")` for more info ### Devel ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ ``` ### CRAN ``` -* installing *source* package ‘paths’ ... -** package ‘paths’ successfully unpacked and MD5 sums checked +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘paths’ -* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ ``` -# PathwaySpace +# pammtools
-* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/PathwaySpace -* Number of recursive dependencies: 70 +* Version: 0.5.93 +* GitHub: https://github.com/adibender/pammtools +* Source code: https://github.com/cran/pammtools +* Date/Publication: 2024-02-25 10:10:02 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info +Run `revdepcheck::cloud_details(, "pammtools")` for more info
@@ -5947,7 +7431,27 @@ Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info ### Devel ``` - +* using log directory ‘/tmp/workdir/pammtools/new/pammtools.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pammtools/DESCRIPTION’ ... OK +... +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking R/sysdata.rda ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: OK @@ -5957,33 +7461,53 @@ Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info ### CRAN ``` - +* using log directory ‘/tmp/workdir/pammtools/old/pammtools.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pammtools/DESCRIPTION’ ... OK +... +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking R/sysdata.rda ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: OK ``` -# pcvr +# paths
-* Version: 1.0.0 -* GitHub: https://github.com/danforthcenter/pcvr -* Source code: https://github.com/cran/pcvr -* Date/Publication: 2024-09-05 17:30:02 UTC -* Number of recursive dependencies: 189 +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/paths +* Date/Publication: 2021-06-18 08:40:02 UTC +* Number of recursive dependencies: 102 -Run `revdepcheck::cloud_details(, "pcvr")` for more info +Run `revdepcheck::cloud_details(, "paths")` for more info
## In both -* checking whether package ‘pcvr’ can be installed ... ERROR +* checking whether package ‘paths’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/paths/new/paths.Rcheck/00install.out’ for details. ``` ## Installation @@ -5991,60 +7515,53 @@ Run `revdepcheck::cloud_details(, "pcvr")` for more info ### Devel ``` -* installing *source* package ‘pcvr’ ... -** package ‘pcvr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pcvr’ -* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/new/paths.Rcheck/paths’ ``` ### CRAN ``` -* installing *source* package ‘pcvr’ ... -** package ‘pcvr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘paths’ ... +** package ‘paths’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘pcvr’ -* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’ +ERROR: lazy loading failed for package ‘paths’ +* removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ ``` -# PlasmaMutationDetector +# PathwaySpace
-* Version: 1.7.2 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/PlasmaMutationDetector -* Date/Publication: 2018-06-11 07:43:09 UTC -* Number of recursive dependencies: 91 +* Source code: https://github.com/cran/PathwaySpace +* Number of recursive dependencies: 69 -Run `revdepcheck::cloud_details(, "PlasmaMutationDetector")` for more info +Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info
@@ -6053,27 +7570,7 @@ Run `revdepcheck::cloud_details(, "PlasmaMutationDetector")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/PlasmaMutationDetector/new/PlasmaMutationDetector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK -... -* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'VariantAnnotation', 'rtracklayer' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR @@ -6083,106 +7580,80 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/PlasmaMutationDetector/old/PlasmaMutationDetector.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK -... -* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'VariantAnnotation', 'rtracklayer' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR ``` -# PlasmaMutationDetector2 +# pcvr
-* Version: 1.1.11 -* GitHub: NA -* Source code: https://github.com/cran/PlasmaMutationDetector2 -* Date/Publication: 2022-05-03 10:00:08 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "PlasmaMutationDetector2")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/new/PlasmaMutationDetector2.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK -... -* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'VariantAnnotation', 'rtracklayer' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* Version: 1.1.1.0 +* GitHub: https://github.com/danforthcenter/pcvr +* Source code: https://github.com/cran/pcvr +* Date/Publication: 2024-11-06 20:50:02 UTC +* Number of recursive dependencies: 192 +Run `revdepcheck::cloud_details(, "pcvr")` for more info +
+## In both +* checking whether package ‘pcvr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details. + ``` -``` -### CRAN +## Installation -``` -* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/old/PlasmaMutationDetector2.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK -... -* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'VariantAnnotation', 'rtracklayer' +### Devel -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’ +``` +### CRAN +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’ ``` @@ -6194,7 +7665,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/PLMIX * Date/Publication: 2019-09-04 11:50:02 UTC -* Number of recursive dependencies: 139 +* Number of recursive dependencies: 128 Run `revdepcheck::cloud_details(, "PLMIX")` for more info @@ -6217,12 +7688,12 @@ Run `revdepcheck::cloud_details(, "PLMIX")` for more info ** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o ... ** data *** moving datasets to lazyload DB @@ -6244,12 +7715,12 @@ ERROR: lazy loading failed for package ‘PLMIX’ ** package ‘PLMIX’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompProbZpartial.cpp -o CompProbZpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateP.cpp -o CompRateP.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CompRateYpartial.cpp -o CompRateYpartial.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c Estep.cpp -o Estep.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c PLMIXsim.cpp -o PLMIXsim.o ... ** data *** moving datasets to lazyload DB @@ -6263,82 +7734,6 @@ ERROR: lazy loading failed for package ‘PLMIX’ * removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ -``` -# polyRAD - -
- -* Version: 2.0.0 -* GitHub: https://github.com/lvclark/polyRAD -* Source code: https://github.com/cran/polyRAD -* Date/Publication: 2022-11-06 21:50:02 UTC -* Number of recursive dependencies: 135 - -Run `revdepcheck::cloud_details(, "polyRAD")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/polyRAD/new/polyRAD.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘polyRAD/DESCRIPTION’ ... OK -... - - When sourcing ‘polyRADtutorial.R’: -Error: Probabilities must be finite and non-negative! -Execution halted - - ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK - ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 3 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/polyRAD/old/polyRAD.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘polyRAD/DESCRIPTION’ ... OK -... - - When sourcing ‘polyRADtutorial.R’: -Error: Probabilities must be finite and non-negative! -Execution halted - - ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK - ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 3 NOTEs - - - - - ``` # popstudy @@ -6348,7 +7743,7 @@ Status: 1 ERROR, 3 NOTEs * GitHub: NA * Source code: https://github.com/cran/popstudy * Date/Publication: 2023-10-17 23:50:02 UTC -* Number of recursive dependencies: 240 +* Number of recursive dependencies: 242 Run `revdepcheck::cloud_details(, "popstudy")` for more info @@ -6418,53 +7813,65 @@ Run `revdepcheck::cloud_details(, "pould")` for more info
-## In both - -* checking whether package ‘pould’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/pould/new/pould.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ +* using log directory ‘/tmp/workdir/pould/new/pould.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pould/DESCRIPTION’ ... OK +... +* this is package ‘pould’ version ‘1.0.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘haplo.stats’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘pould’ ... -** package ‘pould’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘pould’ -* removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ +* using log directory ‘/tmp/workdir/pould/old/pould.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pould/DESCRIPTION’ ... OK +... +* this is package ‘pould’ version ‘1.0.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘haplo.stats’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6540,7 +7947,7 @@ ERROR: lazy loading failed for package ‘PoweREST’ * GitHub: https://github.com/mihaiconstantin/powerly * Source code: https://github.com/cran/powerly * Date/Publication: 2022-09-09 14:10:01 UTC -* Number of recursive dependencies: 181 +* Number of recursive dependencies: 169 Run `revdepcheck::cloud_details(, "powerly")` for more info @@ -6610,7 +8017,7 @@ ERROR: lazy loading failed for package ‘powerly’ * GitHub: https://github.com/marjoleinF/pre * Source code: https://github.com/cran/pre * Date/Publication: 2024-01-12 19:30:02 UTC -* Number of recursive dependencies: 151 +* Number of recursive dependencies: 153 Run `revdepcheck::cloud_details(, "pre")` for more info @@ -6674,7 +8081,7 @@ ERROR: lazy loading failed for package ‘pre’ * GitHub: https://github.com/feiyoung/ProFAST * Source code: https://github.com/cran/ProFAST * Date/Publication: 2024-03-18 08:10:06 UTC -* Number of recursive dependencies: 245 +* Number of recursive dependencies: 248 Run `revdepcheck::cloud_details(, "ProFAST")` for more info @@ -6689,9 +8096,9 @@ Run `revdepcheck::cloud_details(, "ProFAST")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘ProFAST/DESCRIPTION’ ... OK @@ -6719,9 +8126,9 @@ Status: 1 ERROR * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘ProFAST/DESCRIPTION’ ... OK @@ -6750,73 +8157,71 @@ Status: 1 ERROR * GitHub: https://github.com/ocbe-uio/psbcSpeedUp * Source code: https://github.com/cran/psbcSpeedUp * Date/Publication: 2024-07-01 09:00:02 UTC -* Number of recursive dependencies: 130 +* Number of recursive dependencies: 119 Run `revdepcheck::cloud_details(, "psbcSpeedUp")` for more info
-## In both - -* checking whether package ‘psbcSpeedUp’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘psbcSpeedUp’ ... -** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked -** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether the compiler supports GNU C++... yes -checking whether g++ -std=gnu++17 accepts -g... yes +* using log directory ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘psbcSpeedUp/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘psbcSpeedUp’ -* removing ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/psbcSpeedUp’ +* this is package ‘psbcSpeedUp’ version ‘2.0.7’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘psbcSpeedUp’ ... -** package ‘psbcSpeedUp’ successfully unpacked and MD5 sums checked -** using staged installation -checking whether the C++ compiler works... yes -checking for C++ compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether the compiler supports GNU C++... yes -checking whether g++ -std=gnu++17 accepts -g... yes +* using log directory ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘psbcSpeedUp/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘psbcSpeedUp’ -* removing ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck/psbcSpeedUp’ +* this is package ‘psbcSpeedUp’ version ‘2.0.7’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘riskRegression’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6828,7 +8233,7 @@ ERROR: lazy loading failed for package ‘psbcSpeedUp’ * GitHub: https://github.com/JWiley/score-project * Source code: https://github.com/cran/pscore * Date/Publication: 2022-05-13 22:30:02 UTC -* Number of recursive dependencies: 169 +* Number of recursive dependencies: 171 Run `revdepcheck::cloud_details(, "pscore")` for more info @@ -6891,6 +8296,41 @@ ERROR: lazy loading failed for package ‘pscore’ * removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ +``` +# pubh + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/pubh +* Number of recursive dependencies: 161 + +Run `revdepcheck::cloud_details(, "pubh")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # qPCRtools @@ -6900,7 +8340,7 @@ ERROR: lazy loading failed for package ‘pscore’ * GitHub: https://github.com/lixiang117423/qPCRtools * Source code: https://github.com/cran/qPCRtools * Date/Publication: 2023-11-02 13:10:05 UTC -* Number of recursive dependencies: 106 +* Number of recursive dependencies: 110 Run `revdepcheck::cloud_details(, "qPCRtools")` for more info @@ -6960,7 +8400,7 @@ ERROR: lazy loading failed for package ‘qPCRtools’ * GitHub: https://github.com/Kyuhyun07/qris * Source code: https://github.com/cran/qris * Date/Publication: 2024-03-05 14:40:03 UTC -* Number of recursive dependencies: 55 +* Number of recursive dependencies: 54 Run `revdepcheck::cloud_details(, "qris")` for more info @@ -6983,12 +8423,12 @@ Run `revdepcheck::cloud_details(, "qris")` for more info ** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R @@ -7010,12 +8450,12 @@ ERROR: lazy loading failed for package ‘qris’ ** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o ... installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R @@ -7038,7 +8478,7 @@ ERROR: lazy loading failed for package ‘qris’ * GitHub: NA * Source code: https://github.com/cran/qte * Date/Publication: 2022-09-01 14:30:02 UTC -* Number of recursive dependencies: 87 +* Number of recursive dependencies: 123 Run `revdepcheck::cloud_details(, "qte")` for more info @@ -7164,7 +8604,7 @@ ERROR: lazy loading failed for package ‘quantilogram’ * GitHub: NA * Source code: https://github.com/cran/quid * Date/Publication: 2021-12-09 09:00:02 UTC -* Number of recursive dependencies: 95 +* Number of recursive dependencies: 94 Run `revdepcheck::cloud_details(, "quid")` for more info @@ -7224,144 +8664,407 @@ ERROR: lazy loading failed for package ‘quid’
-* Version: 3.2 +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 201 + +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info + +
+ +## In both + +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + +``` +### CRAN + +``` +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + +``` +# rddtools + +
+ +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "rddtools")` for more info + +
+ +## In both + +* checking whether package ‘rddtools’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ + + +``` +### CRAN + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ + + +``` +# relsurv + +
+ +* Version: 2.3-1 +* GitHub: NA +* Source code: https://github.com/cran/relsurv +* Date/Publication: 2025-01-20 15:40:01 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "relsurv")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/relsurv/new/relsurv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘relsurv/DESCRIPTION’ ... OK +... +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking line endings in Makefiles ... OK +* checking compilation flags in Makevars ... OK +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: OK + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/relsurv/old/relsurv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘relsurv/DESCRIPTION’ ... OK +... +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking line endings in Makefiles ... OK +* checking compilation flags in Makevars ... OK +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: OK + + + + + +``` +# ReporterScore + +
+ +* Version: 0.1.9 +* GitHub: https://github.com/Asa12138/ReporterScore +* Source code: https://github.com/cran/ReporterScore +* Date/Publication: 2024-11-28 14:10:06 UTC +* Number of recursive dependencies: 250 + +Run `revdepcheck::cloud_details(, "ReporterScore")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ReporterScore/new/ReporterScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ReporterScore/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘ReporterScore.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ReporterScore/old/ReporterScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ReporterScore/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘ReporterScore.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# RGraphSpace + +
+ +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo -* Date/Publication: 2024-02-06 09:20:02 UTC -* Number of recursive dependencies: 200 +* Source code: https://github.com/cran/RGraphSpace +* Number of recursive dependencies: 64 -Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info +Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info
-## In both - -* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + + + ``` ### CRAN ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ + + + + ``` -# rddtools +# riskRegression
-* Version: 1.6.0 -* GitHub: https://github.com/bquast/rddtools -* Source code: https://github.com/cran/rddtools -* Date/Publication: 2022-01-10 12:42:49 UTC -* Number of recursive dependencies: 106 +* Version: 2023.12.21 +* GitHub: https://github.com/tagteam/riskRegression +* Source code: https://github.com/cran/riskRegression +* Date/Publication: 2023-12-19 17:00:02 UTC +* Number of recursive dependencies: 185 -Run `revdepcheck::cloud_details(, "rddtools")` for more info +Run `revdepcheck::cloud_details(, "riskRegression")` for more info
-## In both - -* checking whether package ‘rddtools’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ +* using log directory ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘riskRegression/DESCRIPTION’ ... OK +... +* this is package ‘riskRegression’ version ‘2023.12.21’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rms’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ +* using log directory ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘riskRegression/DESCRIPTION’ ... OK +... +* this is package ‘riskRegression’ version ‘2023.12.21’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rms’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# RGraphSpace +# rmlnomogram
* Version: NA * GitHub: NA -* Source code: https://github.com/cran/RGraphSpace -* Number of recursive dependencies: 65 +* Source code: https://github.com/cran/rmlnomogram +* Number of recursive dependencies: 181 -Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info +Run `revdepcheck::cloud_details(, "rmlnomogram")` for more info
@@ -7394,7 +9097,7 @@ Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info * Version: NA * GitHub: NA * Source code: https://github.com/cran/rms -* Number of recursive dependencies: 145 +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "rms")` for more info @@ -7422,17 +9125,17 @@ Run `revdepcheck::cloud_details(, "rms")` for more info ``` -# RNAseqQC +# robber
-* Version: 0.2.1 -* GitHub: https://github.com/frederikziebell/RNAseqQC -* Source code: https://github.com/cran/RNAseqQC -* Date/Publication: 2024-07-15 14:40:02 UTC -* Number of recursive dependencies: 162 +* Version: 0.2.4 +* GitHub: https://github.com/Chabert-Liddell/robber +* Source code: https://github.com/cran/robber +* Date/Publication: 2024-02-07 13:50:02 UTC +* Number of recursive dependencies: 143 -Run `revdepcheck::cloud_details(, "RNAseqQC")` for more info +Run `revdepcheck::cloud_details(, "robber")` for more info
@@ -7441,27 +9144,27 @@ Run `revdepcheck::cloud_details(, "RNAseqQC")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/RNAseqQC/new/RNAseqQC.Rcheck’ +* using log directory ‘/tmp/workdir/robber/new/robber.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +* checking for file ‘robber/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ensembldb', 'ComplexHeatmap' - -Package suggested but not available for checking: ‘recount3’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking tests ... OK + Running ‘spelling.R’ + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘topological-analysis.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK @@ -7471,27 +9174,27 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/RNAseqQC/old/RNAseqQC.Rcheck’ +* using log directory ‘/tmp/workdir/robber/old/robber.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +* checking for file ‘robber/DESCRIPTION’ ... OK ... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ensembldb', 'ComplexHeatmap' - -Package suggested but not available for checking: ‘recount3’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking tests ... OK + Running ‘spelling.R’ + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘topological-analysis.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR +Status: OK @@ -7502,11 +9205,11 @@ Status: 1 ERROR
-* Version: 1.0.2 +* Version: 1.2.0 * GitHub: https://github.com/aalfons/robmed * Source code: https://github.com/cran/robmed -* Date/Publication: 2023-06-16 23:00:02 UTC -* Number of recursive dependencies: 60 +* Date/Publication: 2024-12-10 00:00:02 UTC +* Number of recursive dependencies: 59 Run `revdepcheck::cloud_details(, "robmed")` for more info @@ -7566,11 +9269,11 @@ ERROR: lazy loading failed for package ‘robmed’
-* Version: 0.1.0 +* Version: 0.1.1 * GitHub: https://github.com/aalfons/robmedExtra * Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2023-06-02 14:40:02 UTC -* Number of recursive dependencies: 90 +* Date/Publication: 2024-11-03 12:10:01 UTC +* Number of recursive dependencies: 91 Run `revdepcheck::cloud_details(, "robmedExtra")` for more info @@ -7690,7 +9393,7 @@ ERROR: lazy loading failed for package ‘RPPanalyzer’ * GitHub: NA * Source code: https://github.com/cran/RQdeltaCT * Date/Publication: 2024-04-17 15:50:02 UTC -* Number of recursive dependencies: 166 +* Number of recursive dependencies: 163 Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info @@ -7753,7 +9456,7 @@ ERROR: lazy loading failed for package ‘RQdeltaCT’ * Version: NA * GitHub: NA * Source code: https://github.com/cran/RRPP -* Number of recursive dependencies: 68 +* Number of recursive dependencies: 67 Run `revdepcheck::cloud_details(, "RRPP")` for more info @@ -7789,7 +9492,7 @@ Run `revdepcheck::cloud_details(, "RRPP")` for more info * GitHub: https://github.com/stan-dev/rstanarm * Source code: https://github.com/cran/rstanarm * Date/Publication: 2024-01-18 23:00:03 UTC -* Number of recursive dependencies: 138 +* Number of recursive dependencies: 140 Run `revdepcheck::cloud_details(, "rstanarm")` for more info @@ -7808,130 +9511,54 @@ Run `revdepcheck::cloud_details(, "rstanarm")` for more info ### Devel ``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 -rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ - - -``` -### CRAN - -``` -* installing *source* package ‘rstanarm’ ... -** package ‘rstanarm’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan -Wrote C++ file "stan_files/bernoulli.cc" - - -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 -rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc -ERROR: compilation failed for package ‘rstanarm’ -* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ - - -``` -# RTIGER - -
- -* Version: 2.1.0 -* GitHub: NA -* Source code: https://github.com/cran/RTIGER -* Date/Publication: 2023-03-29 09:20:02 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "RTIGER")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/RTIGER/new/RTIGER.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘RTIGER/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" +... +/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/RTIGER/old/RTIGER.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘RTIGER/DESCRIPTION’ ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" +... +/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:0: required from here +/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ ``` @@ -7939,11 +9566,11 @@ Status: 1 NOTE
-* Version: 1.1.0 +* Version: 1.3.0 * GitHub: https://github.com/aidanmorales/rTwig * Source code: https://github.com/cran/rTwig -* Date/Publication: 2024-08-21 00:50:02 UTC -* Number of recursive dependencies: 147 +* Date/Publication: 2024-11-21 21:30:02 UTC +* Number of recursive dependencies: 141 Run `revdepcheck::cloud_details(, "rTwig")` for more info @@ -7966,12 +9593,12 @@ Run `revdepcheck::cloud_details(, "rTwig")` for more info ** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cluster_cloud.cpp -o cluster_cloud.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o ... ** data *** moving datasets to lazyload DB @@ -7993,12 +9620,12 @@ ERROR: lazy loading failed for package ‘rTwig’ ** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cluster_cloud.cpp -o cluster_cloud.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I../inst/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o ... ** data *** moving datasets to lazyload DB @@ -8021,7 +9648,7 @@ ERROR: lazy loading failed for package ‘rTwig’ * GitHub: https://github.com/THERMOSTATS/RVA * Source code: https://github.com/cran/RVA * Date/Publication: 2021-11-01 21:40:02 UTC -* Number of recursive dependencies: 207 +* Number of recursive dependencies: 210 Run `revdepcheck::cloud_details(, "RVA")` for more info @@ -8036,9 +9663,9 @@ Run `revdepcheck::cloud_details(, "RVA")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘RVA/DESCRIPTION’ ... OK @@ -8047,7 +9674,7 @@ Run `revdepcheck::cloud_details(, "RVA")` for more info * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' +Package required but not available: ‘clusterProfiler’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -8066,9 +9693,9 @@ Status: 1 ERROR * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘RVA/DESCRIPTION’ ... OK @@ -8077,7 +9704,7 @@ Status: 1 ERROR * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' +Package required but not available: ‘clusterProfiler’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -8089,79 +9716,132 @@ Status: 1 ERROR ``` -# scCustomize +# S4DM
-* Version: 2.1.2 -* GitHub: https://github.com/samuel-marsh/scCustomize -* Source code: https://github.com/cran/scCustomize -* Date/Publication: 2024-02-28 19:40:02 UTC -* Number of recursive dependencies: 267 +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/S4DM +* Date/Publication: 2025-01-10 21:00:02 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "scCustomize")` for more info +Run `revdepcheck::cloud_details(, "S4DM")` for more info
-## Error before installation +## In both + +* checking whether package ‘S4DM’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/S4DM/new/S4DM.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘scCustomize’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE +* installing *source* package ‘S4DM’ ... +** package ‘S4DM’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘S4DM’ +* removing ‘/tmp/workdir/S4DM/new/S4DM.Rcheck/S4DM’ +``` +### CRAN +``` +* installing *source* package ‘S4DM’ ... +** package ‘S4DM’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘S4DM’ +* removing ‘/tmp/workdir/S4DM/old/S4DM.Rcheck/S4DM’ ``` -### CRAN +# scCustomize + +
+ +* Version: 3.0.1 +* GitHub: https://github.com/samuel-marsh/scCustomize +* Source code: https://github.com/cran/scCustomize +* Date/Publication: 2024-12-18 18:40:02 UTC +* Number of recursive dependencies: 272 + +Run `revdepcheck::cloud_details(, "scCustomize")` for more info + +
+ +## In both + +* checking whether package ‘scCustomize’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘Nebulosa’ + ``` + +## Installation + +### Devel ``` -* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scCustomize/DESCRIPTION’ ... OK -... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘scCustomize’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ +``` +### CRAN +``` +* installing *source* package ‘scCustomize’ ... +** package ‘scCustomize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘scCustomize’ +* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ ``` @@ -8173,7 +9853,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: https://github.com/Liuy12/SCdeconR * Source code: https://github.com/cran/SCdeconR * Date/Publication: 2024-03-22 19:20:02 UTC -* Number of recursive dependencies: 236 +* Number of recursive dependencies: 237 Run `revdepcheck::cloud_details(, "SCdeconR")` for more info @@ -8231,7 +9911,7 @@ ERROR: lazy loading failed for package ‘SCdeconR’ * GitHub: https://github.com/carmonalab/scGate * Source code: https://github.com/cran/scGate * Date/Publication: 2024-04-23 08:50:02 UTC -* Number of recursive dependencies: 179 +* Number of recursive dependencies: 180 Run `revdepcheck::cloud_details(, "scGate")` for more info @@ -8326,9 +10006,9 @@ Run `revdepcheck::cloud_details(, "SCIntRuler")` for more info ** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/SCIntRuler/new/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R @@ -8353,9 +10033,9 @@ ERROR: lazy loading failed for package ‘SCIntRuler’ ** package ‘SCIntRuler’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c crossdist.cpp -o crossdist.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler.so RcppExports.o crossdist.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R @@ -8372,82 +10052,6 @@ ERROR: lazy loading failed for package ‘SCIntRuler’ * removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ -``` -# scITD - -
- -* Version: 1.0.4 -* GitHub: NA -* Source code: https://github.com/cran/scITD -* Date/Publication: 2023-09-08 16:00:02 UTC -* Number of recursive dependencies: 233 - -Run `revdepcheck::cloud_details(, "scITD")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scITD/new/scITD.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scITD/DESCRIPTION’ ... OK -... -* checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Packages suggested but not available for checking: - 'simplifyEnrichment', 'conos', 'pagoda2' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scITD/old/scITD.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scITD/DESCRIPTION’ ... OK -... -* checking package dependencies ... ERROR -Package required but not available: ‘ComplexHeatmap’ - -Packages suggested but not available for checking: - 'simplifyEnrichment', 'conos', 'pagoda2' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # scMappR @@ -8517,11 +10121,11 @@ ERROR: lazy loading failed for package ‘scMappR’
-* Version: 2.2.5 +* Version: 2.2.6 * GitHub: NA * Source code: https://github.com/cran/scpi -* Date/Publication: 2023-11-01 06:10:07 UTC -* Number of recursive dependencies: 98 +* Date/Publication: 2024-11-11 23:40:02 UTC +* Number of recursive dependencies: 96 Run `revdepcheck::cloud_details(, "scpi")` for more info @@ -8590,6 +10194,82 @@ ERROR: lazy loading failed for package ‘scpi’ * removing ‘/tmp/workdir/scpi/old/scpi.Rcheck/scpi’ +``` +# SCpubr + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/enblacar/SCpubr +* Source code: https://github.com/cran/SCpubr +* Date/Publication: 2023-10-11 09:50:02 UTC +* Number of recursive dependencies: 301 + +Run `revdepcheck::cloud_details(, "SCpubr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SCpubr/new/SCpubr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCpubr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘reference_manual.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SCpubr/old/SCpubr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SCpubr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘reference_manual.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + ``` # scRNAstat @@ -8732,82 +10412,6 @@ ERROR: lazy loading failed for package ‘sectorgap’ * removing ‘/tmp/workdir/sectorgap/old/sectorgap.Rcheck/sectorgap’ -``` -# SeedMatchR - -
- -* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/SeedMatchR -* Date/Publication: 2023-10-24 20:30:02 UTC -* Number of recursive dependencies: 167 - -Run `revdepcheck::cloud_details(, "SeedMatchR")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/SeedMatchR/new/SeedMatchR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK -... -* this is package ‘SeedMatchR’ version ‘1.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'msa', 'GenomicFeatures' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/SeedMatchR/old/SeedMatchR.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK -... -* this is package ‘SeedMatchR’ version ‘1.1.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'msa', 'GenomicFeatures' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # SEERaBomb @@ -8840,11 +10444,11 @@ Run `revdepcheck::cloud_details(, "SEERaBomb")` for more info ** package ‘SEERaBomb’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SEERaBomb.so RcppExports.o SEERaBomb_init.o fillPYM.o -L/opt/R/4.3.1/lib/R/lib -lR ... ** R @@ -8867,11 +10471,11 @@ ERROR: lazy loading failed for package ‘SEERaBomb’ ** package ‘SEERaBomb’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SEERaBomb_init.c -o SEERaBomb_init.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fillPYM.cpp -o fillPYM.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SEERaBomb.so RcppExports.o SEERaBomb_init.o fillPYM.o -L/opt/R/4.3.1/lib/R/lib -lR ... ** R @@ -8953,7 +10557,7 @@ ERROR: lazy loading failed for package ‘semicmprskcoxmsm’ * GitHub: https://github.com/IbtihelRebhi/SensMap * Source code: https://github.com/cran/SensMap * Date/Publication: 2022-07-04 19:00:02 UTC -* Number of recursive dependencies: 145 +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "SensMap")` for more info @@ -9008,156 +10612,82 @@ ERROR: lazy loading failed for package ‘SensMap’ * removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ -``` -# sephora - -
- -* Version: 0.1.31 -* GitHub: NA -* Source code: https://github.com/cran/sephora -* Date/Publication: 2024-01-17 18:40:02 UTC -* Number of recursive dependencies: 139 - -Run `revdepcheck::cloud_details(, "sephora")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/sephora/new/sephora.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘sephora/DESCRIPTION’ ... OK -... -* this is package ‘sephora’ version ‘0.1.31’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘spiralize’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/sephora/old/sephora.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘sephora/DESCRIPTION’ ... OK -... -* this is package ‘sephora’ version ‘0.1.31’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘spiralize’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # Seurat
-* Version: 5.1.0 +* Version: 5.2.1 * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat -* Date/Publication: 2024-05-10 17:23:17 UTC -* Number of recursive dependencies: 267 +* Date/Publication: 2025-01-24 06:50:06 UTC +* Number of recursive dependencies: 281 Run `revdepcheck::cloud_details(, "Seurat")` for more info
-## Error before installation +## In both + +* checking whether package ‘Seurat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Seurat’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE - - - +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK +* installing *source* package ‘Seurat’ ... +** package ‘Seurat’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +using C++17 +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o +In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Seurat’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE - - - +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘Seurat’ +* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ ``` @@ -9169,7 +10699,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: https://github.com/YuLab-SMU/shinyTempSignal * Source code: https://github.com/cran/shinyTempSignal * Date/Publication: 2024-03-06 08:00:02 UTC -* Number of recursive dependencies: 137 +* Number of recursive dependencies: 134 Run `revdepcheck::cloud_details(, "shinyTempSignal")` for more info @@ -9229,7 +10759,7 @@ ERROR: lazy loading failed for package ‘shinyTempSignal’ * GitHub: https://github.com/mjuraska/sievePH * Source code: https://github.com/cran/sievePH * Date/Publication: 2024-05-17 23:40:02 UTC -* Number of recursive dependencies: 72 +* Number of recursive dependencies: 76 Run `revdepcheck::cloud_details(, "sievePH")` for more info @@ -9252,42 +10782,120 @@ Run `revdepcheck::cloud_details(, "sievePH")` for more info ** package ‘sievePH’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/sievePH/new/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/new/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/sievePH’ + + +``` +### CRAN + +``` +* installing *source* package ‘sievePH’ ... +** package ‘sievePH’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sievePH/old/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘sievePH’ +* removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ + + +``` +# SiFINeT + +
+ +* Version: 1.13 +* GitHub: NA +* Source code: https://github.com/cran/SiFINeT +* Date/Publication: 2025-01-16 15:10:05 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "SiFINeT")` for more info + +
+ +## In both + +* checking whether package ‘SiFINeT’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SiFINeT’ ... +** package ‘SiFINeT’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c EstNull.cpp -o EstNull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_coexp.cpp -o cal_coexp.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_coexp_sp.cpp -o cal_coexp_sp.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_conn.cpp -o cal_conn.o +... +installing to /tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/00LOCK-SiFINeT/00new/SiFINeT/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘sievePH’ -* removing ‘/tmp/workdir/sievePH/new/sievePH.Rcheck/sievePH’ +ERROR: lazy loading failed for package ‘SiFINeT’ +* removing ‘/tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/SiFINeT’ ``` ### CRAN ``` -* installing *source* package ‘sievePH’ ... -** package ‘sievePH’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SiFINeT’ ... +** package ‘SiFINeT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c kernel_sievePH_utils.cpp -o kernel_sievePH_utils.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sievePH.so RcppExports.o kernel_sievePH_utils.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/sievePH/old/sievePH.Rcheck/00LOCK-sievePH/00new/sievePH/libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c EstNull.cpp -o EstNull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_coexp.cpp -o cal_coexp.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_coexp_sp.cpp -o cal_coexp_sp.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c cal_conn.cpp -o cal_conn.o +... +installing to /tmp/workdir/SiFINeT/old/SiFINeT.Rcheck/00LOCK-SiFINeT/00new/SiFINeT/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘sievePH’ -* removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ +ERROR: lazy loading failed for package ‘SiFINeT’ +* removing ‘/tmp/workdir/SiFINeT/old/SiFINeT.Rcheck/SiFINeT’ ``` @@ -9299,71 +10907,86 @@ ERROR: lazy loading failed for package ‘sievePH’ * GitHub: https://github.com/ShixiangWang/sigminer * Source code: https://github.com/cran/sigminer * Date/Publication: 2024-05-11 08:50:02 UTC -* Number of recursive dependencies: 209 +* Number of recursive dependencies: 212 Run `revdepcheck::cloud_details(, "sigminer")` for more info
-## Error before installation +## Newly broken + +* checking whether package ‘sigminer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/sigminer/new/sigminer.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 7.9Mb + sub-directories of 1Mb or more: + R 1.0Mb + data 2.0Mb + extdata 1.0Mb + help 1.7Mb + libs 1.3Mb + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/sigminer/new/sigminer.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘sigminer/DESCRIPTION’ ... OK +* installing *source* package ‘sigminer’ ... +** package ‘sigminer’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c calc_cosine.cpp -o calc_cosine.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c get_intersect_size.cpp -o get_intersect_size.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sigminer.so RcppExports.o calc_cosine.o get_intersect_size.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sigminer/new/sigminer.Rcheck/00LOCK-sigminer/00new/sigminer/libs ... - 18. └─rlang::abort(...) +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'NMF', details: + call: is.element(models, models.wraps) + error: unused argument (models.wraps) Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘cnsignature.Rmd’ using ‘UTF-8’... OK - ‘sigminer.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 ERROR, 2 NOTEs - - - +ERROR: lazy loading failed for package ‘sigminer’ +* removing ‘/tmp/workdir/sigminer/new/sigminer.Rcheck/sigminer’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/sigminer/old/sigminer.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘sigminer/DESCRIPTION’ ... OK +* installing *source* package ‘sigminer’ ... +** package ‘sigminer’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c calc_cosine.cpp -o calc_cosine.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c get_intersect_size.cpp -o get_intersect_size.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sigminer.so RcppExports.o calc_cosine.o get_intersect_size.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/sigminer/old/sigminer.Rcheck/00LOCK-sigminer/00new/sigminer/libs ... -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘cnsignature.Rmd’ using ‘UTF-8’... OK - ‘sigminer.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - +** help +*** installing help indices +*** copying figures +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (sigminer) ``` @@ -9375,71 +10998,73 @@ Status: 2 NOTEs * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac * Date/Publication: 2024-08-21 07:40:02 UTC -* Number of recursive dependencies: 247 +* Number of recursive dependencies: 246 Run `revdepcheck::cloud_details(, "Signac")` for more info
-## Error before installation +## In both + +* checking whether package ‘Signac’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. + ``` + +## Installation ### Devel ``` -* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Signac’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/new/Signac.Rcheck/Signac’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Signac/DESCRIPTION’ ... OK +* installing *source* package ‘Signac’ ... +** package ‘Signac’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Signac’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/Signac/old/Signac.Rcheck/00install.out’ for details. -* DONE -Status: 1 ERROR, 1 NOTE - - - +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘Signac’ +* removing ‘/tmp/workdir/Signac/old/Signac.Rcheck/Signac’ ``` @@ -9451,7 +11076,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: https://github.com/arcaldwell49/SimplyAgree * Source code: https://github.com/cran/SimplyAgree * Date/Publication: 2024-03-21 14:20:06 UTC -* Number of recursive dependencies: 115 +* Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info @@ -9516,16 +11141,51 @@ ERROR: lazy loading failed for package ‘SimplyAgree’ * removing ‘/tmp/workdir/SimplyAgree/old/SimplyAgree.Rcheck/SimplyAgree’ +``` +# smer + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/smer +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "smer")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # SNPassoc
-* Version: 2.1-0 +* Version: 2.1-2 * GitHub: https://github.com/isglobal-brge/SNPassoc * Source code: https://github.com/cran/SNPassoc -* Date/Publication: 2022-12-14 20:20:02 UTC -* Number of recursive dependencies: 168 +* Date/Publication: 2024-10-28 17:30:02 UTC +* Number of recursive dependencies: 164 Run `revdepcheck::cloud_details(, "SNPassoc")` for more info @@ -9540,23 +11200,23 @@ Run `revdepcheck::cloud_details(, "SNPassoc")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘SNPassoc/DESCRIPTION’ ... OK ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘SNPassoc’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. +* this is package ‘SNPassoc’ version ‘2.1-2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘haplo.stats’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 ERROR, 1 NOTE +Status: 1 ERROR @@ -9570,23 +11230,23 @@ Status: 1 ERROR, 1 NOTE * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘SNPassoc/DESCRIPTION’ ... OK ... -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘SNPassoc’ can be installed ... ERROR -Installation failed. -See ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/00install.out’ for details. +* this is package ‘SNPassoc’ version ‘2.1-2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘haplo.stats’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 ERROR, 1 NOTE +Status: 1 ERROR @@ -9601,7 +11261,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: NA * Source code: https://github.com/cran/snplinkage * Date/Publication: 2024-09-09 19:10:02 UTC -* Number of recursive dependencies: 153 +* Number of recursive dependencies: 155 Run `revdepcheck::cloud_details(, "snplinkage")` for more info @@ -9616,9 +11276,9 @@ Run `revdepcheck::cloud_details(, "snplinkage")` for more info * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK @@ -9646,9 +11306,9 @@ Status: 1 ERROR * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK @@ -9669,26 +11329,90 @@ Status: 1 ERROR ``` -# SoupX +# SoupX + +
+ +* Version: 1.6.2 +* GitHub: https://github.com/constantAmateur/SoupX +* Source code: https://github.com/cran/SoupX +* Date/Publication: 2022-11-01 14:00:03 UTC +* Number of recursive dependencies: 202 + +Run `revdepcheck::cloud_details(, "SoupX")` for more info + +
+ +## In both + +* checking whether package ‘SoupX’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/SoupX’ + + +``` +### CRAN + +``` +* installing *source* package ‘SoupX’ ... +** package ‘SoupX’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SoupX’ +* removing ‘/tmp/workdir/SoupX/old/SoupX.Rcheck/SoupX’ + + +``` +# SpaCCI
-* Version: 1.6.2 -* GitHub: https://github.com/constantAmateur/SoupX -* Source code: https://github.com/cran/SoupX -* Date/Publication: 2022-11-01 14:00:03 UTC -* Number of recursive dependencies: 201 +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/SpaCCI +* Date/Publication: 2025-01-18 23:10:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "SoupX")` for more info +Run `revdepcheck::cloud_details(, "SpaCCI")` for more info
## In both -* checking whether package ‘SoupX’ can be installed ... ERROR +* checking whether package ‘SpaCCI’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/SpaCCI/new/SpaCCI.Rcheck/00install.out’ for details. ``` ## Installation @@ -9696,40 +11420,50 @@ Run `revdepcheck::cloud_details(, "SoupX")` for more info ### Devel ``` -* installing *source* package ‘SoupX’ ... -** package ‘SoupX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SpaCCI’ ... +** package ‘SpaCCI’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c permutation_func.cpp -o permutation_func.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SpaCCI.so RcppExports.o permutation_func.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SpaCCI/new/SpaCCI.Rcheck/00LOCK-SpaCCI/00new/SpaCCI/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SoupX’ -* removing ‘/tmp/workdir/SoupX/new/SoupX.Rcheck/SoupX’ +ERROR: lazy loading failed for package ‘SpaCCI’ +* removing ‘/tmp/workdir/SpaCCI/new/SpaCCI.Rcheck/SpaCCI’ ``` ### CRAN ``` -* installing *source* package ‘SoupX’ ... -** package ‘SoupX’ successfully unpacked and MD5 sums checked +* installing *source* package ‘SpaCCI’ ... +** package ‘SpaCCI’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c permutation_func.cpp -o permutation_func.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SpaCCI.so RcppExports.o permutation_func.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/SpaCCI/old/SpaCCI.Rcheck/00LOCK-SpaCCI/00new/SpaCCI/libs ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘SoupX’ -* removing ‘/tmp/workdir/SoupX/old/SoupX.Rcheck/SoupX’ +ERROR: lazy loading failed for package ‘SpaCCI’ +* removing ‘/tmp/workdir/SpaCCI/old/SpaCCI.Rcheck/SpaCCI’ ``` @@ -9764,11 +11498,11 @@ Run `revdepcheck::cloud_details(, "sparsereg")` for more info ** package ‘sparsereg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/sparsereg/new/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs ** R @@ -9789,11 +11523,11 @@ ERROR: lazy loading failed for package ‘sparsereg’ ** package ‘sparsereg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makeinter.cpp -o makeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c makethreeinter.cpp -o makethreeinter.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c subgroup.cpp -o subgroup.o g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o sparsereg.so RcppExports.o makeinter.o makethreeinter.o subgroup.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/sparsereg/old/sparsereg.Rcheck/00LOCK-sparsereg/00new/sparsereg/libs ** R @@ -9807,79 +11541,75 @@ ERROR: lazy loading failed for package ‘sparsereg’ ``` -# SpatialDDLS +# spectralAnalysis
-* Version: 1.0.2 -* GitHub: https://github.com/diegommcc/SpatialDDLS -* Source code: https://github.com/cran/SpatialDDLS -* Date/Publication: 2024-04-26 16:10:02 UTC -* Number of recursive dependencies: 207 +* Version: 4.3.3 +* GitHub: NA +* Source code: https://github.com/cran/spectralAnalysis +* Date/Publication: 2024-01-30 08:50:02 UTC +* Number of recursive dependencies: 117 -Run `revdepcheck::cloud_details(, "SpatialDDLS")` for more info +Run `revdepcheck::cloud_details(, "spectralAnalysis")` for more info
-## Error before installation - -### Devel +## Newly broken -``` -* using log directory ‘/tmp/workdir/SpatialDDLS/new/SpatialDDLS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SpatialExperiment’ +* checking whether package ‘spectralAnalysis’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/spectralAnalysis/new/spectralAnalysis.Rcheck/00install.out’ for details. + ``` -Package suggested but not available for checking: ‘ComplexHeatmap’ +## Newly fixed -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR +* checking installed package size ... NOTE + ``` + installed size is 6.0Mb + sub-directories of 1Mb or more: + doc 4.6Mb + ``` +## Installation +### Devel +``` +* installing *source* package ‘spectralAnalysis’ ... +** package ‘spectralAnalysis’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'NMF', details: + call: is.element(models, models.wraps) + error: unused argument (models.wraps) +Execution halted +ERROR: lazy loading failed for package ‘spectralAnalysis’ +* removing ‘/tmp/workdir/spectralAnalysis/new/spectralAnalysis.Rcheck/spectralAnalysis’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/SpatialDDLS/old/SpatialDDLS.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK -... -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘SpatialExperiment’ - -Package suggested but not available for checking: ‘ComplexHeatmap’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - +* installing *source* package ‘spectralAnalysis’ ... +** package ‘spectralAnalysis’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Creating a new generic function for ‘smooth’ in package ‘spectralAnalysis’ +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (spectralAnalysis) ``` @@ -9887,10 +11617,10 @@ Status: 1 ERROR
-* Version: 1.1-19 +* Version: 1.1-20 * GitHub: https://github.com/fabian-s/spikeSlabGAM * Source code: https://github.com/cran/spikeSlabGAM -* Date/Publication: 2022-06-10 15:50:07 UTC +* Date/Publication: 2024-10-22 17:30:02 UTC * Number of recursive dependencies: 77 Run `revdepcheck::cloud_details(, "spikeSlabGAM")` for more info @@ -9914,7 +11644,7 @@ Run `revdepcheck::cloud_details(, "spikeSlabGAM")` for more info ** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -9938,7 +11668,7 @@ ERROR: lazy loading failed for package ‘spikeSlabGAM’ ** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -9954,80 +11684,292 @@ ERROR: lazy loading failed for package ‘spikeSlabGAM’ * removing ‘/tmp/workdir/spikeSlabGAM/old/spikeSlabGAM.Rcheck/spikeSlabGAM’ +``` +# stabiliser + +
+ +* Version: 1.0.6 +* GitHub: NA +* Source code: https://github.com/cran/stabiliser +* Date/Publication: 2023-05-17 11:00:05 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "stabiliser")` for more info + +
+ +## In both + +* checking whether package ‘stabiliser’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/stabiliser/new/stabiliser.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘stabiliser’ ... +** package ‘stabiliser’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘maditr’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘stabiliser’ +* removing ‘/tmp/workdir/stabiliser/new/stabiliser.Rcheck/stabiliser’ + + +``` +### CRAN + +``` +* installing *source* package ‘stabiliser’ ... +** package ‘stabiliser’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘maditr’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘stabiliser’ +* removing ‘/tmp/workdir/stabiliser/old/stabiliser.Rcheck/stabiliser’ + + ``` # statsr
-* Version: 0.3.0 -* GitHub: https://github.com/StatsWithR/statsr -* Source code: https://github.com/cran/statsr -* Date/Publication: 2021-01-22 20:40:03 UTC -* Number of recursive dependencies: 97 +* Version: 0.3.0 +* GitHub: https://github.com/StatsWithR/statsr +* Source code: https://github.com/cran/statsr +* Date/Publication: 2021-01-22 20:40:03 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "statsr")` for more info + +
+ +## In both + +* checking whether package ‘statsr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/statsr/new/statsr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘statsr’ ... +** package ‘statsr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘statsr’ +* removing ‘/tmp/workdir/statsr/new/statsr.Rcheck/statsr’ + + +``` +### CRAN + +``` +* installing *source* package ‘statsr’ ... +** package ‘statsr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘statsr’ +* removing ‘/tmp/workdir/statsr/old/statsr.Rcheck/statsr’ + + +``` +# streamDAG + +
+ +* Version: 1.5-9 +* GitHub: NA +* Source code: https://github.com/cran/streamDAG +* Date/Publication: 2025-01-14 21:50:02 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "streamDAG")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5-9’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5-9’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# survex + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/ModelOriented/survex +* Source code: https://github.com/cran/survex +* Date/Publication: 2023-10-24 18:50:07 UTC +* Number of recursive dependencies: 182 -Run `revdepcheck::cloud_details(, "statsr")` for more info +Run `revdepcheck::cloud_details(, "survex")` for more info
-## In both - -* checking whether package ‘statsr’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/statsr/new/statsr.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘statsr’ ... -** package ‘statsr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +* using log directory ‘/tmp/workdir/survex/new/survex.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘survex/DESCRIPTION’ ... OK +... +  A new explainer has been created!  +> +> y <- cph_exp$y +> times <- cph_exp$times +> surv <- cph_exp$predict_survival_function(cph, cph_exp$data, times) +Error in loadNamespace(x) : there is no package called ‘riskRegression’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘statsr’ -* removing ‘/tmp/workdir/statsr/new/statsr.Rcheck/statsr’ +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘statsr’ ... -** package ‘statsr’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘BayesFactor’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +* using log directory ‘/tmp/workdir/survex/old/survex.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘survex/DESCRIPTION’ ... OK +... +  A new explainer has been created!  +> +> y <- cph_exp$y +> times <- cph_exp$times +> surv <- cph_exp$predict_survival_function(cph, cph_exp$data, times) +Error in loadNamespace(x) : there is no package called ‘riskRegression’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘statsr’ -* removing ‘/tmp/workdir/statsr/old/statsr.Rcheck/statsr’ +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` -# streamDAG +# survHE
-* Version: 1.5 -* GitHub: NA -* Source code: https://github.com/cran/streamDAG -* Date/Publication: 2023-10-06 18:50:02 UTC -* Number of recursive dependencies: 132 +* Version: 2.0.2 +* GitHub: https://github.com/giabaio/survHE +* Source code: https://github.com/cran/survHE +* Date/Publication: 2024-10-04 09:50:02 UTC +* Number of recursive dependencies: 129 -Run `revdepcheck::cloud_details(, "streamDAG")` for more info +Run `revdepcheck::cloud_details(, "survHE")` for more info
@@ -10036,20 +11978,22 @@ Run `revdepcheck::cloud_details(, "streamDAG")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’ +* using log directory ‘/tmp/workdir/survHE/new/survHE.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘streamDAG/DESCRIPTION’ ... OK -* this is package ‘streamDAG’ version ‘1.5’ -* checking package namespace information ... OK +* checking for file ‘survHE/DESCRIPTION’ ... OK +... * checking package dependencies ... ERROR -Package required but not available: ‘asbio’ +Package required but not available: ‘rms’ + +Packages suggested but not available for checking: + 'survHEinla', 'survHEhmc' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -10064,20 +12008,22 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’ +* using log directory ‘/tmp/workdir/survHE/old/survHE.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘streamDAG/DESCRIPTION’ ... OK -* this is package ‘streamDAG’ version ‘1.5’ -* checking package namespace information ... OK +* checking for file ‘survHE/DESCRIPTION’ ... OK +... * checking package dependencies ... ERROR -Package required but not available: ‘asbio’ +Package required but not available: ‘rms’ + +Packages suggested but not available for checking: + 'survHEinla', 'survHEhmc' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -10120,9 +12066,9 @@ Run `revdepcheck::cloud_details(, "survidm")` for more info ** package ‘survidm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o survidm.so survidm_init.o survivalBIV.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/survidm/new/survidm.Rcheck/00LOCK-survidm/00new/survidm/libs ** R @@ -10145,9 +12091,9 @@ ERROR: lazy loading failed for package ‘survidm’ ** package ‘survidm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survidm_init.c -o survidm_init.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c survivalBIV.c -o survivalBIV.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o survidm.so survidm_init.o survivalBIV.o -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/survidm/old/survidm.Rcheck/00LOCK-survidm/00new/survidm/libs ** R @@ -10229,69 +12175,75 @@ ERROR: lazy loading failed for package ‘tempted’
-* Version: 1.1.1 +* Version: 1.1.2 * GitHub: https://github.com/jiangyouxiang/TestAnaAPP * Source code: https://github.com/cran/TestAnaAPP -* Date/Publication: 2024-09-10 07:30:02 UTC -* Number of recursive dependencies: 250 +* Date/Publication: 2024-11-09 04:00:02 UTC +* Number of recursive dependencies: 255 Run `revdepcheck::cloud_details(, "TestAnaAPP")` for more info
-## In both - -* checking whether package ‘TestAnaAPP’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘TestAnaAPP’ ... -** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TestAnaAPP’ -* removing ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/TestAnaAPP’ +* using log directory ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘TestAnaAPP/DESCRIPTION’ ... OK +... +* this is package ‘TestAnaAPP’ version ‘1.1.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘lordif’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘TestAnaAPP’ ... -** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘rms’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TestAnaAPP’ -* removing ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck/TestAnaAPP’ +* using log directory ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘TestAnaAPP/DESCRIPTION’ ... OK +... +* this is package ‘TestAnaAPP’ version ‘1.1.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘lordif’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -10365,7 +12317,7 @@ ERROR: lazy loading failed for package ‘tidydr’ * GitHub: NA * Source code: https://github.com/cran/tidyEdSurvey * Date/Publication: 2024-05-14 20:20:03 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 113 Run `revdepcheck::cloud_details(, "tidyEdSurvey")` for more info @@ -10431,7 +12383,7 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ * GitHub: https://github.com/stemangiola/tidyseurat * Source code: https://github.com/cran/tidyseurat * Date/Publication: 2024-01-10 04:50:02 UTC -* Number of recursive dependencies: 208 +* Number of recursive dependencies: 196 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info @@ -10469,42 +12421,182 @@ ERROR: lazy loading failed for package ‘tidyseurat’ ### CRAN ``` -* installing *source* package ‘tidyseurat’ ... -** package ‘tidyseurat’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘tidyseurat’ -* removing ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck/tidyseurat’ +* installing *source* package ‘tidyseurat’ ... +** package ‘tidyseurat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Execution halted +ERROR: lazy loading failed for package ‘tidyseurat’ +* removing ‘/tmp/workdir/tidyseurat/old/tidyseurat.Rcheck/tidyseurat’ + + +``` +# tidyvpc + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/certara/tidyvpc +* Source code: https://github.com/cran/tidyvpc +* Date/Publication: 2024-11-21 23:10:02 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "tidyvpc")` for more info + +
+ +## In both + +* checking whether package ‘tidyvpc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘tidyvpc’ ... +** package ‘tidyvpc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘tidyvpc’ +* removing ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/tidyvpc’ + + +``` +### CRAN + +``` +* installing *source* package ‘tidyvpc’ ... +** package ‘tidyvpc’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘tidyvpc’ +* removing ‘/tmp/workdir/tidyvpc/old/tidyvpc.Rcheck/tidyvpc’ + + +``` +# tinyarray + +
+ +* Version: 2.4.2 +* GitHub: https://github.com/xjsun1221/tinyarray +* Source code: https://github.com/cran/tinyarray +* Date/Publication: 2024-06-13 14:20:02 UTC +* Number of recursive dependencies: 250 + +Run `revdepcheck::cloud_details(, "tinyarray")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/tinyarray/new/tinyarray.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘tinyarray/DESCRIPTION’ ... OK +... +* this is package ‘tinyarray’ version ‘2.4.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/tinyarray/old/tinyarray.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘tinyarray/DESCRIPTION’ ... OK +... +* this is package ‘tinyarray’ version ‘2.4.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# tidyvpc +# treeclim
-* Version: 1.5.1 -* GitHub: https://github.com/certara/tidyvpc -* Source code: https://github.com/cran/tidyvpc -* Date/Publication: 2024-01-18 13:10:02 UTC -* Number of recursive dependencies: 176 +* Version: 2.0.7.1 +* GitHub: https://github.com/cszang/treeclim +* Source code: https://github.com/cran/treeclim +* Date/Publication: 2024-12-16 16:20:02 UTC +* Number of recursive dependencies: 60 -Run `revdepcheck::cloud_details(, "tidyvpc")` for more info +Run `revdepcheck::cloud_details(, "treeclim")` for more info
## In both -* checking whether package ‘tidyvpc’ can be installed ... ERROR +* checking whether package ‘treeclim’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/treeclim/new/treeclim.Rcheck/00install.out’ for details. ``` ## Installation @@ -10512,10 +12604,17 @@ Run `revdepcheck::cloud_details(, "tidyvpc")` for more info ### Devel ``` -* installing *source* package ‘tidyvpc’ ... -** package ‘tidyvpc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘treeclim’ ... +** package ‘treeclim’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun.cpp -o corfun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun_exact.cpp -o corfun_exact.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun_noboot.cpp -o corfun_noboot.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c pcor.cpp -o pcor.o +... ** data *** moving datasets to lazyload DB ** inst @@ -10524,18 +12623,25 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘tidyvpc’ -* removing ‘/tmp/workdir/tidyvpc/new/tidyvpc.Rcheck/tidyvpc’ +ERROR: lazy loading failed for package ‘treeclim’ +* removing ‘/tmp/workdir/treeclim/new/treeclim.Rcheck/treeclim’ ``` ### CRAN ``` -* installing *source* package ‘tidyvpc’ ... -** package ‘tidyvpc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘treeclim’ ... +** package ‘treeclim’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun.cpp -o corfun.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun_exact.cpp -o corfun_exact.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c corfun_noboot.cpp -o corfun_noboot.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c pcor.cpp -o pcor.o +... ** data *** moving datasets to lazyload DB ** inst @@ -10544,8 +12650,8 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘tidyvpc’ -* removing ‘/tmp/workdir/tidyvpc/old/tidyvpc.Rcheck/tidyvpc’ +ERROR: lazy loading failed for package ‘treeclim’ +* removing ‘/tmp/workdir/treeclim/old/treeclim.Rcheck/treeclim’ ``` @@ -10557,7 +12663,7 @@ ERROR: lazy loading failed for package ‘tidyvpc’ * GitHub: https://github.com/alexander-pastukhov/tridim-regression * Source code: https://github.com/cran/TriDimRegression * Date/Publication: 2023-09-13 14:10:03 UTC -* Number of recursive dependencies: 99 +* Number of recursive dependencies: 98 Run `revdepcheck::cloud_details(, "TriDimRegression")` for more info @@ -10609,7 +12715,7 @@ ERROR: configuration failed for package ‘TriDimRegression’ * GitHub: https://github.com/PetoLau/TSrepr * Source code: https://github.com/cran/TSrepr * Date/Publication: 2020-07-13 06:50:15 UTC -* Number of recursive dependencies: 72 +* Number of recursive dependencies: 71 Run `revdepcheck::cloud_details(, "TSrepr")` for more info @@ -10632,12 +12738,12 @@ Run `revdepcheck::cloud_details(, "TSrepr")` for more info ** package ‘TSrepr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o ... ** data *** moving datasets to lazyload DB @@ -10659,12 +12765,12 @@ ERROR: lazy loading failed for package ‘TSrepr’ ** package ‘TSrepr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o +using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c FeatureClippingTrending.cpp -o FeatureClippingTrending.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c helpers.cpp -o helpers.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c measures.cpp -o measures.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c normalizations.cpp -o normalizations.o ... ** data *** moving datasets to lazyload DB @@ -10710,7 +12816,7 @@ Run `revdepcheck::cloud_details(, "twang")` for more info ** package ‘twang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks.c -o ks.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o twang.so init.o ks.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -10735,7 +12841,7 @@ ERROR: lazy loading failed for package ‘twang’ ** package ‘twang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks.c -o ks.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o twang.so init.o ks.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR @@ -10752,158 +12858,6 @@ ERROR: lazy loading failed for package ‘twang’ * removing ‘/tmp/workdir/twang/old/twang.Rcheck/twang’ -``` -# updog - -
- -* Version: 2.1.5 -* GitHub: https://github.com/dcgerard/updog -* Source code: https://github.com/cran/updog -* Date/Publication: 2023-11-29 15:50:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "updog")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/updog/new/updog.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘updog/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘multidog.Rmd’ using ‘UTF-8’... OK - ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK - ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK - ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/updog/old/updog.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘updog/DESCRIPTION’ ... OK -... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘multidog.Rmd’ using ‘UTF-8’... OK - ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK - ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK - ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 2 NOTEs - - - - - -``` -# valr - -
- -* Version: 0.8.2 -* GitHub: https://github.com/rnabioco/valr -* Source code: https://github.com/cran/valr -* Date/Publication: 2024-08-30 22:10:03 UTC -* Number of recursive dependencies: 176 - -Run `revdepcheck::cloud_details(, "valr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/valr/new/valr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘valr/DESCRIPTION’ ... OK -... -* this is package ‘valr’ version ‘0.8.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/valr/old/valr.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘valr/DESCRIPTION’ ... OK -... -* this is package ‘valr’ version ‘0.8.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘rtracklayer’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` # vdg @@ -10936,7 +12890,7 @@ Run `revdepcheck::cloud_details(, "vdg")` for more info ** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gfortran -fpic -g -O2 -c FDS.f -o FDS.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/vdg/new/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs @@ -10960,7 +12914,7 @@ ERROR: lazy loading failed for package ‘vdg’ ** package ‘vdg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using Fortran compiler: ‘GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gfortran -fpic -g -O2 -c FDS.f -o FDS.o gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o vdg.so FDS.o -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR installing to /tmp/workdir/vdg/old/vdg.Rcheck/00LOCK-vdg/00new/vdg/libs @@ -10976,6 +12930,41 @@ ERROR: lazy loading failed for package ‘vdg’ * removing ‘/tmp/workdir/vdg/old/vdg.Rcheck/vdg’ +``` +# VecDep + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/VecDep +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "VecDep")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # visa @@ -10985,7 +12974,7 @@ ERROR: lazy loading failed for package ‘vdg’ * GitHub: https://github.com/kang-yu/visa * Source code: https://github.com/cran/visa * Date/Publication: 2021-04-20 07:20:02 UTC -* Number of recursive dependencies: 140 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "visa")` for more info @@ -11048,7 +13037,7 @@ ERROR: lazy loading failed for package ‘visa’ * Version: NA * GitHub: NA * Source code: https://github.com/cran/VisualizeSimon2Stage -* Number of recursive dependencies: 30 +* Number of recursive dependencies: 36 Run `revdepcheck::cloud_details(, "VisualizeSimon2Stage")` for more info @@ -11075,6 +13064,69 @@ Run `revdepcheck::cloud_details(, "VisualizeSimon2Stage")` for more info +``` +# wppExplorer + +
+ +* Version: 2.3-4 +* GitHub: NA +* Source code: https://github.com/cran/wppExplorer +* Date/Publication: 2020-04-09 09:10:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "wppExplorer")` for more info + +
+ +## Newly broken + +* checking whether package ‘wppExplorer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/wppExplorer/new/wppExplorer.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘wppExplorer’ ... +** package ‘wppExplorer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error in is.element(wpp.data.env$iso3166$uncode, wpp.data.env$popM$country_code) : + unused argument (wpp.data.env$popM$country_code) +Error: unable to load R code in package ‘wppExplorer’ +Execution halted +ERROR: lazy loading failed for package ‘wppExplorer’ +* removing ‘/tmp/workdir/wppExplorer/new/wppExplorer.Rcheck/wppExplorer’ + + +``` +### CRAN + +``` +* installing *source* package ‘wppExplorer’ ... +** package ‘wppExplorer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (wppExplorer) + + ``` # WRTDStidal diff --git a/revdep/problems.md b/revdep/problems.md index 73ee83725d..f698c10792 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,14 +1,14 @@ -# activAnalyzer +# ABHgenotypeR
-* Version: 2.1.1 -* GitHub: https://github.com/pydemull/activAnalyzer -* Source code: https://github.com/cran/activAnalyzer -* Date/Publication: 2024-05-05 22:40:03 UTC -* Number of recursive dependencies: 148 +* Version: 1.0.1 +* GitHub: https://github.com/StefanReuscher/ABHgenotypeR +* Source code: https://github.com/cran/ABHgenotypeR +* Date/Publication: 2016-02-04 11:27:29 +* Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "activAnalyzer")` for more info +Run `revdepcheck::cloud_details(, "ABHgenotypeR")` for more info
@@ -17,47 +17,57 @@ Run `revdepcheck::cloud_details(, "activAnalyzer")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘activAnalyzer.Rmd’ + when running code in ‘ABHgenotypeR-vignette.Rmd’ ... - > p3 <- accum_metrics_sed$p_UBD + + "preprefall025TestData.csv", package = "ABHgenotypeR"), nameA = "NB", + + nameB = "OL ..." ... [TRUNCATED] - > p4 <- accum_metrics_sed$p_gini + > plotGenos(genotypes) - > (p1 | p2)/(p3 | p4) + plot_layout(guides = "collect") & - + theme(legend.position = "bottom") - - When sourcing ‘activAnalyzer.R’: - Error: object is not a unit + When sourcing ‘ABHgenotypeR-vignette.R’: + Error: The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `panel.spacing` argument instead. Execution halted - ‘activAnalyzer.Rmd’ using ‘UTF-8’... failed + ‘ABHgenotypeR-vignette.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘activAnalyzer.Rmd’ using rmarkdown + ... + --- re-building ‘ABHgenotypeR-vignette.Rmd’ using rmarkdown + + Quitting from lines 70-72 [unnamed-chunk-3] (ABHgenotypeR-vignette.Rmd) + Error: processing vignette 'ABHgenotypeR-vignette.Rmd' failed with diagnostics: + The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `panel.spacing` argument instead. + --- failed re-building ‘ABHgenotypeR-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘ABHgenotypeR-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` ## In both -* checking installed package size ... NOTE +* checking LazyData ... NOTE ``` - installed size is 5.8Mb - sub-directories of 1Mb or more: - R 1.5Mb - doc 1.0Mb - extdata 2.0Mb + 'LazyData' is specified without a 'data' directory ``` # actxps
-* Version: 1.5.0 +* Version: 1.6.0 * GitHub: https://github.com/mattheaphy/actxps * Source code: https://github.com/cran/actxps -* Date/Publication: 2024-06-25 12:40:02 UTC +* Date/Publication: 2025-01-07 13:00:02 UTC * Number of recursive dependencies: 130 Run `revdepcheck::cloud_details(, "actxps")` for more info @@ -116,17 +126,17 @@ Run `revdepcheck::cloud_details(, "actxps")` for more info Execution halted ``` -# adaptr +# adklakedata
-* Version: 1.4.0 -* GitHub: https://github.com/INCEPTdk/adaptr -* Source code: https://github.com/cran/adaptr -* Date/Publication: 2024-05-03 12:10:02 UTC -* Number of recursive dependencies: 74 +* Version: 0.6.1 +* GitHub: https://github.com/lawinslow/adklakedata +* Source code: https://github.com/cran/adklakedata +* Date/Publication: 2018-02-16 19:08:16 UTC +* Number of recursive dependencies: 64 -Run `revdepcheck::cloud_details(, "adaptr")` for more info +Run `revdepcheck::cloud_details(, "adklakedata")` for more info
@@ -134,79 +144,139 @@ Run `revdepcheck::cloud_details(, "adaptr")` for more info * checking examples ... ERROR ``` - Running examples in ‘adaptr-Ex.R’ failed + Running examples in ‘adklakedata-Ex.R’ failed The error most likely occurred in: - > ### Name: plot_history - > ### Title: Plot trial metric history - > ### Aliases: plot_history plot_history.trial_result - > ### plot_history.trial_results + > ### Name: adk_lake_shapes + > ### Title: Return path to Lake Polygons Shapefile + > ### Aliases: adk_lake_shapes > > ### ** Examples > - ... - + # Run a single simulation with a fixed random seed - + res <- run_trial(binom_trial, seed = 12345) - + - + # Plot total allocations to each arm according to overall total allocations - + plot_history(res, x_value = "total n", y_value = "n") - + - + } - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot_history ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > library(sf) + Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE + > bl = read_sf(adklakedata::adk_shape()) + Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir, : + package tibble not available: install first? + Calls: read_sf ... st_read -> st_read.character -> process_cpl_read_ogr Execution halted ``` -* checking tests ... ERROR +## In both + +* checking LazyData ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(adaptr) - Loading 'adaptr' package v1.4.0. - For instructions, type 'help("adaptr")' - or see https://inceptdk.github.io/adaptr/. - > - > test_check("adaptr") - ... - • plot_history/history-plot-binomial-single-ratio-ys-look.svg - • plot_metrics_ecdf/errors.svg - • plot_metrics_ecdf/selected.svg - • plot_metrics_ecdf/size-only.svg - • plot_metrics_ecdf/superior.svg - • plot_status/status-plot-across-arms-binomial.svg - • plot_status/status-plot-for-all-arms-binomial.svg - • plot_status/status-plot-for-arm-c-binom.svg - Error: Test failures - Execution halted + 'LazyData' is specified without a 'data' directory + ``` + +# adobeanalyticsr + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/benrwoodard/adobeanalyticsr +* Source code: https://github.com/cran/adobeanalyticsr +* Date/Publication: 2025-01-16 06:10:02 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "adobeanalyticsr")` for more info + +
+ +## Newly broken + +* checking whether package ‘adobeanalyticsr’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(limit[i], ': unused argument (c("within", "after")) + See ‘/tmp/workdir/adobeanalyticsr/new/adobeanalyticsr.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + seg_then: possible error in is.element(limit[i], c("within", "after")): + unused argument (c("within", "after")) + ``` + +# adw + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/PanfengZhang/adw +* Source code: https://github.com/cran/adw +* Date/Publication: 2024-04-15 19:10:16 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "adw")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘adw-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adw + > ### Title: Angular Distance Weighting Interpolation. + > ### Aliases: adw + > + > ### ** Examples + > + > set.seed(2) + ... + 4 111.75 31.25 -0.47570806 + 5 112.25 31.25 -1.57521787 + 6 112.75 31.25 -1.10541492 + > + > # example 2 + > hmap <- cnmap::getMap(code = "410000") |> sf::st_make_valid() # return a 'sf' object. + Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir, : + package tibble not available: install first? + Calls: ... st_read -> st_read.character -> process_cpl_read_ogr + Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Overview.Rmd’ + when running code in ‘Introduction.Rmd’ ... - > plot_convergence(calibrated_binom_trial$best_sims, - + metrics = c("size mean", "prob_superior", "prob_equivalence"), - + n_split = 4) + > tavg <- data.frame(lon = runif(100, min = 110, max = 117), + + lat = runif(100, min = 31, max = 37), value = runif(100, + + min = 20, max .... [TRUNCATED] - > plot_status(calibrated_binom_trial$best_sims, x_value = "total n") + > hmap <- getMap(name = "河南省", returnClass = "sf") - When sourcing ‘Overview.R’: - Error: argument is of length zero + When sourcing ‘Introduction.R’: + Error: package tibble not available: install first? Execution halted - ‘Advanced-example.Rmd’ using ‘UTF-8’... OK - ‘Basic-examples.Rmd’ using ‘UTF-8’... OK - ‘Overview.Rmd’ using ‘UTF-8’... failed + ‘Introduction.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘Advanced-example.Rmd’ using rmarkdown + ... + --- re-building ‘Introduction.Rmd’ using rmarkdown + + Quitting from lines 48-74 [unnamed-chunk-3] (Introduction.Rmd) + Error: processing vignette 'Introduction.Rmd' failed with diagnostics: + package tibble not available: install first? + --- failed re-building ‘Introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘Introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` # AeRobiology @@ -217,7 +287,7 @@ Run `revdepcheck::cloud_details(, "adaptr")` for more info * GitHub: NA * Source code: https://github.com/cran/AeRobiology * Date/Publication: 2019-06-03 06:20:03 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 97 Run `revdepcheck::cloud_details(, "AeRobiology")` for more info @@ -225,14 +295,6 @@ Run `revdepcheck::cloud_details(, "AeRobiology")` for more info ## Newly broken -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘my-vignette.Rmd’ using rmarkdown - ``` - -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: @@ -252,15 +314,21 @@ Run `revdepcheck::cloud_details(, "AeRobiology")` for more info ‘my-vignette.Rmd’ using ‘UTF-8’... failed ``` +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘my-vignette.Rmd’ using rmarkdown + ``` + # agricolaeplotr
-* Version: 0.5.0 +* Version: 0.6.0 * GitHub: https://github.com/jensharbers/agricolaeplotr * Source code: https://github.com/cran/agricolaeplotr -* Date/Publication: 2024-01-17 16:42:04 UTC -* Number of recursive dependencies: 144 +* Date/Publication: 2025-01-22 13:20:02 UTC +* Number of recursive dependencies: 143 Run `revdepcheck::cloud_details(, "agricolaeplotr")` for more info @@ -293,60 +361,50 @@ Run `revdepcheck::cloud_details(, "agricolaeplotr")` for more info Execution halted ``` -# alien - -
- -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/alien -* Date/Publication: 2024-06-19 16:20:02 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "alien")` for more info - -
- -## Newly broken - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘basic_usage.Rmd’ + when running code in ‘FielDHub.Rmd’ ... - 2 0.3330822 6.848124e-06 1.620061e+04 - 3 0.3377835 1.902532e-07 5.997150e+05 - 4 0.3425512 5.285577e-09 2.220028e+07 + 3 3 IBAGUE 103 1 ND-10 + 4 4 IBAGUE 104 1 ND-13 + 5 5 IBAGUE 105 1 ND-6 + 6 6 IBAGUE 106 1 ND-14 - > plot_snc(model, cumulative = T) + coord_cartesian(ylim = c(0, - + 150)) + scale_y_continuous(breaks = seq(0, 150, 50)) + ylab("Cumulative discove ..." ... [TRUNCATED] + > plt <- plot(rcbd2) - When sourcing ‘basic_usage.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + When sourcing ‘FielDHub.R’: + Error: unused argument (dn) Execution halted - ‘basic_usage.Rmd’ using ‘UTF-8’... failed - ‘native_discoveries.Rmd’ using ‘UTF-8’... OK - ‘simulations.Rmd’ using ‘UTF-8’... OK + ‘FielDHub.Rmd’ using ‘UTF-8’... failed + ‘vignette.Rmd’ using ‘UTF-8’... OK ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘basic_usage.Rmd’ using rmarkdown + --- re-building ‘FielDHub.Rmd’ using rmarkdown + + Quitting from lines 40-44 [unnamed-chunk-2] (FielDHub.Rmd) + Error: processing vignette 'FielDHub.Rmd' failed with diagnostics: + unused argument (dn) + --- failed re-building ‘FielDHub.Rmd’ + + --- re-building ‘vignette.Rmd’ using rmarkdown ``` -# AlphaPart +# agridat
-* Version: 0.9.8 -* GitHub: NA -* Source code: https://github.com/cran/AlphaPart -* Date/Publication: 2022-11-15 21:40:05 UTC -* Number of recursive dependencies: 83 +* Version: 1.24 +* GitHub: https://github.com/kwstat/agridat +* Source code: https://github.com/cran/agridat +* Date/Publication: 2024-10-27 17:00:02 UTC +* Number of recursive dependencies: 226 -Run `revdepcheck::cloud_details(, "AlphaPart")` for more info +Run `revdepcheck::cloud_details(, "agridat")` for more info
@@ -354,49 +412,59 @@ Run `revdepcheck::cloud_details(, "AlphaPart")` for more info * checking examples ... ERROR ``` - Running examples in ‘AlphaPart-Ex.R’ failed + Running examples in ‘agridat-Ex.R’ failed The error most likely occurred in: - > ### Name: print.plotSummaryAlphaPart - > ### Title: Print a plot generate by the function 'plotSummaryAlphaPart' - > ### Aliases: print.plotSummaryAlphaPart + > ### Name: connolly.potato + > ### Title: Potato yields in single-drill plots + > ### Aliases: connolly.potato + > ### Keywords: datasets > > ### ** Examples > - > ## Partition additive genetic values ... - 4 4 1 105.00000 66 39.00000 - + > dat <- connolly.potato > - > ## Plot the partitions - > p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation") - > print(p[[1]]) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + > # Field plan + > libs(desplot) + > desplot(dat, yield~col*row, + + out1=rep, # aspect unknown + + main="connolly.potato yields (reps not contiguous)") + Error in is.element(x, dn) : unused argument (dn) + Calls: desplot -> checkvars Execution halted ``` -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘alphapart-variance.Rmd’ + when running code in ‘agridat_graphical_gems.Rmd’ ... - > data <- readRDS("./../inst/extdata/AlphaPartCattleSim.rds") %>% - + dplyr::mutate(across(generation:mother, as.numeric)) %>% - + dplyr::rename .... [TRUNCATED] - Warning in gzfile(file, "rb") : - cannot open compressed file './../inst/extdata/AlphaPartCattleSim.rds', probable reason 'No such file or directory' + > dat <- gomez.stripsplitplot - When sourcing ‘alphapart-variance.R’: - Error: cannot open the connection + > if (require("desplot")) { + + desplot(dat, gen ~ col * row, out1 = rep, col = nitro, text = planting, + + cex = 1, main = "gomez.stripsplit ..." ... [TRUNCATED] + + When sourcing ‘agridat_graphical_gems.R’: + Error: unused argument (dn) Execution halted - ‘alphapart-variance.Rmd’ using ‘UTF-8’... failed - ‘alphapart-vignette.Rmd’ using ‘UTF-8’... OK + ‘agridat_data.Rmd’ using ‘UTF-8’... OK + ‘agridat_graphical_gems.Rmd’ using ‘UTF-8’... failed + ‘agridat_intro.Rmd’ using ‘UTF-8’... OK + ‘agridat_mixed_model_example.Rmd’ using ‘UTF-8’... OK + ‘agridat_uniformity_data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘agridat_data.Rmd’ using rmarkdown + --- finished re-building ‘agridat_data.Rmd’ + + --- re-building ‘agridat_graphical_gems.Rmd’ using rmarkdown ``` # AnalysisLin @@ -482,7 +550,7 @@ Run `revdepcheck::cloud_details(, "animbook")` for more info * GitHub: https://github.com/bflammers/ANN2 * Source code: https://github.com/cran/ANN2 * Date/Publication: 2020-12-01 10:00:02 UTC -* Number of recursive dependencies: 52 +* Number of recursive dependencies: 51 Run `revdepcheck::cloud_details(, "ANN2")` for more info @@ -524,10 +592,10 @@ Run `revdepcheck::cloud_details(, "ANN2")` for more info * checking installed package size ... NOTE ``` - installed size is 58.9Mb + installed size is 48.8Mb sub-directories of 1Mb or more: cereal 1.4Mb - libs 57.3Mb + libs 47.2Mb ``` * checking LazyData ... NOTE @@ -535,58 +603,58 @@ Run `revdepcheck::cloud_details(, "ANN2")` for more info 'LazyData' is specified without a 'data' directory ``` -# AnnoProbe +# APCI
-* Version: 0.1.7 -* GitHub: https://github.com/jmzeng1314/AnnoProbe -* Source code: https://github.com/cran/AnnoProbe -* Date/Publication: 2022-11-14 08:30:11 UTC -* Number of recursive dependencies: 121 +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/APCI +* Date/Publication: 2024-09-02 20:20:06 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "AnnoProbe")` for more info +Run `revdepcheck::cloud_details(, "APCI")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘AnnoProbe-Ex.R’ failed - The error most likely occurred in: - - > ### Name: check_diff_genes - > ### Title: Check a list of genes how they show difference. - > ### Aliases: check_diff_genes - > - > ### ** Examples - > - > attach(GSE95166) + Running ‘1_tests.R’ + Running the tests in ‘tests/1_tests.R’ failed. + Complete output: + > # install the package and use this script to test the package + > library("APCI") + > # or: remotes::install_github("jiahui1902/APCI") + > test_data <- APCI::women9017 + > test_data$acc <- as.factor(test_data$acc) + > test_data$pcc <- as.factor(test_data$pcc) + > test_data$educc <- as.factor(test_data$educc) ... - 11. │ └─ggplot2:::`+.gg`(...) - 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 13. │ ├─ggplot2::ggplot_add(object, p, objectname) - 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 16. └─base::.handleSimpleError(...) - 17. └─purrr (local) h(simpleError(msg, call)) - 18. └─cli::cli_abort(...) - 19. └─rlang::abort(...) - Execution halted + -0.330681588 0.124972726 0.151208824 -0.350044237 0.160268300 + acc8:pcc3 acc9:pcc3 acc1:pcc4 acc2:pcc4 acc3:pcc4 + -0.124023962 0.184278037 -0.415952378 0.038103374 0.173343774 + acc4:pcc4 acc5:pcc4 acc6:pcc4 acc7:pcc4 acc8:pcc4 + 0.274042725 0.250469135 -0.098811727 -0.063004131 -0.355449149 + acc9:pcc4 acc1:pcc5 acc2:pcc5 acc3:pcc5 acc4:pcc5 + 0.147098521 0.009963326 0.321744801 -0.080742516 -0.199308789 + acc5:pcc5 acc6:pcc5 acc7:pcc5 acc8:pcc5 acc9:pcc5 + -0.509084301 -0.328667274 0.352292245 0.698949422 -0.291285834 + Killed ``` -# ANOFA +# APCtools
-* Version: 0.1.3 -* GitHub: https://github.com/dcousin3/ANOFA -* Source code: https://github.com/cran/ANOFA -* Date/Publication: 2023-11-18 14:20:08 UTC -* Number of recursive dependencies: 81 +* Version: 1.0.4 +* GitHub: https://github.com/bauer-alex/APCtools +* Source code: https://github.com/cran/APCtools +* Date/Publication: 2023-01-13 23:30:02 UTC +* Number of recursive dependencies: 114 -Run `revdepcheck::cloud_details(, "ANOFA")` for more info +Run `revdepcheck::cloud_details(, "APCtools")` for more info
@@ -594,26 +662,26 @@ Run `revdepcheck::cloud_details(, "ANOFA")` for more info * checking examples ... ERROR ``` - Running examples in ‘ANOFA-Ex.R’ failed + Running examples in ‘APCtools-Ex.R’ failed The error most likely occurred in: - > ### Name: Gillet1993 - > ### Title: Gillet1993 - > ### Aliases: Gillet1993 - > ### Keywords: datasets + > ### Name: plot_densityMatrix + > ### Title: Create a matrix of density plots + > ### Aliases: plot_densityMatrix > > ### ** Examples > + > library(APCtools) ... - > # run the base analysis - > w <- anofa( Freq ~ species * location * florished, Gillet1993) - > - > # display a plot of the results - > anofaPlot(w) - superb::FYI: The variables will be plotted in that order: species, location, florished (use factorOrder to change). - Error in superb::superbPlot(cdata, BSFactors = bsfact, variables = as.character(w$freqColumn), : - superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - Calls: anofaPlot -> + 2.2.0 and is now defunct. + ℹ Please use the `rows` argument instead. + Backtrace: + ▆ + 1. └─APCtools::plot_densityMatrix(...) + 2. └─ggplot2::facet_grid(facets = facet_formula, switch = "y") + 3. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") + 4. └─lifecycle:::deprecate_stop0(msg) + 5. └─rlang::cnd_signal(...) Execution halted ``` @@ -623,21 +691,21 @@ Run `revdepcheck::cloud_details(, "ANOFA")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > test_check("ANOFA") - Loading required package: ANOFA - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-ANOFA-2.R:36:5'): TESTS of emFrequencies function (2/3) ──────── + > library(APCtools) + > + > test_check("APCtools") + Loading required package: nlme + This is mgcv 1.8-42. For overview type 'help("mgcv-package")'. + Excluding 9565 missing observations of mainTrip_distance... ... - statistic = "count", errorbar = "CI", gamma = confidenceLevel, - plotStyle = plotStyle, errorbarParams = errorbarParams, ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - Backtrace: ▆ - 1. └─ANOFA::anofaPlot(w, Freq ~ B) at test-ANOFA-3.R:46:5 - 2. └─superb::superbPlot(...) + 1. └─APCtools::plot_densityMatrix(...) at test-plots_descriptive.R:148:3 + 2. └─ggplot2::facet_grid(facets = facet_formula, switch = "y") + 3. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") + 4. └─lifecycle:::deprecate_stop0(msg) + 5. └─rlang::cnd_signal(...) - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] + [ FAIL 2 | WARN 51 | SKIP 0 | PASS 84 ] Error: Test failures Execution halted ``` @@ -645,452 +713,230 @@ Run `revdepcheck::cloud_details(, "ANOFA")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘ConfidenceIntervals.Rmd’ + when running code in ‘main_functionality.Rmd’ ... - > library(ANOFA) - - > w <- anofa(obsfreq ~ vocation * gender, LightMargolin1971) - - > anofaPlot(w) - superb::FYI: The variables will be plotted in that order: vocation, gender (use factorOrder to change). - ... - - > anofaPlot(w) + > plot_densityMatrix(dat = travel, y_var = "mainTrip_distance", + + age_groups = age_groups, period_groups = period_groups, log_scale = TRUE) + Excluding 9149 missing observations of mainTrip_distance... - When sourcing ‘WhatIsANOFA.R’: - Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + When sourcing ‘main_functionality.R’: + Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `rows` argument instead. Execution halted - ‘ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed - ‘DataFormatsForFrequencies.Rmd’ using ‘UTF-8’... OK - ‘WhatIsANOFA.Rmd’ using ‘UTF-8’... failed + ‘main_functionality.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘ConfidenceIntervals.Rmd’ using rmarkdown - - Quitting from lines 70-73 [unnamed-chunk-2] (ConfidenceIntervals.Rmd) - Error: processing vignette 'ConfidenceIntervals.Rmd' failed with diagnostics: - superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - --- failed re-building ‘ConfidenceIntervals.Rmd’ - - --- re-building ‘DataFormatsForFrequencies.Rmd’ using rmarkdown - ... - Quitting from lines 108-109 [unnamed-chunk-4] (WhatIsANOFA.Rmd) - Error: processing vignette 'WhatIsANOFA.Rmd' failed with diagnostics: - superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - --- failed re-building ‘WhatIsANOFA.Rmd’ - - SUMMARY: processing the following files failed: - ‘ConfidenceIntervals.Rmd’ ‘WhatIsANOFA.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘main_functionality.Rmd’ using rmarkdown ``` -# ANOPA +# applicable
-* Version: 0.1.3 -* GitHub: https://github.com/dcousin3/ANOPA -* Source code: https://github.com/cran/ANOPA -* Date/Publication: 2024-03-22 19:40:05 UTC -* Number of recursive dependencies: 81 +* Version: 0.1.1 +* GitHub: https://github.com/tidymodels/applicable +* Source code: https://github.com/cran/applicable +* Date/Publication: 2024-04-25 00:00:04 UTC +* Number of recursive dependencies: 116 -Run `revdepcheck::cloud_details(, "ANOPA")` for more info +Run `revdepcheck::cloud_details(, "applicable")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘ANOPA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ArringtonEtAl2002 - > ### Title: Arrington et al. (2002) dataset - > ### Aliases: ArringtonEtAl2002 - > ### Keywords: datasets - > - > ### ** Examples - > - ... - Africa Nocturnal Omnivore 0 0 - North America Nocturnal Detritivore 0 0 - Warning: ANOPA::warning(1): Some cells have zero over zero data. Imputing... - > - > # make a plot with all the factors - > anopaPlot(w) - Error in superb::superbPlot(wdata, BSFactors = bsfact, WSFactors = wsfact, : - superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - Calls: anopaPlot -> - Execution halted - ``` - * checking tests ... ERROR ``` + Running ‘spelling.R’ Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > test_check("ANOPA") - Loading required package: ANOPA - ------------------------------------------------------------ - Design is: 2 x ( 3 ) with 2 independent groups. - ------------------------------------------------------------ - 1.Between-Subject Factors ( 2 groups ) : - ... - 1) "UA" else "none"), plotStyle = plotStyle, errorbarParams = errorbarParams, - ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - Backtrace: - ▆ - 1. └─ANOPA::anopaPlot(w) at test-ANOPA-4.R:106:9 - 2. └─superb::superbPlot(...) + > library(applicable) + Loading required package: ggplot2 + + Attaching package: 'ggplot2' + + ... + `expected` is a character vector ('percentile') + ── Failure ('test-plot.R:36:3'): output of autoplot.apd_pca is correct when options=distance are provided ── + ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`). - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + `actual` is NULL + `expected` is a character vector ('percentile') + + [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ] Error: Test failures Execution halted ``` -* checking running R code from vignettes ... ERROR +# ARPALData + +
+ +* Version: 1.6.1 +* GitHub: NA +* Source code: https://github.com/cran/ARPALData +* Date/Publication: 2025-01-10 14:00:10 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "ARPALData")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘A-WhatIsANOPA.Rmd’ - ... - > w <- anopa({ - + nSuccess - + nParticipants - + } ~ DistractingTask, ArticleExample1) - - > anopaPlot(w) + Running examples in ‘ARPALData-Ex.R’ failed + The error most likely occurred in: + > ### Name: is_ARPALdf + > ### Title: Check if a given object belongs to class 'ARPALdf' + > ### Aliases: is_ARPALdf + > + > ### ** Examples + > + > d <- get_ARPA_Lombardia_AQ_registry() ... - When sourcing ‘E-ArcsineIsAsinine.R’: - Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - Execution halted + dbl (5): IDSensor, IDStation, Altitude, Latitude, Longitude + date (2): DateStart, DateStop - ‘A-WhatIsANOPA.Rmd’ using ‘UTF-8’... failed - ‘B-DataFormatsForProportions.Rmd’ using ‘UTF-8’... OK - ‘C-ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed - ‘D-ArringtonExample.Rmd’ using ‘UTF-8’... failed - ‘E-ArcsineIsAsinine.Rmd’ using ‘UTF-8’... failed - ‘F-TestingTypeIError.Rmd’ using ‘UTF-8’... OK + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + > is_ARPALdf(d) + Error in is.element("ARPALdf", attr(Data, "class")) : + unused argument (attr(Data, "class")) + Calls: is_ARPALdf + Execution halted ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘ARPALData’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘A-WhatIsANOPA.Rmd’ using rmarkdown - - Quitting from lines 182-183 [unnamed-chunk-5] (A-WhatIsANOPA.Rmd) - Error: processing vignette 'A-WhatIsANOPA.Rmd' failed with diagnostics: - superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... - --- failed re-building ‘A-WhatIsANOPA.Rmd’ - - --- re-building ‘B-DataFormatsForProportions.Rmd’ using rmarkdown - --- finished re-building ‘B-DataFormatsForProportions.Rmd’ - ... - - --- re-building ‘F-TestingTypeIError.Rmd’ using rmarkdown - --- finished re-building ‘F-TestingTypeIError.Rmd’ - - SUMMARY: processing the following files failed: - ‘A-WhatIsANOPA.Rmd’ ‘C-ConfidenceIntervals.Rmd’ - ‘D-ArringtonExample.Rmd’ ‘E-ArcsineIsAsinine.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# AntMAN - -
- -* Version: 1.1.0 -* GitHub: https://github.com/bbodin/AntMAN -* Source code: https://github.com/cran/AntMAN -* Date/Publication: 2021-07-23 10:00:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "AntMAN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘AntMAN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: AM_mix_hyperparams_uninorm - > ### Title: univariate Normal mixture hyperparameters - > ### Aliases: AM_mix_hyperparams_uninorm - > - > ### ** Examples - > - > - ... - Press [enter] to continue - Plotting pmf for M,K - NULL - Press [enter] to continue - Plotting traces from M,K - Press [enter] to continue - Plotting values from M,K - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘UnitTest_AM_binder.R’ - Running ‘UnitTest_AM_coclustering.R’ - Running ‘UnitTest_AM_demo.R’ - Running ‘UnitTest_AM_extract.R’ - Running ‘UnitTest_AM_mcmc.R’ - Running the tests in ‘tests/UnitTest_AM_mcmc.R’ failed. - Complete output: - > ####################################################################################### - > ############### - > ############### AntMAN Package : Tests and Examples - ... - Press [enter] to continue - Plotting pmf for M,K - NULL - Press [enter] to continue - Plotting traces from M,K - Press [enter] to continue - Plotting values from M,K - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking C++ specification ... NOTE - ``` - Specified C++11: please drop specification unless essential - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - libs 6.4Mb + Found the following significant warnings: + Note: possible error in 'is.element("try-error", ': unused argument (attr(Meteo2, "class")) + Note: possible error in 'is.element("ARPALdf", ': unused argument (attr(Data, "class")) + Note: possible error in 'is.element("ARPALdf_AQ", ': unused argument (attr(Data, "class")) + Note: possible error in 'is.element("ARPALdf_AQ_mun", ': unused argument (attr(Data, "class")) + Note: possible error in 'is.element("ARPALdf_W", ': unused argument (attr(Data, "class")) + See ‘/tmp/workdir/ARPALData/new/ARPALData.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -* checking dependencies in R code ... NOTE +* checking R code for possible problems ... NOTE ``` - Namespaces in Imports field not imported from: - ‘Rdpack’ ‘mcclust’ - All declared Imports should be used. + get_ARPA_Lombardia_W_data: possible error in is.element("try-error", + attr(Meteo2, "class")): unused argument (attr(Meteo2, "class")) + is_ARPALdf: possible error in is.element("ARPALdf", attr(Data, + "class")): unused argument (attr(Data, "class")) + is_ARPALdf_AQ: possible error in is.element("ARPALdf_AQ", attr(Data, + "class")): unused argument (attr(Data, "class")) + is_ARPALdf_AQ_mun: possible error in is.element("ARPALdf_AQ_mun", + attr(Data, "class")): unused argument (attr(Data, "class")) + is_ARPALdf_W: possible error in is.element("ARPALdf_W", attr(Data, + "class")): unused argument (attr(Data, "class")) ``` -# APCI +# arulesViz
-* Version: 1.0.8 -* GitHub: NA -* Source code: https://github.com/cran/APCI -* Date/Publication: 2024-09-02 20:20:06 UTC -* Number of recursive dependencies: 73 +* Version: 1.5.3 +* GitHub: https://github.com/mhahsler/arulesViz +* Source code: https://github.com/cran/arulesViz +* Date/Publication: 2024-04-26 09:20:02 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "APCI")` for more info +Run `revdepcheck::cloud_details(, "arulesViz")` for more info
## Newly broken -* checking tests ... ERROR +* checking whether package ‘arulesViz’ can be installed ... WARNING ``` - Running ‘1_tests.R’ - Running the tests in ‘tests/1_tests.R’ failed. - Complete output: - > # install the package and use this script to test the package - > library("APCI") - > # or: remotes::install_github("jiahui1902/APCI") - > test_data <- APCI::women9017 - > test_data$acc <- as.factor(test_data$acc) - > test_data$pcc <- as.factor(test_data$pcc) - > test_data$educc <- as.factor(test_data$educc) - ... - -0.335818939 0.165402344 0.138957101 -0.357703237 0.229441985 - acc8:pcc3 acc9:pcc3 acc1:pcc4 acc2:pcc4 acc3:pcc4 - -0.147848556 0.146360984 -0.436635793 0.062363971 0.289676120 - acc4:pcc4 acc5:pcc4 acc6:pcc4 acc7:pcc4 acc8:pcc4 - 0.266502847 0.199035811 -0.082410026 -0.140171983 -0.274808726 - acc9:pcc4 acc1:pcc5 acc2:pcc5 acc3:pcc5 acc4:pcc5 - 0.070541348 0.052280642 0.320968547 -0.136111903 -0.102002632 - acc5:pcc5 acc6:pcc5 acc7:pcc5 acc8:pcc5 acc9:pcc5 - -0.553458810 -0.333938836 0.340338956 0.670285259 -0.300340437 - Killed + Found the following significant warnings: + Warning: replacing previous import ‘arules::is.element’ by ‘ggplot2::is.element’ when loading ‘arulesViz’ + See ‘/tmp/workdir/arulesViz/new/arulesViz.Rcheck/00install.out’ for details. ``` -# aplot +# asremlPlus
-* Version: 0.2.3 -* GitHub: https://github.com/YuLab-SMU/aplot -* Source code: https://github.com/cran/aplot -* Date/Publication: 2024-06-17 09:50:01 UTC -* Number of recursive dependencies: 50 +* Version: 4.4.43 +* GitHub: https://github.com/briencj/asremlPlus +* Source code: https://github.com/cran/asremlPlus +* Date/Publication: 2024-12-10 08:30:01 UTC +* Number of recursive dependencies: 176 -Run `revdepcheck::cloud_details(, "aplot")` for more info +Run `revdepcheck::cloud_details(, "asremlPlus")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘asremlPlus’ can be installed ... WARNING ``` - Running examples in ‘aplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: insert_left - > ### Title: plot-insertion - > ### Aliases: insert_left insert_right insert_top insert_bottom - > - > ### ** Examples - > - > library(ggplot2) - ... - > ap - > ap[2, 1] <- ap[2, 1] + theme_bw() - > ap[2, 1] <- ap[2, 1] + - + aes(color = as.factor(am)) + - + scale_color_manual(values = c('steelblue', 'darkgreen')) - > ap[1, 1] <- ap[1, 1] + theme(axis.line.x.bottom=element_line()) - > ap - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element(fixed.labels[[1]], ': unused argument (fixed.labels[[i]]) + Note: possible error in 'is.element(sparse.labels[[1]], ': unused argument (sparse.labels[[i]]) + See ‘/tmp/workdir/asremlPlus/new/asremlPlus.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -# applicable - -
- -* Version: 0.1.1 -* GitHub: https://github.com/tidymodels/applicable -* Source code: https://github.com/cran/applicable -* Date/Publication: 2024-04-25 00:00:04 UTC -* Number of recursive dependencies: 116 - -Run `revdepcheck::cloud_details(, "applicable")` for more info - -
- -## Newly broken - -* checking tests ... ERROR +* checking R code for possible problems ... NOTE ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(applicable) - Loading required package: ggplot2 - > - > test_check("applicable") - Loading required package: dplyr - ... - `expected` is a character vector ('percentile') - ── Failure ('test-plot.R:36:3'): output of autoplot.apd_pca is correct when options=distance are provided ── - ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`). - - `actual` is NULL - `expected` is a character vector ('percentile') - - [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ] - Error: Test failures - Execution halted + REMLRT.asreml: possible error in is.element(fixed.labels[[1]], + fixed.labels[[i]]): unused argument (fixed.labels[[i]]) + REMLRT.asreml: possible error in is.element(sparse.labels[[1]], + sparse.labels[[i]]): unused argument (sparse.labels[[i]]) + bootREMLRT.asreml: possible error in is.element(fixed.labels[[1]], + fixed.labels[[i]]): unused argument (fixed.labels[[i]]) + bootREMLRT.asreml: possible error in is.element(sparse.labels[[1]], + sparse.labels[[i]]): unused argument (sparse.labels[[i]]) ``` -# ASRgenomics - -
- -* Version: 1.1.4 -* GitHub: NA -* Source code: https://github.com/cran/ASRgenomics -* Date/Publication: 2024-01-29 21:20:02 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "ASRgenomics")` for more info - -
- -## Newly broken +## In both * checking examples ... ERROR ``` - Running examples in ‘ASRgenomics-Ex.R’ failed + Running examples in ‘asremlPlus-Ex.R’ failed The error most likely occurred in: - > ### Name: kinship.pca - > ### Title: Performs a Principal Component Analysis (PCA) based on a kinship - > ### matrix K - > ### Aliases: kinship.pca + > ### Name: LSD.frame + > ### Title: Description of an LSD frame + > ### Aliases: LSD.frame + > ### Keywords: asreml htest > > ### ** Examples > ... - 13. │ └─ggplot2:::`+.gg`(...) - 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. │ ├─ggplot2::ggplot_add(object, p, objectname) - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) + + } + Warning in check_dep_version() : + ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original ‘Matrix’ package + Error in initializePtr() : + function 'cholmod_factor_ldetA' not provided by package 'Matrix' + Calls: ... initialize -> -> initializePtr -> .Call Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - ... - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) - - [ FAIL 2 | WARN 2 | SKIP 0 | PASS 249 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE +* checking package dependencies ... NOTE ``` - installed size is 8.9Mb - sub-directories of 1Mb or more: - data 8.5Mb + Package which this enhances but not available for checking: ‘asreml’ ``` # autocogs @@ -1101,7 +947,7 @@ Run `revdepcheck::cloud_details(, "ASRgenomics")` for more info * GitHub: https://github.com/schloerke/autocogs * Source code: https://github.com/cran/autocogs * Date/Publication: 2021-05-29 17:00:05 UTC -* Number of recursive dependencies: 74 +* Number of recursive dependencies: 73 Run `revdepcheck::cloud_details(, "autocogs")` for more info @@ -1151,7 +997,7 @@ Run `revdepcheck::cloud_details(, "autocogs")` for more info * GitHub: https://github.com/terrytangyuan/autoplotly * Source code: https://github.com/cran/autoplotly * Date/Publication: 2021-04-18 06:50:11 UTC -* Number of recursive dependencies: 88 +* Number of recursive dependencies: 87 Run `revdepcheck::cloud_details(, "autoplotly")` for more info @@ -1171,11 +1017,16 @@ Run `revdepcheck::cloud_details(, "autoplotly")` for more info > > ### ** Examples > - > # Automatically generate interactive plot for results produced by `stats::prcomp` + ... > p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris, + colour = 'Species', label = TRUE, label.size = 3, frame = TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: autoplotly ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Warning: `aes_string()` was deprecated in ggplot2 3.0.0. + ℹ Please use tidy evaluation idioms with `aes()`. + ℹ See also `vignette("ggplot2-in-packages")` for more information. + ℹ The deprecated feature was likely used in the ggfortify package. + Please report the issue at . + Error in pm[[2]] : subscript out of bounds + Calls: autoplotly ... autoplotly.default -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` @@ -1188,110 +1039,88 @@ Run `revdepcheck::cloud_details(, "autoplotly")` for more info > library(autoplotly) > > test_check("autoplotly") - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ... - 5. └─ggfortify::ggbiplot(...) - 6. └─ggplot2:::`+.gg`(...) - 7. └─ggplot2:::add_ggplot(e1, e2, e2name) - 8. ├─ggplot2::ggplot_add(object, p, objectname) - 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + ▆ + 1. ├─autoplotly::autoplotly(...) at test_all.R:26:3 + 2. └─autoplotly:::autoplotly.default(...) + 3. ├─plotly::ggplotly(...) + 4. └─plotly:::ggplotly.ggplot(...) + 5. └─plotly::gg2list(...) - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted ``` -# autoReg +# autoTS
-* Version: 0.3.3 -* GitHub: https://github.com/cardiomoon/autoReg -* Source code: https://github.com/cran/autoReg -* Date/Publication: 2023-11-14 05:53:27 UTC -* Number of recursive dependencies: 214 +* Version: 0.9.11 +* GitHub: https://github.com/vivienroussez/autots +* Source code: https://github.com/cran/autoTS +* Date/Publication: 2020-06-05 12:20:06 UTC +* Number of recursive dependencies: 119 -Run `revdepcheck::cloud_details(, "autoReg")` for more info +Run `revdepcheck::cloud_details(, "autoTS")` for more info
## Newly broken -* checking examples ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Running examples in ‘autoReg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: adjustedPlot.survreg - > ### Title: Draw predicted survival curve with an object survreg - > ### Aliases: adjustedPlot.survreg - > - > ### ** Examples - > - > library(survival) - > x=survreg(Surv(time, status) ~ rx, data=anderson,dist="exponential") - > adjustedPlot(x) - > adjustedPlot(x,addCox=TRUE) - Warning: Removed 42 rows containing missing values or values outside the scale range - (`geom_line()`). - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted + Error(s) in re-building vignettes: + --- re-building ‘autoTS_vignette.Rmd’ using rmarkdown ``` +## In both + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Automatic_Regression_Modeling.Rmd’ + when running code in ‘autoTS_vignette.Rmd’ ... - Species setosa (N=50) Mean ± SD 5.0 ± 0.4 - versicolor (N=50) Mean ± SD 5.9 ± 0.5 1.46 (1.24 to 1.68, p<.001) 1.44 (1.16 to 1.71, p<.001) 1.47 (1.23 to 1.70, p<.001) - virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.87 (1.62 to 2.11, p<.001) 1.97 (1.76 to 2.17, p<.001) - ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— + Warning in unzip(zipfile = "../inst/extdata/namq_10_gdp.zip", exdir = tmp_dir) : + error 1 in extracting from zip file - > modelPlot(fit1, imputed = TRUE) + > dat <- read.csv(paste0(tmp_dir, "/namq_10_gdp_1_Data.csv")) + Warning in file(file, "rt") : + cannot open file '/tmp/RtmpJMEUNu/namq_10_gdp_1_Data.csv': No such file or directory - ... - - When sourcing ‘Survival.R’: - Error: argument is of length zero + When sourcing ‘autoTS_vignette.R’: + Error: cannot open the connection Execution halted - ‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... failed - ‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK - ‘Getting_started.Rmd’ using ‘UTF-8’... failed - ‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK - ‘Survival.Rmd’ using ‘UTF-8’... failed + ‘autoTS_vignette.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE +* checking dependencies in R code ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘Automatic_Regression_Modeling.Rmd’ using rmarkdown - - Quitting from lines 142-143 [unnamed-chunk-15] (Automatic_Regression_Modeling.Rmd) - Error: processing vignette 'Automatic_Regression_Modeling.Rmd' failed with diagnostics: - object is not a unit - --- failed re-building ‘Automatic_Regression_Modeling.Rmd’ - - --- re-building ‘Bootstrap_Prediction.Rmd’ using rmarkdown + Namespaces in Imports field not imported from: + ‘plotly’ ‘shinycssloaders’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory ``` -# baggr +# backShift
-* Version: 0.7.8 -* GitHub: https://github.com/wwiecek/baggr -* Source code: https://github.com/cran/baggr -* Date/Publication: 2024-02-12 18:20:02 UTC -* Number of recursive dependencies: 104 +* Version: 0.1.4.3 +* GitHub: https://github.com/christinaheinze/backShift +* Source code: https://github.com/cran/backShift +* Date/Publication: 2020-05-06 11:30:03 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "baggr")` for more info +Run `revdepcheck::cloud_details(, "backShift")` for more info
@@ -1299,334 +1128,261 @@ Run `revdepcheck::cloud_details(, "baggr")` for more info * checking examples ... ERROR ``` - Running examples in ‘baggr-Ex.R’ failed + Running examples in ‘backShift-Ex.R’ failed The error most likely occurred in: - > ### Name: baggr_plot - > ### Title: Plotting method in baggr package - > ### Aliases: baggr_plot + > ### Name: metricsThreshold + > ### Title: Performance metrics for estimate of connectiviy matrix A. + > ### Aliases: metricsThreshold > > ### ** Examples > - > fit <- baggr(schools, pooling = "none") - Automatically chose Rubin model with aggregate data based on input data. - Setting prior for mean in each group using 10 times the max effect : - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(baggr) - Loading required package: Rcpp - This is baggr; see vignette('baggr') for tutorial, ?baggr for basic help. - For execution on a local, multicore CPU with excess RAM call: - options(mc.cores = parallel::detectCores()) - > + > # true A ... - 10. └─bayesplot::mcmc_areas(...) - 11. └─ggplot2:::`+.gg`(...) - 12. └─ggplot2:::add_ggplot(e1, e2, e2name) - 13. ├─ggplot2::ggplot_add(object, p, objectname) - 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 6 | WARN 0 | SKIP 6 | PASS 488 ] - Error: Test failures - Execution halted + > diag(A.est) <- 0 + > A.est[1,2] <- 0.76 + > A.est[2,3] <- -0.68 + > A.est[3,1] <- 0.83 + > + > # compute metrics with threshold 0.25 + > metricsThreshold(A, A.est, thres = 0.25) + Error in is.element(-1, errs$diff) : unused argument (errs$diff) + Calls: metricsThreshold -> unlist -> metrics + Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘baggr.Rmd’ + when running code in ‘exampleBackShift.Rmd’ ... - 2.5% 0.4303903 - mean 0.8619752 - 97.5% 0.9998572 + > plotGraphEdgeAttr(estimate = Ahat.structure, plotStabSelec = TRUE, + + labels = colnames(A), thres.point = thres.pe, edgeWeights = Ahat, + + t .... [TRUNCATED] - > plot(baggr_schools, order = FALSE) + > metricsThresholdedA <- metricsThreshold(A, Ahat, thres = thres.pe) - When sourcing ‘baggr.R’: - Error: argument is of length zero + When sourcing ‘exampleBackShift.R’: + Error: unused argument (errs$diff) Execution halted - ‘baggr.Rmd’ using ‘UTF-8’... failed - ‘baggr_binary.Rmd’ using ‘UTF-8’... OK + ‘exampleBackShift.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘backShift’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘baggr.Rmd’ using rmarkdown - - Quitting from lines 272-273 [unnamed-chunk-9] (baggr.Rmd) - Error: processing vignette 'baggr.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘baggr.Rmd’ - - --- re-building ‘baggr_binary.Rmd’ using rmarkdown - --- finished re-building ‘baggr_binary.Rmd’ - - SUMMARY: processing the following file failed: - ‘baggr.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element(-1, errs$diff)': unused argument (errs$diff) + Note: possible error in 'is.element(1, errs$diff)': unused argument (errs$diff) + See ‘/tmp/workdir/backShift/new/backShift.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -## In both +* checking R code for possible problems ... NOTE + ``` + metrics: possible error in is.element(-1, errs$diff): unused argument + (errs$diff) + metrics: possible error in is.element(1, errs$diff): unused argument + (errs$diff) + ``` -* checking installed package size ... NOTE +* checking re-building of vignette outputs ... NOTE ``` - installed size is 196.3Mb - sub-directories of 1Mb or more: - libs 194.5Mb + Error(s) in re-building vignettes: + --- re-building ‘exampleBackShift.Rmd’ using rmarkdown ``` -* checking for GNU extensions in Makefiles ... NOTE +## In both + +* checking Rd cross-references ... NOTE ``` - GNU make is a SystemRequirements. + Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ ``` -# banter +# bartMan
-* Version: 0.9.6 +* Version: 0.1.1 * GitHub: NA -* Source code: https://github.com/cran/banter -* Date/Publication: 2023-02-12 21:32:29 UTC -* Number of recursive dependencies: 95 +* Source code: https://github.com/cran/bartMan +* Date/Publication: 2024-07-24 12:10:02 UTC +* Number of recursive dependencies: 135 -Run `revdepcheck::cloud_details(, "banter")` for more info +Run `revdepcheck::cloud_details(, "bartMan")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘bartMan’ can be installed ... ERROR ``` - Running examples in ‘banter-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotDetectorTrace - > ### Title: Plot BANTER Detector Traces - > ### Aliases: plotDetectorTrace - > - > ### ** Examples - > - > data(train.data) - ... - > bant.mdl <- addBanterDetector( - + bant.mdl, train.data$detectors, - + ntree = 50, sampsize = 1, num.cores = 1 - + ) - > - > plotDetectorTrace(bant.mdl) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: plotDetectorTrace ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted + Installation failed. + See ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/00install.out’ for details. ``` -# bartMan +## Installation -
+### Devel -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/bartMan -* Date/Publication: 2024-07-24 12:10:02 UTC -* Number of recursive dependencies: 135 +``` +* installing *source* package ‘bartMan’ ... +** package ‘bartMan’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in eval(exprs[i], envir) : object 'justify_grobs' not found +Error: unable to load R code in package ‘bartMan’ +Execution halted +ERROR: lazy loading failed for package ‘bartMan’ +* removing ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/bartMan’ -Run `revdepcheck::cloud_details(, "bartMan")` for more info -
+``` +### CRAN -## Newly broken +``` +* installing *source* package ‘bartMan’ ... +** package ‘bartMan’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (bartMan) -* checking examples ... ERROR - ``` - Running examples in ‘bartMan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mdsBart - > ### Title: mdsBart - > ### Aliases: mdsBart - > - > ### ** Examples - > - > if (requireNamespace("dbarts", quietly = TRUE)) { - ... - | - |======================================================================| 100% - Extracting Observation Data... - - Getting proximites... - Getting MDS... - Performing procrustes... - Error in if (new_name %in% existing) { : argument is of length zero - Calls: mdsBart -> suppressMessages -> withCallingHandlers - Execution halted - ``` -# BasketballAnalyzeR +``` +# bayesAB
-* Version: 0.5.0 -* GitHub: https://github.com/sndmrc/BasketballAnalyzeR -* Source code: https://github.com/cran/BasketballAnalyzeR -* Date/Publication: 2020-06-26 09:00:11 UTC -* Number of recursive dependencies: 83 +* Version: 1.1.3 +* GitHub: https://github.com/FrankPortman/bayesAB +* Source code: https://github.com/cran/bayesAB +* Date/Publication: 2021-06-25 00:50:02 UTC +* Number of recursive dependencies: 73 -Run `revdepcheck::cloud_details(, "BasketballAnalyzeR")` for more info +Run `revdepcheck::cloud_details(, "bayesAB")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘BasketballAnalyzeR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scatterplot - > ### Title: Draws a scatter plot or a matrix of scatter plots - > ### Aliases: scatterplot - > - > ### ** Examples - > - > # Single scatter plot - ... - > X <- data.frame(AST=Pbox.sel$AST/Pbox.sel$MIN,TOV=Pbox.sel$TOV/Pbox.sel$MIN) - > X$PTSpm <- Pbox.sel$PTS/Pbox.sel$MIN - > mypal <- colorRampPalette(c("blue","yellow","red")) - > scatterplot(X, data.var=c("AST","TOV"), z.var="PTSpm", labels=1:nrow(X), palette=mypal) - > # Matrix of scatter plots - > data <- Pbox[1:50, c("PTS","P3M","P2M","OREB","Team")] - > scatterplot(data, data.var=1:4, z.var="Team") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.9Mb - sub-directories of 1Mb or more: - data 6.5Mb - ``` - -* checking dependencies in R code ... NOTE +* checking tests ... ERROR ``` - Namespaces in Imports field not imported from: - ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’ - All declared Imports should be used. + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayesAB) + > + > test_check("bayesAB") + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-dists.R:34:3'): Success ────────────────────────────────────── + plotNormalInvGamma(3, 1, 1, 1)$labels$y not equal to "sig_sq". + target is NULL, current is character + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + Error: Test failures + Execution halted ``` -# bayefdr +# bayesforecast
-* Version: 0.2.1 -* GitHub: https://github.com/VallejosGroup/bayefdr -* Source code: https://github.com/cran/bayefdr -* Date/Publication: 2022-10-26 19:35:06 UTC -* Number of recursive dependencies: 96 +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/bayesforecast +* Date/Publication: 2021-06-17 10:00:02 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "bayefdr")` for more info +Run `revdepcheck::cloud_details(, "bayesforecast")` for more info
## Newly broken -* checking examples ... ERROR +* checking running R code from vignettes ... ERROR ``` - Running examples in ‘bayefdr-Ex.R’ failed - The error most likely occurred in: + Errors in running code in vignettes: + when running code in ‘ARIMA.Rmd’ + ... + ma -0.4547 0.0033 -0.6145 -0.2713 1008.0532 1.0008 + sar -0.2735 0.0023 -0.3902 -0.1508 1034.6555 0.9992 + sma -0.3322 0.0027 -0.4979 -0.2091 1022.9639 1.0007 + loglik -443.0979 0.0588 -446.7919 -440.8711 935.8408 0.9999 - > ### Name: traceplot - > ### Title: Trace, marginal density histogram, and autocorrelation plot of - > ### MCMC draws. - > ### Aliases: traceplot - > - > ### ** Examples - > - > x <- rnorm(1000) - > traceplot(x) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > mcmc_plot(object = sf1) + + ... + [1] "df [ ] ~ gamma ( shape = 2 ,rate = 0.1 )" + + > mcmc_plot(sf1) + + When sourcing ‘GARCH.R’: + Error: unused argument (code) Execution halted + + ‘ARIMA.Rmd’ using ‘UTF-8’... failed + ‘GARCH.Rmd’ using ‘UTF-8’... failed ``` -* checking tests ... ERROR +* checking whether package ‘bayesforecast’ can be installed ... WARNING ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(bayefdr) - > - > test_check("bayefdr") - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - 8. └─base::Reduce(`+`, c(list(noGeomPlot), layers)) - 9. └─ggplot2:::`+.gg`(init, x[[i]]) - 10. └─ggplot2:::add_ggplot(e1, e2, e2name) - 11. ├─ggplot2::ggplot_add(object, p, objectname) - 12. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 13. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] - Error: Test failures - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element(NA, code)': unused argument (code) + See ‘/tmp/workdir/bayesforecast/new/bayesforecast.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -# bayesAB - -
+* checking R code for possible problems ... NOTE + ``` + mcmc_plot.varstan: possible error in is.element(NA, code): unused + argument (code) + ``` -* Version: 1.1.3 -* GitHub: https://github.com/FrankPortman/bayesAB -* Source code: https://github.com/cran/bayesAB -* Date/Publication: 2021-06-25 00:50:02 UTC -* Number of recursive dependencies: 74 +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ARIMA.Rmd’ using rmarkdown + ``` -Run `revdepcheck::cloud_details(, "bayesAB")` for more info +## In both -
+* checking installed package size ... NOTE + ``` + installed size is 163.5Mb + sub-directories of 1Mb or more: + libs 162.0Mb + ``` -## Newly broken +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘StanHeaders’ ‘astsa’ + All declared Imports should be used. + ``` -* checking tests ... ERROR +* checking for GNU extensions in Makefiles ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(bayesAB) - > - > test_check("bayesAB") - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-dists.R:34:3'): Success ────────────────────────────────────── - plotNormalInvGamma(3, 1, 1, 1)$labels$y not equal to "sig_sq". - target is NULL, current is character - - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] - Error: Test failures - Execution halted + GNU make is a SystemRequirements. ``` # BayesGrowth @@ -1658,7 +1414,7 @@ Run `revdepcheck::cloud_details(, "BayesGrowth")` for more info When sourcing ‘MCMC-example.R’: Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 14, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, FALSE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NUL + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, Execution halted ‘MCMC-example.Rmd’ using ‘UTF-8’... failed @@ -1674,10 +1430,10 @@ Run `revdepcheck::cloud_details(, "BayesGrowth")` for more info * checking installed package size ... NOTE ``` - installed size is 84.8Mb + installed size is 82.3Mb sub-directories of 1Mb or more: data 1.5Mb - libs 82.6Mb + libs 80.1Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1685,84 +1441,133 @@ Run `revdepcheck::cloud_details(, "BayesGrowth")` for more info GNU make is a SystemRequirements. ``` -# BayesianReasoning +# BayesianMCPMod
-* Version: 0.4.2 -* GitHub: https://github.com/gorkang/BayesianReasoning -* Source code: https://github.com/cran/BayesianReasoning -* Date/Publication: 2023-11-14 11:33:20 UTC -* Number of recursive dependencies: 107 +* Version: 1.0.1 +* GitHub: https://github.com/Boehringer-Ingelheim/BayesianMCPMod +* Source code: https://github.com/cran/BayesianMCPMod +* Date/Publication: 2024-04-05 13:53:00 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info +Run `revdepcheck::cloud_details(, "BayesianMCPMod")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘BayesianMCPMod-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getBootstrapQuantiles + > ### Title: getBootstrapQuantiles + > ### Aliases: getBootstrapQuantiles + > + > ### ** Examples + > + > posterior_list <- list(Ctrl = RBesT::mixnorm(comp1 = c(w = 1, m = 0, s = 1), sigma = 2), + ... + + DG_4 = RBesT::mixnorm(comp1 = c(w = 1, m = 6.5, s = 1.1), sigma = 2)) + > models <- c("exponential", "linear") + > dose_levels <- c(0, 1, 2, 4, 8) + > fit <- getModelFits(models = models, + + posterior = posterior_list, + + dose_levels = dose_levels, + + simple = TRUE) + Error in is.element(modelNum, 1:4) : unused argument (1:4) + Calls: getModelFits -> lapply -> FUN -> -> fitMod.raw + Execution halted + ``` + * checking tests ... ERROR ``` + Running ‘spelling.R’ Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: - > library(testthat) - > library(BayesianReasoning) - > - > test_check("BayesianReasoning") - - Plot created in: ./FP_10_sens_100_screening_1667_diagnostic_44.png - + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html ... - `names(expected)` is absent - ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ─────────────── - vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`). - - `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect') - `names(expected)` is absent - - [ FAIL 8 | WARN 56 | SKIP 4 | PASS 115 ] - Error: Test failures + 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) + 11. │ ├─base::withCallingHandlers(...) + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─DoseFinding::Mods(linear = NULL, doses = dose_levels) at tests/testthat/setup.R:106:1 + 15. │ └─DoseFinding:::fullMod(...) + 16. └─base::.handleSimpleError(...) + 17. └─testthat (local) h(simpleError(msg, call)) + 18. └─rlang::abort(...) Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘PPV_NPV.Rmd’ + when running code in ‘Simulation_Example.Rmd’ ... - ℹ Please consider using `annotate()` or provide this layer with data containing - a single row. - Warning in ggforce::geom_mark_rect(aes(label = paste0(translated_labels$label_PPV_NPV, : - All aesthetics have length 1, but the data has 10201 rows. - ℹ Please consider using `annotate()` or provide this layer with data containing - a single row. + > sigemax2 <- DoseFinding::guesst(d = c(2, 4), p = c(0.3, + + 0.8), model = "sigEmax") + + > mods <- DoseFinding::Mods(linear = NULL, emax = emax, + + exponential = exp, sigEmax = rbind(sigemax, sigemax2), doses = dose_levels, + + maxE .... [TRUNCATED] + + ... + > mods <- DoseFinding::Mods(linear = NULL, emax = emax_guesst, + + exponential = exp_guesst, doses = dose_levels, maxEff = -1, + + placEff = -12 .... [TRUNCATED] - When sourcing ‘PPV_NPV.R’: - Error: object is not coercible to a unit + When sourcing ‘analysis_normal.R’: + Error: unused argument (c("emax", "quadratic", "exponential")) Execution halted - ‘PPV_NPV.Rmd’ using ‘UTF-8’... failed - ‘introduction.Rmd’ using ‘UTF-8’... OK + ‘Simulation_Example.Rmd’ using ‘UTF-8’... failed + ‘analysis_normal.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘PPV_NPV.Rmd’ using rmarkdown + ... + --- re-building ‘Simulation_Example.Rmd’ using rmarkdown + + Quitting from lines 93-124 [unnamed-chunk-2] (Simulation_Example.Rmd) + Error: processing vignette 'Simulation_Example.Rmd' failed with diagnostics: + unused argument (c("emax", "quadratic", "exponential")) + --- failed re-building ‘Simulation_Example.Rmd’ + + --- re-building ‘analysis_normal.Rmd’ using rmarkdown + ... + Quitting from lines 130-148 [Pre-Specification of candidate models] (analysis_normal.Rmd) + Error: processing vignette 'analysis_normal.Rmd' failed with diagnostics: + unused argument (c("emax", "quadratic", "exponential")) + --- failed re-building ‘analysis_normal.Rmd’ + + SUMMARY: processing the following files failed: + ‘Simulation_Example.Rmd’ ‘analysis_normal.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# BayesMallows +# BayesianReasoning
-* Version: 2.2.2 -* GitHub: https://github.com/ocbe-uio/BayesMallows -* Source code: https://github.com/cran/BayesMallows -* Date/Publication: 2024-08-17 13:00:03 UTC -* Number of recursive dependencies: 82 +* Version: 0.4.2 +* GitHub: https://github.com/gorkang/BayesianReasoning +* Source code: https://github.com/cran/BayesianReasoning +* Date/Publication: 2023-11-14 11:33:20 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "BayesMallows")` for more info +Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info
@@ -1773,106 +1578,75 @@ Run `revdepcheck::cloud_details(, "BayesMallows")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html + > library(testthat) + > library(BayesianReasoning) + > + > test_check("BayesianReasoning") + + Attaching package: 'ggplot2' + ... - `expected` is a character vector ('interaction(chain, cluster)') - ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ── - p$labels$colour (`actual`) not equal to "cluster" (`expected`). + `names(expected)` is absent + ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ─────────────── + vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`). - `actual` is NULL - `expected` is a character vector ('cluster') + `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect') + `names(expected)` is absent - [ FAIL 10 | WARN 0 | SKIP 6 | PASS 435 ] + [ FAIL 8 | WARN 56 | SKIP 4 | PASS 115 ] Error: Test failures Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 23.7Mb - sub-directories of 1Mb or more: - doc 2.7Mb - libs 20.1Mb - ``` - -# bayesplay +# BayesMallows
-* Version: 0.9.3 -* GitHub: https://github.com/bayesplay/bayesplay -* Source code: https://github.com/cran/bayesplay -* Date/Publication: 2023-04-13 12:10:02 UTC -* Number of recursive dependencies: 84 +* Version: 2.2.3 +* GitHub: https://github.com/ocbe-uio/BayesMallows +* Source code: https://github.com/cran/BayesMallows +* Date/Publication: 2025-01-14 11:30:02 UTC +* Number of recursive dependencies: 81 -Run `revdepcheck::cloud_details(, "bayesplay")` for more info +Run `revdepcheck::cloud_details(, "BayesMallows")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘bayesplay-Ex.R’ failed - The error most likely occurred in: - - > ### Name: visual_compare - > ### Title: Visually compare two models - > ### Aliases: visual_compare - > - > ### ** Examples - > - > # define two models + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html ... - > h1_mod <- prior(family = "normal", mean = 0, sd = 10) - > m0 <- extract_predictions(data_model * h0_mod) - > m1 <- extract_predictions(data_model * h1_mod) - > - > # visually compare the model - > visual_compare(m0, m1) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted + `expected` is a character vector ('interaction(chain, cluster)') + ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ── + p$labels$colour (`actual`) not equal to "cluster" (`expected`). + + `actual` is NULL + `expected` is a character vector ('cluster') + + [ FAIL 10 | WARN 0 | SKIP 10 | PASS 363 ] + Error: Test failures + Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘advanced.Rmd’ - ... - > plot(posterior1, add_prior = TRUE) + labs(title = "prior and posterior distribution", - + subtitle = "for a binomial likelihood and beta prior") - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for - - ... - > visual_compare(d_model1, d_model2) - - When sourcing ‘plots.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘advanced.Rmd’ using ‘UTF-8’... failed - ‘basic.Rmd’ using ‘UTF-8’... OK - ‘default_ttests.Rmd’ using ‘UTF-8’... OK - ‘plots.Rmd’ using ‘UTF-8’... failed - ``` +## In both -* checking re-building of vignette outputs ... NOTE +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘advanced.Rmd’ using rmarkdown + installed size is 23.6Mb + sub-directories of 1Mb or more: + doc 2.7Mb + libs 20.0Mb ``` # bayesplot @@ -1883,7 +1657,7 @@ Run `revdepcheck::cloud_details(, "bayesplay")` for more info * GitHub: https://github.com/stan-dev/bayesplot * Source code: https://github.com/cran/bayesplot * Date/Publication: 2024-02-15 05:30:11 UTC -* Number of recursive dependencies: 126 +* Number of recursive dependencies: 128 Run `revdepcheck::cloud_details(, "bayesplot")` for more info @@ -1891,31 +1665,6 @@ Run `revdepcheck::cloud_details(, "bayesplot")` for more info ## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘bayesplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MCMC-intervals - > ### Title: Plot interval estimates from MCMC draws - > ### Aliases: MCMC-intervals mcmc_intervals mcmc_areas mcmc_areas_ridges - > ### mcmc_intervals_data mcmc_areas_data mcmc_areas_ridges_data - > - > ### ** Examples - > - ... - - $Parameter - [1] "alpha" "sigma" "beta[1]" "beta[2]" "beta[3]" "beta[4]" - - > - > color_scheme_set("brightblue") - > mcmc_intervals(x) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - * checking tests ... ERROR ``` Running ‘testthat.R’ @@ -1929,14 +1678,14 @@ Run `revdepcheck::cloud_details(, "bayesplot")` for more info * Does _not_ affect other ggplot2 plots * See ?bayesplot_theme_set for details on theme setting ... - 5. └─bayesplot::ppc_violin_grouped(y, yrep, group) - 6. └─ggplot2:::`+.gg`(...) - 7. └─ggplot2:::add_ggplot(e1, e2, e2name) - 8. ├─ggplot2::ggplot_add(object, p, objectname) - 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-mcmc-traces.R:55:3'): mcmc_trace options work ──────────────── + all(c("xmin", "xmax", "ymin", "ymax") %in% names(ll)) is not TRUE + + `actual`: FALSE + `expected`: TRUE - [ FAIL 6 | WARN 1 | SKIP 73 | PASS 994 ] + [ FAIL 1 | WARN 1 | SKIP 73 | PASS 1024 ] Error: Test failures Execution halted ``` @@ -1946,16 +1695,12 @@ Run `revdepcheck::cloud_details(, "bayesplot")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘plotting-mcmc-draws.Rmd’ + when running code in ‘visual-mcmc-diagnostics.Rmd’ ... + > schools_dat <- list(J = 8, y = c(28, 8, -3, 7, -1, + + 1, 18, 12), sigma = c(15, 10, 16, 11, 9, 11, 10, 18)) - > color_scheme_set("red") - - > mcmc_intervals(posterior, pars = c("cyl", "drat", - + "am", "sigma")) - - ... > fit_cp <- sampling(schools_mod_cp, data = schools_dat, + seed = 803214055, control = list(adapt_delta = 0.9)) @@ -1964,7 +1709,7 @@ Run `revdepcheck::cloud_details(, "bayesplot")` for more info Execution halted ‘graphical-ppcs.Rmd’ using ‘UTF-8’... OK - ‘plotting-mcmc-draws.Rmd’ using ‘UTF-8’... failed + ‘plotting-mcmc-draws.Rmd’ using ‘UTF-8’... OK ‘visual-mcmc-diagnostics.Rmd’ using ‘UTF-8’... failed ``` @@ -1976,83 +1721,15 @@ Run `revdepcheck::cloud_details(, "bayesplot")` for more info doc 3.8Mb ``` -# bayestestR - -
- -* Version: 0.14.0 -* GitHub: https://github.com/easystats/bayestestR -* Source code: https://github.com/cran/bayestestR -* Date/Publication: 2024-07-24 14:10:02 UTC -* Number of recursive dependencies: 209 - -Run `revdepcheck::cloud_details(, "bayestestR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bayestestR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bayesfactor_restricted - > ### Title: Bayes Factors (BF) for Order Restricted Models - > ### Aliases: bayesfactor_restricted bf_restricted - > ### bayesfactor_restricted.stanreg bayesfactor_restricted.brmsfit - > ### bayesfactor_restricted.blavaan bayesfactor_restricted.emmGrid - > ### as.logical.bayesfactor_restricted - > - ... - + ) - > - > - > (b <- bayesfactor_restricted(posterior, hypothesis = hyps, prior = prior)) - Bayes Factor (Order-Restriction) - - Hypothesis P(Prior) P(Posterior) BF - A > B & B > C 0.16 0.23 1.39 - A > B & A > C 0.36 0.59 1.61 - C > A 0.46 0.34 0.742 - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(bayestestR) - > - > test_check("bayestestR") - Starting 2 test processes - [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] - - ... - 14. └─brms:::eval2(call, envir = args, enclos = envir) - 15. └─base::eval(expr, envir, ...) - 16. └─base::eval(expr, envir, ...) - 17. └─rstan (local) .fun(model_code = .x1) - 18. └─rstan:::cxxfunctionplus(...) - 19. └─base::sink(type = "output") - - [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] - Error: Test failures - Execution halted - ``` - # BCEA
-* Version: 2.4.6 +* Version: 2.4.7 * GitHub: https://github.com/n8thangreen/BCEA * Source code: https://github.com/cran/BCEA -* Date/Publication: 2024-02-16 15:00:08 UTC -* Number of recursive dependencies: 125 +* Date/Publication: 2025-01-14 12:30:08 UTC +* Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "BCEA")` for more info @@ -2065,23 +1742,23 @@ Run `revdepcheck::cloud_details(, "BCEA")` for more info Running examples in ‘BCEA-Ex.R’ failed The error most likely occurred in: - > ### Name: ceac.plot.bcea - > ### Title: Cost-Effectiveness Acceptability Curve (CEAC) Plot - > ### Aliases: ceac.plot.bcea ceac.plot - > ### Keywords: hplot + > ### Name: bcea + > ### Title: Create Bayesian Cost-Effectiveness Analysis Object + > ### Aliases: bcea bcea.default bcea.rjags bcea.rstan bcea.bugs + > ### Keywords: manip > > ### ** Examples > ... - > he <- BCEA::bcea(eff, cost) - No reference selected. Defaulting to first intervention. - > ceac.plot(he) - > - > ceac.plot(he, graph = "base") - > ceac.plot(he, graph = "ggplot2") - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + + # with each intervention + + Kmax=50000, # maximum value possible for the willingness + + # to pay threshold; implies that k is chosen + + # in a grid from the interval (0, Kmax) + + plot=TRUE # plots the results + + ) + Error in is.element("point", names(extra_args)) : + unused argument (names(extra_args)) + Calls: bcea -> bcea.default -> plot -> plot.bcea Execution halted ``` @@ -2092,20 +1769,20 @@ Run `revdepcheck::cloud_details(, "BCEA")` for more info Complete output: > library(testthat) > library(BCEA) - The BCEA version loaded is: 2.4.6 + Registered S3 method overwritten by 'BCEA': + method from + plot.evppi voi + The BCEA version loaded is: 2.4.7 - Attaching package: 'BCEA' - - The following object is masked from 'package:graphics': ... - 3. └─BCEA:::eib_plot_ggplot(he, graph_params, ...) - 4. └─ggplot2:::`+.gg`(...) - 5. └─ggplot2:::add_ggplot(e1, e2, e2name) - 6. ├─ggplot2::ggplot_add(object, p, objectname) - 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 6. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 7. │ │ │ └─base::force(code) + 8. │ │ └─base::withVisible(code) + 9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 10. ├─base::summary(smoke_bcea) + 11. └─BCEA:::summary.bcea(smoke_bcea) - [ FAIL 1 | WARN 1 | SKIP 7 | PASS 159 ] + [ FAIL 3 | WARN 0 | SKIP 3 | PASS 89 ] Error: Test failures Execution halted ``` @@ -2113,90 +1790,66 @@ Run `revdepcheck::cloud_details(, "BCEA")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘CEriskav.Rmd’ + when running code in ‘bcea.Rmd’ ... + is.element - > CEriskav(bcea_smoke) <- r - > plot(bcea_smoke) + > library(purrr) - > plot(bcea_smoke, graph = "ggplot") + > plot(bcea_smoke) ... - ‘CEriskav.Rmd’ using ‘UTF-8’... failed + ‘CEriskav.Rmd’ using ‘UTF-8’... OK ‘bcea.Rmd’ using ‘UTF-8’... failed - ‘ceac.Rmd’ using ‘UTF-8’... failed + ‘ceac.Rmd’ using ‘UTF-8’... OK ‘ceef.Rmd’ using ‘UTF-8’... OK - ‘ceplane.Rmd’ using ‘UTF-8’... failed - ‘contour.Rmd’ using ‘UTF-8’... failed - ‘eib.Rmd’ using ‘UTF-8’... failed + ‘ceplane.Rmd’ using ‘UTF-8’... OK + ‘contour.Rmd’ using ‘UTF-8’... OK + ‘eib.Rmd’ using ‘UTF-8’... OK ‘paired_vs_multiple_comps.Rmd’ using ‘UTF-8’... OK ‘Set_bcea_parameters.Rmd’ using ‘UTF-8’... OK ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘CEriskav.Rmd’ using rmarkdown - - Quitting from lines 41-46 [unnamed-chunk-3] (CEriskav.Rmd) - Error: processing vignette 'CEriskav.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘CEriskav.Rmd’ - - --- re-building ‘bcea.Rmd’ using rmarkdown - ``` - -# BDgraph - -
- -* Version: 2.73 -* GitHub: NA -* Source code: https://github.com/cran/BDgraph -* Date/Publication: 2024-08-23 13:20:02 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "BDgraph")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR +* checking whether package ‘BCEA’ can be installed ... WARNING ``` - Errors in running code in vignettes: - when running code in ‘BDgraph-Examples.Rmd’ - ... - Sensitivity 1 0.714 0.714 - MCC 1 0.827 0.827 - - > plotroc(list(bdgraph.obj, bdgraph.mpl.obj), data.sim, - + cut = 200, labels = c("BDgraph", "BDgraph.mpl"), color = c("blue", - + "red")) - - When sourcing ‘BDgraph-Examples.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘BDgraph-Examples.Rmd’ using ‘UTF-8’... failed - ‘Introduction-BDgraph.Rmd’ using ‘UTF-8’... OK + Found the following significant warnings: + Note: possible error in 'is.element(wtp, he$k)': unused argument (he$k) + Note: possible error in 'is.element("point", names(extra_args))': unused argument (names(extra_args)) + Note: possible error in 'is.element("color", names(extra_args$point))': unused argument (names(extra_args$point)) + Note: possible error in 'is.element(names(Table), ': unused argument (paste0("U", c(he$ref, he$comp))) + See ‘/tmp/workdir/BCEA/new/BCEA.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + ib_plot_base: possible error in is.element(wtp, he$k): unused argument + (he$k) + ib_plot_ggplot: possible error in is.element(wtp, he$k): unused + argument (he$k) + plot.bcea: possible error in is.element("point", names(extra_args)): + unused argument (names(extra_args)) + plot.bcea: possible error in is.element("color", + names(extra_args$point)): unused argument (names(extra_args$point)) + sim_table.bcea: possible error in is.element(wtp, he$k): unused + argument (he$k) + summary.bcea: possible error in is.element(wtp, he$k): unused argument + (he$k) + summary.bcea: possible error in is.element(names(Table), paste0("U", + c(he$ref, he$comp))): unused argument (paste0("U", c(he$ref, + he$comp))) + summary.pairwise: possible error in is.element(wtp, he$k): unused + argument (he$k) ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘BDgraph-Examples.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.3Mb - sub-directories of 1Mb or more: - libs 6.8Mb + --- re-building ‘CEriskav.Rmd’ using rmarkdown ``` # BEAMR @@ -2207,7 +1860,7 @@ Run `revdepcheck::cloud_details(, "BDgraph")` for more info * GitHub: https://github.com/annaSeffernick/BEAMR * Source code: https://github.com/cran/BEAMR * Date/Publication: 2024-07-27 16:00:06 UTC -* Number of recursive dependencies: 148 +* Number of recursive dependencies: 152 Run `revdepcheck::cloud_details(, "BEAMR")` for more info @@ -2220,26 +1873,62 @@ Run `revdepcheck::cloud_details(, "BEAMR")` for more info Running examples in ‘BEAMR-Ex.R’ failed The error most likely occurred in: - > ### Name: gen_beam_plot_list - > ### Title: Generate BEAM Plot List - > ### Aliases: gen_beam_plot_list + > ### Name: check_beam_specs + > ### Title: Check that beam.specs satisfies all necessary conditions + > ### Aliases: check_beam_specs > > ### ** Examples > - > data(beam_stats) - ... - + beam.specs=beam_stats$beam.specs) - > plot.list <- gen_beam_plot_list(beam.result=beam_stats, beam.specs=plot.specs, - + beam.feat.pvals=test.feat.pvals, - + number.pairs=1, set.id="ENSG00000099810", - + feat.id=NULL, title.size=11, - + pair.order="omic", endpt.order=NULL) - Error in if (new_name %in% existing) { : argument is of length zero - Error in plot.temp$plot : $ operator is invalid for atomic vectors - Calls: gen_beam_plot_list + > data(beam_dat) + > data(beam_specs) + > test_specs <- check_beam_specs(beam_specs, names(beam_dat$mtx.data)) + Error in is.element(beam.specs[, "mtx"], mtx.names) : + unused argument (mtx.names) + Calls: check_beam_specs Execution halted ``` +* checking whether package ‘BEAMR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(beam.specs[, ': unused argument (mtx.names) + Note: possible error in 'is.element("name", colnames(beam.specs))': unused argument (colnames(beam.specs)) + Note: possible error in 'is.element(cls, required.class)': unused argument (required.class) + Note: possible error in 'is.element(obj.cls, "list")': unused argument ("list") + Note: possible error in 'is.element(set.data$mtx.id, ': unused argument (specs.mtx) + Note: possible error in 'is.element(colnames(set.anns), ': unused argument ("set.id") + Note: possible error in 'is.element(c("set.id", ': unused argument (colnames(set.data)) + Note: possible error in 'is.element(set.index$mtx.id[i], ': unused argument (mtx.names) + Note: possible error in 'is.element(set.data$row.id[row.index], ': unused argument (row.ids) + See ‘/tmp/workdir/BEAMR/new/BEAMR.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + check_beam_specs: possible error in is.element(beam.specs[, "mtx"], + mtx.names): unused argument (mtx.names) + check_beam_specs: possible error in is.element("name", + colnames(beam.specs)): unused argument (colnames(beam.specs)) + check_list_class: possible error in is.element(cls, required.class): + unused argument (required.class) + check_list_class: possible error in is.element(obj.cls, "list"): unused + argument ("list") + compute_set_pvalues: possible error in is.element(set.data$mtx.id, + specs.mtx): unused argument (specs.mtx) + prep_beam_data: possible error in is.element(colnames(set.anns), + "set.id"): unused argument ("set.id") + prep_beam_data: possible error in is.element(c("set.id", "mtx.id", + "row.id"), colnames(set.data)): unused argument (colnames(set.data)) + prep_beam_data: possible error in is.element(set.index$mtx.id[i], + mtx.names): unused argument (mtx.names) + prep_beam_data: possible error in + is.element(set.data$row.id[row.index], row.ids): unused argument + (row.ids) + ``` + # beastt
@@ -2248,7 +1937,7 @@ Run `revdepcheck::cloud_details(, "BEAMR")` for more info * GitHub: https://github.com/GSK-Biostatistics/beastt * Source code: https://github.com/cran/beastt * Date/Publication: 2024-06-20 15:50:16 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 Run `revdepcheck::cloud_details(, "beastt")` for more info @@ -2299,7 +1988,7 @@ Run `revdepcheck::cloud_details(, "beastt")` for more info ℹ Error occurred in the 1st layer. Caused by error in `use_defaults()`: ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, Execution halted ‘binary.Rmd’ using ‘UTF-8’... failed @@ -2312,17 +2001,17 @@ Run `revdepcheck::cloud_details(, "beastt")` for more info --- re-building ‘binary.Rmd’ using rmarkdown ``` -# BeeGUTS +# biclust
-* Version: 1.1.3 -* GitHub: https://github.com/bgoussen/BeeGUTS -* Source code: https://github.com/cran/BeeGUTS -* Date/Publication: 2023-09-18 15:40:02 UTC -* Number of recursive dependencies: 86 +* Version: 2.0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/biclust +* Date/Publication: 2023-05-19 07:18:34 UTC +* Number of recursive dependencies: 41 -Run `revdepcheck::cloud_details(, "BeeGUTS")` for more info +Run `revdepcheck::cloud_details(, "biclust")` for more info
@@ -2330,207 +2019,85 @@ Run `revdepcheck::cloud_details(, "BeeGUTS")` for more info * checking examples ... ERROR ``` - Running examples in ‘BeeGUTS-Ex.R’ failed + Running examples in ‘biclust-Ex.R’ failed The error most likely occurred in: - > ### Name: traceplot - > ### Title: Plotting method for traces and densities for 'beeSurvFit' - > ### objects - > ### Aliases: traceplot traceplot.beeSurvFit + > ### Name: BCPlaid + > ### Title: The Plaid Model Bicluster algorithm + > ### Aliases: BCPlaid plaid 'plaid model' BCPlaid BCPlaid-class 'turner + > ### biclustering' biclust,matrix,BCPlaid-method + > ### Keywords: cluster classif models > > ### ** Examples > - > data(fitBetacyfluthrin_Chronic) - > traceplot(fitBetacyfluthrin_Chronic) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Tutorial.Rmd’ - ... - Chain 1: Elapsed Time: 137.867 seconds (Warm-up) - Chain 1: 75.093 seconds (Sampling) - Chain 1: 212.96 seconds (Total) - Chain 1: - - > traceplot(fit) - - When sourcing ‘Tutorial.R’: - Error: argument is of length zero - Execution halted - - ‘Tutorial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Tutorial.Rmd’ using rmarkdown - - Quitting from lines 45-58 [example] (Tutorial.Rmd) - Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘Tutorial.Rmd’ - - Error: Vignette re-building failed. + > #Random matrix with embedded bicluster + > test <- matrix(rnorm(5000),100,50) + > test[11:20,11:20] <- rnorm(100,3,0.3) + > res<-biclust(test, method=BCPlaid()) + Error in is.element("a", model) : unused argument (model) + Calls: biclust -> biclust -> -> plaid -> fitLayer Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 78.9Mb - sub-directories of 1Mb or more: - data 4.0Mb - libs 74.3Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE +* checking whether package ‘biclust’ can be installed ... WARNING ``` - GNU make is a SystemRequirements. + Found the following significant warnings: + Note: possible error in 'is.element("a", model)': unused argument (model) + Note: possible error in 'is.element("b", model)': unused argument (model) + Note: possible error in 'is.element("c", model)': unused argument (model) + Note: possible error in 'is.element("a", fit.model)': unused argument (fit.model) + Note: possible error in 'is.element("b", fit.model)': unused argument (fit.model) + Note: possible error in 'is.element("c", fit.model)': unused argument (fit.model) + Note: possible error in 'is.element(cluster, c("r", ': unused argument (c("r", "b")) + Note: possible error in 'is.element(cluster, c("c", ': unused argument (c("c", "b")) + See ‘/tmp/workdir/biclust/new/biclust.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + fitLayer: possible error in is.element("a", model): unused argument + (model) + fitLayer: possible error in is.element("b", model): unused argument + (model) + fitLayer: possible error in is.element("c", model): unused argument + (model) + plaid: possible error in is.element("a", fit.model): unused argument + (fit.model) + plaid: possible error in is.element("b", fit.model): unused argument + (fit.model) + ... + updatePlaid: possible error in is.element(cluster, c("r", "b")): unused + argument (c("r", "b")) + updatePlaid: possible error in is.element(cluster, c("c", "b")): unused + argument (c("c", "b")) + updatePlaid: possible error in is.element("a", model): unused argument + (model) + updatePlaid: possible error in is.element("b", model): unused argument + (model) + updatePlaid: possible error in is.element("c", model): unused argument + (model) ``` -# besthr +# biclustermd
-* Version: 0.3.2 -* GitHub: NA -* Source code: https://github.com/cran/besthr -* Date/Publication: 2023-04-14 08:50:08 UTC -* Number of recursive dependencies: 67 +* Version: 0.2.3 +* GitHub: https://github.com/jreisner/biclustermd +* Source code: https://github.com/cran/biclustermd +* Date/Publication: 2021-06-17 15:10:06 UTC +* Number of recursive dependencies: 83 -Run `revdepcheck::cloud_details(, "besthr")` for more info +Run `revdepcheck::cloud_details(, "biclustermd")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘besthr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.hrest - > ### Title: plots the 'hrest' object - > ### Aliases: plot.hrest - > - > ### ** Examples - > - > - > d1 <- make_data() - > hr_est <- estimate(d1, score, group) - > plot(hr_est) - Picking joint bandwidth of 0.68 - Error in as.unit(value) : object is not coercible to a unit - Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘basic-use.Rmd’ - ... - Confidence Intervals (0.025, 0.975) - 3.7475, 8.2525 - - 100 bootstrap resamples. - > plot(hr_est_1) - Picking joint bandwidth of 0.381 - - When sourcing ‘basic-use.R’: - Error: object is not coercible to a unit - Execution halted - - ‘basic-use.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘basic-use.Rmd’ using rmarkdown - - Quitting from lines 34-44 [unnamed-chunk-2] (basic-use.Rmd) - Error: processing vignette 'basic-use.Rmd' failed with diagnostics: - object is not coercible to a unit - --- failed re-building ‘basic-use.Rmd’ - - SUMMARY: processing the following file failed: - ‘basic-use.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# betaclust - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/betaclust -* Date/Publication: 2023-09-29 10:20:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "betaclust")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘vignettes.Rmd’ - ... - + data = pca.methylation.data[, 2:5], patient_number = 1, plot_type = "ggplot") - - > plot(threshold_out, what = "kernel density", threshold = TRUE, - + data = pca.methylation.data[, 2:5], plot_type = "ggplot") - - > plot(threshold_out, what = "uncertainty") - - When sourcing ‘vignettes.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘vignettes.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘vignettes.Rmd’ using rmarkdown - ``` - -# biclustermd - -
- -* Version: 0.2.3 -* GitHub: https://github.com/jreisner/biclustermd -* Source code: https://github.com/cran/biclustermd -* Date/Publication: 2021-06-17 15:10:06 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "biclustermd")` for more info - -
- -## Newly broken - -* checking tests ... ERROR +* checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. @@ -2538,10 +2105,10 @@ Run `revdepcheck::cloud_details(, "biclustermd")` for more info > library(testthat) > library(biclustermd) Loading required package: ggplot2 - Loading required package: tidyr - Attaching package: 'tidyr' + Attaching package: 'ggplot2' + The following object is masked from 'package:base': ... ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. @@ -2571,7 +2138,7 @@ Run `revdepcheck::cloud_details(, "biclustermd")` for more info * GitHub: https://github.com/biodosetools-team/biodosetools * Source code: https://github.com/cran/biodosetools * Date/Publication: 2022-11-16 16:00:02 UTC -* Number of recursive dependencies: 121 +* Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "biodosetools")` for more info @@ -2604,144 +2171,6 @@ Run `revdepcheck::cloud_details(, "biodosetools")` for more info Execution halted ``` -# BioPred - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/BioPred -* Date/Publication: 2024-06-06 16:50:09 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "BioPred")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Tutorial.Rmd’ - ... - - > tutorial_data$biogroup = ifelse(tutorial_data$x2 <= - + 0.5, "biomarker_positive", "biomarker_negative") - - > res = subgrp_perf_pred(yvar = "y.time", censorvar = "y.event", - + grpvar = "biogroup", grpname = c("biomarker_positive", "biomarker_negative"), .... [TRUNCATED] - - When sourcing ‘Tutorial.R’: - Error: argument is of length zero - Execution halted - - ‘Tutorial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Tutorial.Rmd’ using rmarkdown - ``` - -# BlandAltmanLeh - -
- -* Version: 0.3.1 -* GitHub: NA -* Source code: https://github.com/cran/BlandAltmanLeh -* Date/Publication: 2015-12-23 23:32:17 -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "BlandAltmanLeh")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Intro.Rmd’ - ... - > b <- 0.02 * a + 0.3 * rnorm(150) - - > library(ggExtra) - - > print(ggMarginal(bland.altman.plot(a, b, graph.sys = "ggplot2"), - + type = "histogram", size = 4)) - - When sourcing ‘Intro.R’: - Error: argument is of length zero - Execution halted - - ‘Intro.Rmd’... failed - ``` - -# bmggum - -
- -* Version: 0.1.0 -* GitHub: https://github.com/Naidantu/bmggum -* Source code: https://github.com/cran/bmggum -* Date/Publication: 2021-04-09 08:50:06 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "bmggum")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bmggum-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bayesplot - > ### Title: bayesian convergence diagnosis plotting function - > ### Aliases: bayesplot - > - > ### ** Examples - > - > Data <- c(1,4,2,3) - ... - Chain 1: - Warning: There were 3 divergent transitions after warmup. See - https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup - to find out why this is a problem and how to eliminate them. - Warning: Examine the pairs() plot to diagnose sampling problems - - > bayesplot(mod, 'alpha', 'density', inc_warmup=FALSE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: bayesplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 206.7Mb - sub-directories of 1Mb or more: - libs 206.1Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - # boxly
@@ -2750,7 +2179,7 @@ Run `revdepcheck::cloud_details(, "bmggum")` for more info * GitHub: https://github.com/Merck/boxly * Source code: https://github.com/cran/boxly * Date/Publication: 2023-10-24 02:40:02 UTC -* Number of recursive dependencies: 91 +* Number of recursive dependencies: 90 Run `revdepcheck::cloud_details(, "boxly")` for more info @@ -2783,17 +2212,17 @@ Run `revdepcheck::cloud_details(, "boxly")` for more info Execution halted ``` -# braidReports +# brolgar
-* Version: 0.5.4 -* GitHub: NA -* Source code: https://github.com/cran/braidReports -* Date/Publication: 2021-01-05 18:20:09 UTC -* Number of recursive dependencies: 30 +* Version: 1.0.1 +* GitHub: https://github.com/njtierney/brolgar +* Source code: https://github.com/cran/brolgar +* Date/Publication: 2024-05-10 14:50:34 UTC +* Number of recursive dependencies: 103 -Run `revdepcheck::cloud_details(, "braidReports")` for more info +Run `revdepcheck::cloud_details(, "brolgar")` for more info
@@ -2801,273 +2230,74 @@ Run `revdepcheck::cloud_details(, "braidReports")` for more info * checking examples ... ERROR ``` - Running examples in ‘braidReports-Ex.R’ failed + Running examples in ‘brolgar-Ex.R’ failed The error most likely occurred in: - > ### Name: makeBRAIDreport - > ### Title: Make a BRAID Report Page - > ### Aliases: makeBRAIDreport - > ### Keywords: hplot + > ### Name: facet_sample + > ### Title: Facet data into groups to facilitate exploration + > ### Aliases: facet_sample > > ### ** Examples > + > library(ggplot2) ... - 22. │ └─grid::convertUnit(short, "cm", valueOnly = TRUE) - 23. │ ├─grid:::upgradeUnit(x) - 24. │ └─grid:::upgradeUnit.default(x) - 25. │ └─base::stop("Not a unit object") - 26. └─base::.handleSimpleError(``, "Not a unit object", base::quote(upgradeUnit.default(x))) - 27. └─rlang (local) h(simpleError(msg, call)) - 28. └─handlers[[1L]](cnd) - 29. └─cli::cli_abort(...) - 30. └─rlang::abort(...) - Execution halted - ``` - -# BRcal - -
- -* Version: 0.0.4 -* GitHub: https://github.com/apguthrie/BRcal -* Source code: https://github.com/cran/BRcal -* Date/Publication: 2024-06-25 11:30:08 UTC -* Number of recursive dependencies: 116 - -Run `revdepcheck::cloud_details(, "BRcal")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BRcal-Ex.R’ failed - The error most likely occurred in: - > ### Name: lineplot - > ### Title: Lineplot for LLO-adjusted Probability Predictions - > ### Aliases: lineplot - > - > ### ** Examples - > - > - ... - > # Simulated 100 binary event outcomes using x - > y <- rbinom(100, 1, x) # By construction, x is well calibrated. - > - > # Lineplot show change in probabilities from original to MLE-recalibration to - > # specified Levels of Boldness-Recalibration via t_levels - > # Return a list with dataframe used to construct plot with return_df=TRUE - > lp1 <- lineplot(x, y, t_levels=c(0.98, 0.95), return_df=TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: lineplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > ggplot(heights, + + aes(x = year, + + y = height_cm, + + group = country)) + + + geom_line() + + + facet_sample() + Error in if (params$as.table) { : argument is of length zero + Calls: ... -> setup -> -> compute_layout Execution halted ``` +## In both + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘hockey_vignette.Rmd’ + when running code in ‘exploratory-modelling.Rmd’ ... - [841] 0.4804441 0.7670617 0.4668403 0.4104682 0.6058493 0.4249086 0.6581869 - [848] 0.7194199 0.4534938 0.7421488 0.6726924 0.3255808 0.5005185 0.6483056 - [855] 0.7210362 0.6593455 0.4586214 0.7750603 0.5841900 0.4826292 0.4080026 - [862] 0.6701504 0.6561462 0.4814185 0.7421488 0.6786381 0.3255808 0.4814569 - - > lineplot(hockey$x, hockey$y) + Warning in is.na(non_null_default_aes[[aes_param_name]]) : + is.na() applied to non-(list or vector) of type 'language' - When sourcing ‘hockey_vignette.R’: + When sourcing ‘exploratory-modelling.R’: + Error: ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + ... Error: argument is of length zero Execution halted - ‘hockey_vignette.Rmd’ using ‘UTF-8’... failed + ‘exploratory-modelling.Rmd’ using ‘UTF-8’... failed + ‘finding-features.Rmd’ using ‘UTF-8’... failed + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK + ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK + ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed + ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘hockey_vignette.Rmd’ using rmarkdown - - Quitting from lines 180-181 [unnamed-chunk-11] (hockey_vignette.Rmd) - Error: processing vignette 'hockey_vignette.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘hockey_vignette.Rmd’ + --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown - SUMMARY: processing the following file failed: - ‘hockey_vignette.Rmd’ + Quitting from lines 47-56 [use-gg-highlight] (exploratory-modelling.Rmd) + Error: processing vignette 'exploratory-modelling.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + aes_param_name]])`: + ! 'length = 2' in coercion to 'logical(1)' + --- failed re-building ‘exploratory-modelling.Rmd’ - Error: Vignette re-building failed. - Execution halted + --- re-building ‘finding-features.Rmd’ using rmarkdown ``` -# breathtestcore - -
- -* Version: 0.8.7 -* GitHub: https://github.com/dmenne/breathtestcore -* Source code: https://github.com/cran/breathtestcore -* Date/Publication: 2024-01-24 15:02:47 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "breathtestcore")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Complete output: - > library(testthat) - > - > options(Ncpus = parallelly::availableCores(omit = 1)) - > test_check("breathtestcore") - Loading required package: breathtestcore - Starting 1 test process - [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] - ... - `expected`: 10 - ── Failure ('test_plot_breathtestfit.R:81:3'): Plot multiple groups data only (no fit) ── - length(p) (`actual`) not equal to length(ggplot()) (`expected`). - - `actual`: 11 - `expected`: 10 - - [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] - Error: Test failures - Execution halted - ``` - -# brolgar - -
- -* Version: 1.0.1 -* GitHub: https://github.com/njtierney/brolgar -* Source code: https://github.com/cran/brolgar -* Date/Publication: 2024-05-10 14:50:34 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "brolgar")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘brolgar-Ex.R’ failed - The error most likely occurred in: - - > ### Name: facet_sample - > ### Title: Facet data into groups to facilitate exploration - > ### Aliases: facet_sample - > - > ### ** Examples - > - > library(ggplot2) - > ggplot(heights, - + aes(x = year, - + y = height_cm, - + group = country)) + - + geom_line() + - + facet_sample() - Error in if (params$as.table) { : argument is of length zero - Calls: ... -> setup -> -> compute_layout - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘exploratory-modelling.Rmd’ - ... - Warning in is.na(non_null_default_aes[[aes_param_name]]) : - is.na() applied to non-(list or vector) of type 'language' - - When sourcing ‘exploratory-modelling.R’: - Error: ℹ In index: 1. - ℹ With name: geom_line. - Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ - ... - Error: argument is of length zero - Execution halted - - ‘exploratory-modelling.Rmd’ using ‘UTF-8’... failed - ‘finding-features.Rmd’ using ‘UTF-8’... failed - ‘getting-started.Rmd’ using ‘UTF-8’... failed - ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK - ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK - ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed - ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown - - Quitting from lines 47-56 [use-gg-highlight] (exploratory-modelling.Rmd) - Error: processing vignette 'exploratory-modelling.Rmd' failed with diagnostics: - ℹ In index: 1. - ℹ With name: geom_line. - Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ - aes_param_name]])`: - ! 'length = 2' in coercion to 'logical(1)' - --- failed re-building ‘exploratory-modelling.Rmd’ - - --- re-building ‘finding-features.Rmd’ using rmarkdown - ``` - -# calibrationband - -
- -* Version: 0.2.1 -* GitHub: https://github.com/marius-cp/calibrationband -* Source code: https://github.com/cran/calibrationband -* Date/Publication: 2022-08-09 14:40:02 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "calibrationband")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘calibrationband-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.calibrationband - > ### Title: Plotting monotone confidence bands - > ### Aliases: plot.calibrationband autoplot.calibrationband - > ### autolayer.calibrationband - > - > ### ** Examples - > - ... - > p <- function(x,s){p = 1/(1+((1/x*(1-x))^(s+1)));return(p)} - > dat <- data.frame(pr=x, y=rbinom(n,1,p(x,s))) - > - > cb <- calibration_bands(x=dat$pr, y=dat$y,alpha=0.05, method="round", digits =3) - > - > #simple plotting - > plot(cb) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# cartograflow +# cartograflow
@@ -3075,7 +2305,7 @@ Run `revdepcheck::cloud_details(, "calibrationband")` for more info * GitHub: https://github.com/fbahoken/cartogRaflow * Source code: https://github.com/cran/cartograflow * Date/Publication: 2023-10-17 22:40:21 UTC -* Number of recursive dependencies: 102 +* Number of recursive dependencies: 101 Run `revdepcheck::cloud_details(, "cartograflow")` for more info @@ -3108,72 +2338,6 @@ Run `revdepcheck::cloud_details(, "cartograflow")` for more info Execution halted ``` -# cases - -
- -* Version: 0.1.1 -* GitHub: https://github.com/maxwestphal/cases -* Source code: https://github.com/cran/cases -* Date/Publication: 2023-05-18 08:30:02 UTC -* Number of recursive dependencies: 129 - -Run `revdepcheck::cloud_details(, "cases")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘example_wdbc.Rmd’ - ... - 13 TRUE FALSE - 14 FALSE FALSE - 15 FALSE FALSE - - - > visualize(results_bm) - - ... - + regu = TRU .... [TRUNCATED] - - > visualize(results_comp) - - When sourcing ‘package_overview.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘example_wdbc.Rmd’ using ‘UTF-8’... failed - ‘package_overview.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘example_wdbc.Rmd’ using rmarkdown - data_wdbc package:cases R Documentation - - _B_r_e_a_s_t _C_a_n_c_e_r _W_i_s_c_o_n_s_i_n (_D_i_a_g_n_o_s_t_i_c) _D_a_t_a _S_e_t - - _D_e_s_c_r_i_p_t_i_o_n: - - Dataset documentation can be found at the source website and - references below. - ... - Quitting from lines 160-168 [viz_comp] (package_overview.Rmd) - Error: processing vignette 'package_overview.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘package_overview.Rmd’ - - SUMMARY: processing the following files failed: - ‘example_wdbc.Rmd’ ‘package_overview.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - # cats
@@ -3224,71 +2388,17 @@ Run `revdepcheck::cloud_details(, "cats")` for more info All declared Imports should be used. ``` -# ceterisParibus - -
- -* Version: 0.4.2 -* GitHub: https://github.com/pbiecek/ceterisParibus -* Source code: https://github.com/cran/ceterisParibus -* Date/Publication: 2020-03-28 03:10:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "ceterisParibus")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ceterisParibus) - Loading required package: ggplot2 - Loading required package: gower - > - > test_check("ceterisParibus") - Welcome to DALEX (version: 2.4.3). - ... - 5. └─ceterisParibus:::plot_interactive.what_if_explainer(wi_rf_all) - 6. └─ggplot2:::`+.gg`(...) - 7. └─ggplot2:::add_ggplot(e1, e2, e2name) - 8. ├─ggplot2::ggplot_add(object, p, objectname) - 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 3 | SKIP 0 | PASS 29 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘knitr’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# cfda +# CausalImpact
-* Version: 0.11.0 -* GitHub: https://github.com/modal-inria/cfda -* Source code: https://github.com/cran/cfda -* Date/Publication: 2023-10-07 15:50:05 UTC -* Number of recursive dependencies: 98 +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/CausalImpact +* Date/Publication: 2022-11-09 08:40:40 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "cfda")` for more info +Run `revdepcheck::cloud_details(, "CausalImpact")` for more info
@@ -3296,108 +2406,344 @@ Run `revdepcheck::cloud_details(, "cfda")` for more info * checking examples ... ERROR ``` - Running examples in ‘cfda-Ex.R’ failed + Running examples in ‘CausalImpact-Ex.R’ failed The error most likely occurred in: - > ### Name: compute_duration - > ### Title: Compute duration of individuals - > ### Aliases: compute_duration + > ### Name: CausalImpact + > ### Title: Inferring causal impact using structural time-series models + > ### Aliases: CausalImpact > > ### ** Examples > - > # Simulate the Jukes-Cantor model of nucleotide replacement + > # Example 1 ... - > d_JK <- generate_Markov(n = 10, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10) - > - > - > # compute duration of each individual - > duration <- compute_duration(d_JK) - > - > hist(duration) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: hist ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > y <- 1.2 * x1 + rnorm(52) + > y[41:52] <- y[41:52] + 10 + > data <- cbind(y, x1) + > pre.period <- c(1, 40) + > post.period <- c(41, 52) + > impact <- CausalImpact(data, pre.period, post.period) + Error in is.element(letter, c("B", "M", "K")) : + unused argument (c("B", "M", "K")) + Calls: CausalImpact ... InterpretSummaryTable -> IdentifyNumberAbbreviation Execution halted ``` * checking tests ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. + Running ‘CausalImpact_import_test.R’ + Running the tests in ‘tests/CausalImpact_import_test.R’ failed. Complete output: - > library(testthat) - > library(cfda) - Loading required package: fda - Loading required package: splines - Loading required package: fds - Loading required package: rainbow - Loading required package: MASS - ... - 7. └─cfda:::hist.njump(njump) - 8. └─ggplot2:::`+.gg`(...) - 9. └─ggplot2:::add_ggplot(e1, e2, e2name) - 10. ├─ggplot2::ggplot_add(object, p, objectname) - 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 2 | WARN 1 | SKIP 12 | PASS 351 ] - Error: Test failures + > # Copyright 2014-2022 Google Inc. All rights reserved. + > # + > # Licensed under the Apache License, Version 2.0 (the "License"); + > # you may not use this file except in compliance with the License. + > # You may obtain a copy of the License at + > # + > # http://www.apache.org/licenses/LICENSE-2.0 + ... + > y <- 1.2 * x1 + rnorm(100) + > y[71:100] <- y[71:100] + 10 + > data <- cbind(y, x1) + > + > # Test that a `CausalImpact` object is created when the package is not loaded. + > impact <- CausalImpact::CausalImpact(data, c(1, 70), c(71, 100)) + Error in is.element(letter, c("B", "M", "K")) : + unused argument (c("B", "M", "K")) + Calls: ... InterpretSummaryTable -> IdentifyNumberAbbreviation Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘cfda.Rmd’ + when running code in ‘CausalImpact.Rmd’ ... - > head(nJump) - 1 2 3 4 5 6 - 17 9 3 13 10 13 + > pre.period <- c(1, 70) - > hist(nJump) + > post.period <- c(71, 100) - When sourcing ‘cfda.R’: - Error: argument is of length zero + > impact <- CausalImpact(data, pre.period, post.period) + + When sourcing ‘CausalImpact.R’: + Error: unused argument (c("B", "M", "K")) Execution halted - ‘cfda.Rmd’ using ‘UTF-8’... failed + ‘CausalImpact.Rmd’ using ‘UTF-8’... failed + ``` + +* checking whether package ‘CausalImpact’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(letter, c("B", ': unused argument (c("B", "M", "K")) + See ‘/tmp/workdir/CausalImpact/new/CausalImpact.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + IdentifyNumberAbbreviation: possible error in is.element(letter, c("B", + "M", "K")): unused argument (c("B", "M", "K")) ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘cfda.Rmd’ using rmarkdown + --- re-building ‘CausalImpact.Rmd’ using rmarkdown ``` -# cheem +# celltrackR
-* Version: 0.4.0.0 -* GitHub: https://github.com/nspyrison/cheem -* Source code: https://github.com/cran/cheem -* Date/Publication: 2023-11-08 21:30:02 UTC -* Number of recursive dependencies: 153 +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/celltrackR +* Date/Publication: 2024-08-26 12:20:02 UTC +* Number of recursive dependencies: 94 -Run `revdepcheck::cloud_details(, "cheem")` for more info +Run `revdepcheck::cloud_details(, "celltrackR")` for more info
## Newly broken -* checking tests ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(cheem) - -------------------------------------------------------- - cheem --- version 0.4.0.0 - Please share bugs, suggestions, and feature requests at: - https://github.com/nspyrison/cheem/issues/ - -------------------------------------------------------- - ... + Error(s) in re-building vignettes: + --- re-building ‘QC.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘clustering.Rmd’ + ... + + squareDisplacement, maxDisplacement, outreachRatio), method = "MDS", + + labels = r .... [TRUNCATED] + + > trackFeatureMap(all.tracks, c(speed, meanTurningAngle, + + squareDisplacement, maxDisplacement, outreachRatio), method = "UMAP", + + labels = .... [TRUNCATED] + + ... + When sourcing ‘data-QC.R’: + Error: unused argument (names(TCells)) + Execution halted + + ‘QC.Rmd’ using ‘UTF-8’... OK + ‘ana-methods.Rmd’ using ‘UTF-8’... OK + ‘clustering.Rmd’ using ‘UTF-8’... failed + ‘data-QC.Rmd’ using ‘UTF-8’... failed + ‘reading-converting-data.Rmd’ using ‘UTF-8’... OK + ‘simulation.Rmd’ using ‘UTF-8’... OK + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + doc 3.6Mb + ``` + +# cellularautomata + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/cellularautomata +* Date/Publication: 2024-11-20 19:10:06 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "cellularautomata")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic-usage.Rmd’ + ... + + > plot(ca(45)) + + > plot(ca(195)) + + > plot(ca(30, ncols = 20, steps = 30), animate = TRUE) + + When sourcing ‘basic-usage.R’: + Error: argument "theme" is missing, with no default + Execution halted + + ‘basic-usage.Rmd’ using ‘UTF-8’... failed + ``` + +# CensMFM + +
+ +* Version: 3.1 +* GitHub: NA +* Source code: https://github.com/cran/CensMFM +* Date/Publication: 2024-05-14 07:33:36 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "CensMFM")` for more info + +
+ +## Newly broken + +* checking whether package ‘CensMFM’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(NA, y)': unused argument (y) + See ‘/tmp/workdir/CensMFM/new/CensMFM.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + fit.EM.MSNC: possible error in is.element(NA, y): unused argument (y) + ``` + +# CFO + +
+ +* Version: 2.2.0 +* GitHub: NA +* Source code: https://github.com/cran/CFO +* Date/Publication: 2024-11-15 12:00:09 UTC +* Number of recursive dependencies: 34 + +Run `revdepcheck::cloud_details(, "CFO")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CFO-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CFO.oc + > ### Title: Generate operating characteristics of phase I trials single-drug + > ### trials in multiple simulations + > ### Aliases: CFO.oc + > + > ### ** Examples + > + ... + Percentage of patients allocated to the MTD: 0.340 + Percentage of selecting a dose above the MTD: 0.200 + Percentage of allocating patients at dose levels above the MTD: 0.240 + Percentage of the patients suffering DLT: 0.227 + Average trial duration: 17.9 + > plot(faCFOoc) + Error in is.element(strpattern, c("none", names(objectPlot))) : + unused argument (c("none", names(objectPlot))) + Calls: plot -> plot.cfo + Execution halted + ``` + +* checking whether package ‘CFO’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(strpattern, ': unused argument (c("none", names(objectPlot))) + See ‘/tmp/workdir/CFO/new/CFO.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + plot.cfo: possible error in is.element(strpattern, c("none", + names(objectPlot))): unused argument (c("none", names(objectPlot))) + ``` + +# changepoint.geo + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/grundy95/changepoint.geo +* Source code: https://github.com/cran/changepoint.geo +* Date/Publication: 2023-09-23 22:50:09 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "changepoint.geo")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(changepoint.geo) + Loading required package: changepoint + Loading required package: zoo + + Attaching package: 'zoo' + + ... + Angle Changepoints : 60 90 + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 152 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-geomcp.R:74:2'): (code run outside of `test_that()`) ─────────── + Error in `is.element(NA, data[[d]])`: unused argument (data[[d]]) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 152 ] + Error: Test failures + Execution halted + ``` + +# cheem + +
+ +* Version: 0.4.0.0 +* GitHub: https://github.com/nspyrison/cheem +* Source code: https://github.com/cran/cheem +* Date/Publication: 2023-11-08 21:30:02 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "cheem")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cheem) + -------------------------------------------------------- + cheem --- version 0.4.0.0 + Please share bugs, suggestions, and feature requests at: + https://github.com/nspyrison/cheem/issues/ + -------------------------------------------------------- + ... 13. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) 14. │ │ └─base::stopifnot(is.list(x), is.list(val)) 15. │ └─x %||% list() @@ -3435,11 +2781,11 @@ Run `revdepcheck::cloud_details(, "cheem")` for more info
-* Version: 0.75 +* Version: 0.76 * GitHub: NA * Source code: https://github.com/cran/chillR -* Date/Publication: 2023-11-27 22:20:02 UTC -* Number of recursive dependencies: 138 +* Date/Publication: 2024-11-14 09:40:02 UTC +* Number of recursive dependencies: 137 Run `revdepcheck::cloud_details(, "chillR")` for more info @@ -3452,26 +2798,38 @@ Run `revdepcheck::cloud_details(, "chillR")` for more info Running examples in ‘chillR-Ex.R’ failed The error most likely occurred in: - > ### Name: plot_scenarios - > ### Title: Plot historic and future scenarios for climate-related metrics - > ### ('ggplot2' version) - > ### Aliases: plot_scenarios + > ### Name: interpolate_gaps_hourly + > ### Title: Interpolate gaps in hourly temperature records + > ### Aliases: interpolate_gaps_hourly + > ### Keywords: utility > > ### ** Examples > - ... - > - > # Plot the climate scenarios > - > plot_scenarios(climate_scenario_list, metric = 'Chill_Portions', - + add_historic = TRUE, size = 2, shape = 3, color = 'blue', - + outlier_shape = 12, historic_color = 'skyblue', - + group_by = c("Year", "Scenario")) - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + > + > Winters_gaps<-make_JDay(Winters_hours_gaps[1:2000,]) + Error in is.element(c("Day", "Month", "Year"), colnames(dateframe)) : + unused argument (colnames(dateframe)) + Calls: make_JDay Execution halted ``` +* checking whether package ‘chillR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(c("Day", "Month", ': unused argument (colnames(dateframe)) + See ‘/tmp/workdir/chillR/new/chillR.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + make_JDay: possible error in is.element(c("Day", "Month", "Year"), + colnames(dateframe)): unused argument (colnames(dateframe)) + ``` + # chronicle
@@ -3480,7 +2838,7 @@ Run `revdepcheck::cloud_details(, "chillR")` for more info * GitHub: NA * Source code: https://github.com/cran/chronicle * Date/Publication: 2021-06-25 05:00:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "chronicle")` for more info @@ -3553,17 +2911,17 @@ Run `revdepcheck::cloud_details(, "chronicle")` for more info All declared Imports should be used. ``` -# CINNA +# cjoint
-* Version: 1.2.2 +* Version: 2.1.1 * GitHub: NA -* Source code: https://github.com/cran/CINNA -* Date/Publication: 2023-08-08 16:40:02 UTC -* Number of recursive dependencies: 140 +* Source code: https://github.com/cran/cjoint +* Date/Publication: 2023-08-22 07:50:07 UTC +* Number of recursive dependencies: 85 -Run `revdepcheck::cloud_details(, "CINNA")` for more info +Run `revdepcheck::cloud_details(, "cjoint")` for more info
@@ -3571,199 +2929,151 @@ Run `revdepcheck::cloud_details(, "CINNA")` for more info * checking examples ... ERROR ``` - Running examples in ‘CINNA-Ex.R’ failed + Running examples in ‘cjoint-Ex.R’ failed The error most likely occurred in: - > ### Name: pca_centralities - > ### Title: PCA Centrality Measures - > ### Aliases: pca_centralities + > ### Name: japan2014conjoint + > ### Title: Japan 2014 Conjoint Experiment Dataset from Horiuchi et. al. + > ### (2014) + > ### Aliases: japan2014conjoint + > ### Keywords: datasets > > ### ** Examples - > - > # Create a data frame with multiple observations ... - 13. │ └─e1 %+% e2 - 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. │ ├─ggplot2::ggplot_add(object, p, objectname) - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) + > # Run AMCE estimator using all attributes and uniform design + > results <- amce(selected ~ `Consumption tax` + `Employment` + `Monetary and fiscal policy` + + + `Economic growth strategy` + `Nuclear power` + `TPP` + + + `Collective self-defense` + `Constitutional revision` + + + `National assembly seat reduction`, data=japan2014conjoint, cluster=TRUE, + + respondent.id="respondentIndex", weights="wgt", design="uniform") + Error in is.element(full_terms, orig_effects) : + unused argument (orig_effects) + Calls: amce Execution halted ``` -* checking running R code from vignettes ... ERROR +* checking tests ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘CINNA.Rmd’ - ... - > calc_cent <- calculate_centralities(zachary, include = pr_cent[1:10]) - - > pca_centralities(calc_cent) - - When sourcing ‘CINNA.R’: - Error: ℹ In index: 1. - ℹ With name: contrib. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - Execution halted - - ‘CINNA.Rmd’ using ‘UTF-8’... failed + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cjoint) + Loading required package: sandwich + Loading required package: lmtest + Loading required package: zoo + + Attaching package: 'zoo' + ... + 2. └─cjoint::amce(...) at test-main.r:16:3 + ── Error ('test-plot.R:3:1'): (code run outside of `test_that()`) ────────────── + Error in `is.element(full_terms, orig_effects)`: unused argument (orig_effects) + Backtrace: + ▆ + 1. └─cjoint::amce(...) at test-plot.R:3:1 + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘cjoint’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘CINNA.Rmd’ using rmarkdown - - Quitting from lines 231-234 [unnamed-chunk-11] (CINNA.Rmd) - Error: processing vignette 'CINNA.Rmd' failed with diagnostics: - ℹ In index: 1. - ℹ With name: contrib. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - --- failed re-building ‘CINNA.Rmd’ - - SUMMARY: processing the following file failed: - ‘CINNA.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element(full_terms, ': unused argument (orig_effects) + Note: possible error in 'is.element(unique_vars, ': unused argument (respondent_vars) + Note: possible error in 'is.element(y, respondent_vars)': unused argument (respondent_vars) + Note: possible error in 'is.element(all_prof, ': unused argument (all_run_vars) + Note: possible error in 'is.element(substrings, ': unused argument (y) + Note: possible error in 'is.element(all_depends, ': unused argument (profile_effects[i]) + Note: possible error in 'is.element(substrings_d, ': unused argument (substrings) + Note: possible error in 'is.element(all_depends, ': unused argument (resp_effects[i]) + Note: possible error in 'is.element(respondent_vars, ': unused argument (substrings) + ... + Note: possible error in 'is.element(facet.names, ': unused argument (amce_obj$respondent.varying) + Note: possible error in 'is.element(raw_attributes, ': unused argument (attr_remove) + Note: possible error in 'is.element(subs, names(amce_obj$estimates))': unused argument (names(amce_obj$estimates)) + Note: possible error in 'is.element(facet.name, ': unused argument (names(amce_obj$estimates)) + Note: possible error in 'is.element(all.vars, ': unused argument (this.var) + Note: possible error in 'is.element(subs, all_prof)': unused argument (all_prof) + See ‘/tmp/workdir/cjoint/new/cjoint.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + amce: possible error in is.element(full_terms, orig_effects): unused + argument (orig_effects) + amce: possible error in is.element(unique_vars, respondent_vars): + unused argument (respondent_vars) + amce : : possible error in is.element(y, respondent_vars): + unused argument (respondent_vars) + amce: possible error in is.element(all_prof, all_run_vars): unused + argument (all_run_vars) + amce : : possible error in is.element(substrings, y): unused + argument (y) + ... + plot.amce : : possible error in is.element(subs, + names(amce_obj$estimates)): unused argument + (names(amce_obj$estimates)) + plot.amce: possible error in is.element(facet.name, + names(amce_obj$estimates)): unused argument + (names(amce_obj$estimates)) + print.summary.amce: possible error in is.element(all.vars, this.var): + unused argument (this.var) + summary.amce : : possible error in is.element(subs, + all_prof): unused argument (all_prof) ``` ## In both -* checking dependencies in R code ... NOTE +* checking data for non-ASCII characters ... NOTE ``` - Namespaces in Imports field not imported from: - ‘circlize’ ‘utils’ - All declared Imports should be used. + Note: found 29 marked UTF-8 strings ``` -# circhelp +# clickstream
-* Version: 1.1 -* GitHub: https://github.com/achetverikov/circhelp -* Source code: https://github.com/cran/circhelp -* Date/Publication: 2024-07-04 17:10:02 UTC -* Number of recursive dependencies: 106 +* Version: 1.3.3 +* GitHub: NA +* Source code: https://github.com/cran/clickstream +* Date/Publication: 2023-09-27 14:50:02 UTC +* Number of recursive dependencies: 43 -Run `revdepcheck::cloud_details(, "circhelp")` for more info +Run `revdepcheck::cloud_details(, "clickstream")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘circhelp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: remove_cardinal_biases - > ### Title: Remove cardinal biases - > ### Aliases: remove_cardinal_biases - > - > ### ** Examples - > - > - > # Data in orientation domain from Pascucci et al. (2019, PLOS Bio), - > # https://doi.org/10.5281/zenodo.2544946 - > - > ex_data <- Pascucci_et_al_2019_data[observer == 4, ] - > remove_cardinal_biases(ex_data$err, ex_data$orientation, plots = "show") - Error in as.unit(value) : object is not coercible to a unit - Calls: remove_cardinal_biases ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘cardinal_biases.Rmd’ - ... - + 90)) + .... [TRUNCATED] - - > ex_subj_data <- data[observer == 4, ] - - > res <- remove_cardinal_biases(ex_subj_data$err, ex_subj_data$orientation, - + plots = "show") - - When sourcing ‘cardinal_biases.R’: - Error: object is not coercible to a unit - Execution halted - - ‘cardinal_biases.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘clickstream’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘cardinal_biases.Rmd’ using rmarkdown + Found the following significant warnings: + Warning: replacing previous import ‘arules::is.element’ by ‘ggplot2::is.element’ when loading ‘clickstream’ + See ‘/tmp/workdir/clickstream/new/clickstream.Rcheck/00install.out’ for details. ``` -# clifro +# clinDataReview
-* Version: 3.2-5 -* GitHub: https://github.com/ropensci/clifro -* Source code: https://github.com/cran/clifro -* Date/Publication: 2021-05-24 05:50:02 UTC -* Number of recursive dependencies: 84 +* Version: 1.6.1 +* GitHub: https://github.com/openanalytics/clinDataReview +* Source code: https://github.com/cran/clinDataReview +* Date/Publication: 2024-06-18 09:10:05 UTC +* Number of recursive dependencies: 120 -Run `revdepcheck::cloud_details(, "clifro")` for more info +Run `revdepcheck::cloud_details(, "clinDataReview")` for more info
## Newly broken -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Complete output: - > library(testthat) - > library(clifro) - > - > test_check("clifro") - [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] - - ... - • On CRAN (4): 'test-cf_find_station.R:4:3', 'test-cf_last_query.R:4:3', - 'test-cf_query.R:4:3', 'test-cf_station.R:4:3' - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-windrose.R:15:3'): windrose ────────────────────────────────── - tt$labels inherits from `'NULL'` not `'character'`. - - [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -# clinDataReview - -
- -* Version: 1.6.1 -* GitHub: https://github.com/openanalytics/clinDataReview -* Source code: https://github.com/cran/clinDataReview -* Date/Publication: 2024-06-18 09:10:05 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "clinDataReview")` for more info - -
- -## Newly broken - -* checking examples ... ERROR +* checking examples ... ERROR ``` Running examples in ‘clinDataReview-Ex.R’ failed The error most likely occurred in: @@ -3783,8 +3093,8 @@ Run `revdepcheck::cloud_details(, "clinDataReview")` for more info + aesLineVar = list(group = "USUBJID", color = "TRTP"), + labelVars = labelVars + ) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: scatterplotClinData ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Error in pm[[2]] : subscript out of bounds + Calls: scatterplotClinData -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` @@ -3798,17 +3108,17 @@ Run `revdepcheck::cloud_details(, "clinDataReview")` for more info > > test_check("clinDataReview") adding: report.html (deflated 63%) - adding: report_dependencies169f5c7b66d/ (stored 0%) - adding: report_dependencies169f5c7b66d/file169f105f2e2e.html (deflated 8%) + adding: report_dependencies16a96c1c4532/ (stored 0%) + adding: report_dependencies16a96c1c4532/file16a9248230f.html (deflated 8%) ... - 11. ├─base::withCallingHandlers(...) - 12. └─ggplot2:::`+.gg`(gg, do.call(layerFunction, argsGeom)) - 13. └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. ├─ggplot2::ggplot_add(object, p, objectname) - 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + Backtrace: + ▆ + 1. └─clinDataReview::scatterplotClinData(...) at test_scatterplotClinData.R:1001:3 + 2. ├─plotly::ggplotly(p = gg, width = width, height = height, tooltip = if (!is.null(hoverVars)) "text") + 3. └─plotly:::ggplotly.ggplot(...) + 4. └─plotly::gg2list(...) - [ FAIL 35 | WARN 0 | SKIP 31 | PASS 453 ] + [ FAIL 31 | WARN 0 | SKIP 31 | PASS 466 ] Error: Test failures Execution halted ``` @@ -3824,7 +3134,7 @@ Run `revdepcheck::cloud_details(, "clinDataReview")` for more info Quitting from lines 167-208 [timeProfiles] (clinDataReview-dataVisualization.Rmd) Error: processing vignette 'clinDataReview-dataVisualization.Rmd' failed with diagnostics: - argument is of length zero + subscript out of bounds ... --- failed re-building ‘clinDataReview-dataVisualization.Rmd’ @@ -3847,6 +3157,47 @@ Run `revdepcheck::cloud_details(, "clinDataReview")` for more info doc 4.3Mb ``` +# clinDR + +
+ +* Version: 2.4.1 +* GitHub: NA +* Source code: https://github.com/cran/clinDR +* Date/Publication: 2023-08-09 04:20:05 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "clinDR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clinDR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: "Extract.emaxsim" + > ### Title: Extract a simulation from the output of emaxsim + > ### Aliases: [.emaxsim + > ### Keywords: nonlinear + > + > ### ** Examples + > + ... + > meanlev<-emaxfun(doselev,pop) + > + > ###FixedMean is specialized constructor function for emaxsim + > gen.parm<-FixedMean(n,doselev,meanlev,sdy) + > + > D1 <- emaxsim(nsim=2,gen.parm,modType=3,nproc=1) + Error in is.element(x, c("emax", "quadratic", "exponential")) : + unused argument (c("emax", "quadratic", "exponential")) + Calls: emaxsim -> Mods -> fullMod -> modCount -> lapply -> FUN + Execution halted + ``` + # clinUtils
@@ -3855,7 +3206,7 @@ Run `revdepcheck::cloud_details(, "clinDataReview")` for more info * GitHub: https://github.com/openanalytics/clinUtils * Source code: https://github.com/cran/clinUtils * Date/Publication: 2024-05-17 14:50:06 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 110 Run `revdepcheck::cloud_details(, "clinUtils")` for more info @@ -3918,74 +3269,40 @@ Run `revdepcheck::cloud_details(, "clinUtils")` for more info doc 6.5Mb ``` -# cloneRate +# CLONETv2
-* Version: 0.2.3 -* GitHub: https://github.com/bdj34/cloneRate -* Source code: https://github.com/cran/cloneRate -* Date/Publication: 2023-09-22 15:40:02 UTC -* Number of recursive dependencies: 121 +* Version: 2.2.1 +* GitHub: NA +* Source code: https://github.com/cran/CLONETv2 +* Date/Publication: 2021-10-13 20:40:14 UTC +* Number of recursive dependencies: 34 -Run `revdepcheck::cloud_details(, "cloneRate")` for more info +Run `revdepcheck::cloud_details(, "CLONETv2")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘cloneRate-dataAnalysis.Rmd’ - ... - - > fitColor <- colorPal[6] - - > ggplot(PD9478_long, aes(x = Age, y = VAF)) + theme_bw() + - + coord_cartesian(xlim = c(min(x), max(x)), ylim = c(-0.01, - + 0.52), expand .... [TRUNCATED] - - When sourcing ‘cloneRate-dataAnalysis.R’: - Error: `expand` must be a logical vector, not the number 0. - Execution halted - - ‘cloneRate-dataAnalysis.Rmd’ using ‘UTF-8’... failed - ‘cloneRate-simulate.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘cloneRate-dataAnalysis.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 47.4Mb - sub-directories of 1Mb or more: - doc 1.0Mb - libs 45.2Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE +* checking whether package ‘CLONETv2’ can be installed ... WARNING ``` - GNU make is a SystemRequirements. + Found the following significant warnings: + Warning: replacing previous import ‘arules::is.element’ by ‘ggplot2::is.element’ when loading ‘CLONETv2’ + See ‘/tmp/workdir/CLONETv2/new/CLONETv2.Rcheck/00install.out’ for details. ``` -# clustEff +# ClusROC
-* Version: 0.3.1 -* GitHub: NA -* Source code: https://github.com/cran/clustEff -* Date/Publication: 2024-01-23 08:52:55 UTC -* Number of recursive dependencies: 125 +* Version: 1.0.2 +* GitHub: https://github.com/toduckhanh/ClusROC +* Source code: https://github.com/cran/ClusROC +* Date/Publication: 2022-11-17 15:00:02 UTC +* Number of recursive dependencies: 113 -Run `revdepcheck::cloud_details(, "clustEff")` for more info +Run `revdepcheck::cloud_details(, "ClusROC")` for more info
@@ -3993,40 +3310,97 @@ Run `revdepcheck::cloud_details(, "clustEff")` for more info * checking examples ... ERROR ``` - Running examples in ‘clustEff-Ex.R’ failed + Running examples in ‘ClusROC-Ex.R’ failed The error most likely occurred in: - > ### Name: clustEff-package - > ### Title: Clusters of effects curves - > ### Aliases: clustEff-package - > ### Keywords: package + > ### Name: clus_lme + > ### Title: Linear Mixed-Effects Models for a continuous diagnostic test or + > ### a biomarker (or a classifier). + > ### Aliases: clus_lme > > ### ** Examples > ... - 13. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) - 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. │ ├─ggplot2::ggplot_add(object, p, objectname) - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) + 3 1 -0.5174383 2 0.36460260 1 + 4 2 2.0831761 1 2.55955171 0 + 5 2 2.5393980 2 -0.57296509 1 + 6 2 -1.6553751 1 0.06360181 0 + > ## A model with two covariate + > out1 <- clus_lme(fixed_formula = Y ~ X1 + X2, name_class = "D", + + name_clust = "id_Clus", data = data_3class) + Error in is.element(name_test, names_vars) : unused argument (names_vars) + Calls: clus_lme -> check_fixed_formula Execution halted ``` -# ClustImpute +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ClusROC) + Loading required package: nlme + Loading required package: Rcpp + > library(rgl) + > + > options(rgl.useNULL = TRUE) + ... + without newdata ── + Error in `is.element(name_test, names_vars)`: unused argument (names_vars) + Backtrace: + ▆ + 1. └─ClusROC::clus_lme(...) at test-clus_vus.R:31:3 + 2. └─ClusROC:::check_fixed_formula(fixed_formula, call, names_vars) + + [ FAIL 31 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +* checking whether package ‘ClusROC’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(name_class, ': unused argument (names_vars) + Note: possible error in 'is.element(name_clust, ': unused argument (names_vars) + Note: possible error in 'is.element(name_clust, ': unused argument (c(name_test, names_covars, name_class)) + Note: possible error in 'is.element(name_test, ': unused argument (names_vars) + Note: possible error in 'is.element(names_covars, ': unused argument (names_vars) + Note: possible error in 'is.element(x, ok_method)': unused argument (ok_method) + See ‘/tmp/workdir/ClusROC/new/ClusROC.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + check_class: possible error in is.element(name_class, names_vars): + unused argument (names_vars) + check_clust: possible error in is.element(name_clust, names_vars): + unused argument (names_vars) + check_clust: possible error in is.element(name_clust, c(name_test, + names_covars, name_class)): unused argument (c(name_test, + names_covars, name_class)) + check_fixed_formula: possible error in is.element(name_test, + names_vars): unused argument (names_vars) + check_fixed_formula: possible error in is.element(names_covars, + names_vars): unused argument (names_vars) + get_method_opt_thres3 : : possible error in is.element(x, + ok_method): unused argument (ok_method) + ``` + +# clustcurv
-* Version: 0.2.4 -* GitHub: NA -* Source code: https://github.com/cran/ClustImpute -* Date/Publication: 2021-05-31 07:40:11 UTC -* Number of recursive dependencies: 121 +* Version: 2.0.2 +* GitHub: https://github.com/noramvillanueva/clustcurv +* Source code: https://github.com/cran/clustcurv +* Date/Publication: 2024-10-25 08:20:07 UTC +* Number of recursive dependencies: 109 -Run `revdepcheck::cloud_details(, "ClustImpute")` for more info +Run `revdepcheck::cloud_details(, "clustcurv")` for more info
@@ -4035,61 +3409,97 @@ Run `revdepcheck::cloud_details(, "ClustImpute")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Example_on_simulated_data.Rmd’ + when running code in ‘clustcurv.Rmd’ ... - > dat4plot$true_clust_fct <- factor(true_clust) - - > p_base <- ggplot(dat4plot, aes(x = x, y = y, color = true_clust_fct)) + - + geom_point() + > autoplot(res, groups_by_colour = FALSE, interactive = TRUE) + Warning: `aes_string()` was deprecated in ggplot2 3.0.0. + ℹ Please use tidy evaluation idioms with `aes()`. + ℹ See also `vignette("ggplot2-in-packages")` for more information. + ℹ The deprecated feature was likely used in the ggfortify package. + Please report the issue at . - > ggExtra::ggMarginal(p_base, groupColour = TRUE, groupFill = TRUE) - - When sourcing ‘Example_on_simulated_data.R’: - Error: argument is of length zero + When sourcing ‘clustcurv.R’: + Error: subscript out of bounds Execution halted - ‘Example_on_simulated_data.Rmd’ using ‘UTF-8’... failed - ‘description_of_algorithm.Rnw’ using ‘UTF-8’... OK + ‘clustcurv.Rmd’ using ‘UTF-8’... failed ``` -## In both - * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘Example_on_simulated_data.Rmd’ using rmarkdown - - Quitting from lines 49-53 [unnamed-chunk-3] (Example_on_simulated_data.Rmd) - Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Example_on_simulated_data.Rmd’ + ... + --- re-building ‘clustcurv.Rmd’ using rmarkdown - --- re-building ‘description_of_algorithm.Rnw’ using Sweave - Error: processing vignette 'description_of_algorithm.Rnw' failed with diagnostics: - ... - l.6 \usepackage - {Sweave}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘description_of_algorithm.Rnw’ + Quitting from lines 93-94 [unnamed-chunk-5] (clustcurv.Rmd) + Error: processing vignette 'clustcurv.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘clustcurv.Rmd’ - SUMMARY: processing the following files failed: - ‘Example_on_simulated_data.Rmd’ ‘description_of_algorithm.Rnw’ + SUMMARY: processing the following file failed: + ‘clustcurv.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# cmstatr +# clustMD
-* Version: 0.9.3 -* GitHub: https://github.com/cmstatr/cmstatr -* Source code: https://github.com/cran/cmstatr -* Date/Publication: 2024-03-14 14:30:02 UTC -* Number of recursive dependencies: 87 +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/clustMD +* Date/Publication: 2017-05-08 17:19:20 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "clustMD")` for more info + +
+ +## Newly broken + +* checking whether package ‘clustMD’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(model, c("EII", ': unused argument (c("EII", "VII", "EEI", "VEI", "EVI", "VVI", "BD")) + Note: possible error in 'is.element(covModel, ': unused argument (resParallel$models) + Note: possible error in 'is.element(nClus, resParallel$G)': unused argument (resParallel$G) + See ‘/tmp/workdir/clustMD/new/clustMD.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + M.step: possible error in is.element(model, c("EII", "VII", "EEI", + "VEI", "EVI", "VVI", "BD")): unused argument (c("EII", "VII", "EEI", + "VEI", "EVI", "VVI", "BD")) + getOutput_clustMDparallel: possible error in is.element(covModel, + resParallel$models): unused argument (resParallel$models) + getOutput_clustMDparallel: possible error in is.element(nClus, + resParallel$G): unused argument (resParallel$G) + ``` + +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \& + ``` + +# cnmap + +
-Run `revdepcheck::cloud_details(, "cmstatr")` for more info +* Version: 0.1.0 +* GitHub: https://github.com/PanfengZhang/cnmap +* Source code: https://github.com/cran/cnmap +* Date/Publication: 2024-04-02 12:42:06 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "cnmap")` for more info
@@ -4097,84 +3507,59 @@ Run `revdepcheck::cloud_details(, "cmstatr")` for more info * checking examples ... ERROR ``` - Running examples in ‘cmstatr-Ex.R’ failed + Running examples in ‘cnmap-Ex.R’ failed The error most likely occurred in: - > ### Name: nested_data_plot - > ### Title: Create a plot of nested sources of variation - > ### Aliases: nested_data_plot + > ### Name: getMap + > ### Title: China Map Data from AutoNavi Map + > ### Aliases: getMap > > ### ** Examples > - > library(dplyr) - ... - - intersect, setdiff, setequal, union - - > carbon.fabric.2 %>% - + filter(test == "WT" & condition == "RTD") %>% - + nested_data_plot(strength, - + groups = c(batch, panel)) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > library(cnmap) + > + > map1 <- getMap(code = "110000") # get the map data of Beijing City + Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir, : + package tibble not available: install first? + Calls: getMap ... st_read -> st_read.character -> process_cpl_read_ogr Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(cmstatr) - > - > test_check("cmstatr") - Starting 2 test processes - [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] - ... - 6. └─cmstatr:::draw_vert_lines_to_labels(g, elm_list, vline_args) - 7. └─ggplot2:::`+.gg`(...) - 8. └─ggplot2:::add_ggplot(e1, e2, e2name) - 9. ├─ggplot2::ggplot_add(object, p, objectname) - 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] - Error: Test failures - Execution halted - ``` - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘cmstatr_Graphing.Rmd’ + when running code in ‘Introduction.Rmd’ ... - + by = "condition") %>% inner_join(a_basis_pooled_results, - + by = "condition") .... [TRUNCATED] + > library(sf) + Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE - > carbon.fabric.2 %>% mutate(panel = as.character(panel)) %>% - + filter(test == "WT") %>% nested_data_plot(strength, groups = c(batch, - + pane .... [TRUNCATED] + > library(cnmap) - When sourcing ‘cmstatr_Graphing.R’: - Error: argument is of length zero + > map1 <- getMap(name = "中国") + + When sourcing ‘Introduction.R’: + Error: package tibble not available: install first? Execution halted - ‘adktest.Rmd’ using ‘UTF-8’... OK - ‘cmstatr_Graphing.Rmd’ using ‘UTF-8’... failed - ‘cmstatr_Tutorial.Rmd’ using ‘UTF-8’... OK - ‘cmstatr_Validation.Rmd’ using ‘UTF-8’... OK - ‘hk_ext.Rmd’ using ‘UTF-8’... OK + ‘Introduction.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘adktest.Rmd’ using rmarkdown - --- finished re-building ‘adktest.Rmd’ + ... + --- re-building ‘Introduction.Rmd’ using rmarkdown + + Quitting from lines 29-35 [unnamed-chunk-3] (Introduction.Rmd) + Error: processing vignette 'Introduction.Rmd' failed with diagnostics: + package tibble not available: install first? + --- failed re-building ‘Introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘Introduction.Rmd’ - --- re-building ‘cmstatr_Graphing.Rmd’ using rmarkdown + Error: Vignette re-building failed. + Execution halted ``` # codaredistlm @@ -4185,7 +3570,7 @@ Run `revdepcheck::cloud_details(, "cmstatr")` for more info * GitHub: https://github.com/tystan/codaredistlm * Source code: https://github.com/cran/codaredistlm * Date/Publication: 2022-12-22 19:50:06 UTC -* Number of recursive dependencies: 67 +* Number of recursive dependencies: 66 Run `revdepcheck::cloud_details(, "codaredistlm")` for more info @@ -4218,45 +3603,27 @@ Run `revdepcheck::cloud_details(, "codaredistlm")` for more info --- ``` -# coefplot +# codez
-* Version: 1.2.8 +* Version: 1.0.0 * GitHub: NA -* Source code: https://github.com/cran/coefplot -* Date/Publication: 2022-01-14 09:42:47 UTC -* Number of recursive dependencies: 110 +* Source code: https://github.com/cran/codez +* Date/Publication: 2022-09-23 15:10:02 UTC +* Number of recursive dependencies: 136 -Run `revdepcheck::cloud_details(, "coefplot")` for more info +Run `revdepcheck::cloud_details(, "codez")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘codez’ can be installed ... WARNING ``` - Running examples in ‘coefplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: buildModelCI - > ### Title: buildModelCI - > ### Aliases: buildModelCI - > - > ### ** Examples - > - > - ... - cut.C 327.4816 model1 - cut.Q -574.8626 model1 - cut.L 1187.6004 model1 - carat 7843.1229 model1 - (Intercept) -2732.2382 model1 - > coefplot(model1) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::is.scale’ by ‘greybox::is.scale’ when loading ‘codez’ + See ‘/tmp/workdir/codez/new/codez.Rcheck/00install.out’ for details. ``` # CohortPlat @@ -4337,17 +3704,17 @@ Run `revdepcheck::cloud_details(, "CohortPlat")` for more info Execution halted ``` -# complmrob +# colorrepel
-* Version: 0.7.0 -* GitHub: https://github.com/dakep/complmrob -* Source code: https://github.com/cran/complmrob -* Date/Publication: 2019-09-17 18:10:02 UTC -* Number of recursive dependencies: 31 +* Version: 0.4.1 +* GitHub: https://github.com/raysinensis/color_repel +* Source code: https://github.com/cran/colorrepel +* Date/Publication: 2025-01-19 04:50:02 UTC +* Number of recursive dependencies: 89 -Run `revdepcheck::cloud_details(, "complmrob")` for more info +Run `revdepcheck::cloud_details(, "colorrepel")` for more info
@@ -4355,35 +3722,36 @@ Run `revdepcheck::cloud_details(, "complmrob")` for more info * checking examples ... ERROR ``` - Running examples in ‘complmrob-Ex.R’ failed + Running examples in ‘colorrepel-Ex.R’ failed The error most likely occurred in: - > ### Name: plot.complmrob - > ### Title: Diagnostic plots for the robust regression model with - > ### compositional covariates - > ### Aliases: plot.complmrob + > ### Name: ggplotly_background + > ### Title: Prepare ggplot object to ggplotly-compatible layer and image + > ### layer + > ### Aliases: ggplotly_background > > ### ** Examples > - > data <- data.frame(lifeExp = state.x77[, "Life Exp"], USArrests[ , -3]) - > mUSArr <- complmrob(lifeExp ~ ., data = data) - > plot(mUSArr) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > a <- ggplot2::ggplot(ggplot2::mpg, ggplot2::aes(displ, hwy)) + + + ggplot2::geom_point(ggplot2::aes(color = as.factor(cyl))) + > new_colors <- color_repel(a) + > b <- ggplotly_background(a, filename = NULL) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly_background -> -> ggplotly.ggplot -> gg2list Execution halted ``` -# conjoint +# CoreMicrobiomeR
-* Version: 1.41 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/conjoint -* Date/Publication: 2018-07-26 13:00:03 UTC -* Number of recursive dependencies: 53 +* Source code: https://github.com/cran/CoreMicrobiomeR +* Date/Publication: 2024-04-03 20:03:02 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "conjoint")` for more info +Run `revdepcheck::cloud_details(, "CoreMicrobiomeR")` for more info
@@ -4391,137 +3759,46 @@ Run `revdepcheck::cloud_details(, "conjoint")` for more info * checking examples ... ERROR ``` - Running examples in ‘conjoint-Ex.R’ failed + Running examples in ‘CoreMicrobiomeR-Ex.R’ failed The error most likely occurred in: - > ### Name: caSegmentation - > ### Title: Function caSegmentation divides respondents on clusters - > ### Aliases: caSegmentation - > ### Keywords: multivariate + > ### Name: group_bar_plots + > ### Title: Grouped Bar Plots Based on Sample Size + > ### Aliases: group_bar_plots > > ### ** Examples > + > #To run input data ... - Available components: - - [1] "cluster" "centers" "totss" "withinss" "tot.withinss" - [6] "betweenss" "size" "iter" "ifault" - > util<-as.data.frame(segments$util) - > set.seed(123) - > ggplot2::autoplot(kmeans(util,3),data=util,label=TRUE,label.size=4,frame=TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + + top_percentage = 10 # Adjust the percentage as needed for core/non-core OTUs + + ) + Warning encountered during diversity analysis:you have empty rows: their dissimilarities may be + meaningless in method “bray” + > #To run grouped bar plot function + > plot_group_bar <- group_bar_plots(core_1$final_otu_table_bef_filter, + + core_1$final_otu_aft_filter, 10) + Error in pm[[2]] : subscript out of bounds + Calls: group_bar_plots -> -> ggplotly.ggplot -> gg2list Execution halted ``` -# conquestr +# correlationfunnel
-* Version: 1.3.4 -* GitHub: NA -* Source code: https://github.com/cran/conquestr -* Date/Publication: 2024-07-24 06:00:01 UTC -* Number of recursive dependencies: 80 +* Version: 0.2.0 +* GitHub: https://github.com/business-science/correlationfunnel +* Source code: https://github.com/cran/correlationfunnel +* Date/Publication: 2020-06-09 04:40:03 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "conquestr")` for more info +Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘plotting.Rmd’ - ... - > myRout <- ConQuestRout() - no rout file provided, loading the example rout file instead - - > myPlot <- plotRout(myRout) - - > myPlot - - ... - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘data-cleaning-functions-in-conquestr.Rmd’ using ‘UTF-8’... OK - ‘generateResponses.Rmd’ using ‘UTF-8’... OK - ‘intro-to-conquestr.Rmd’ using ‘UTF-8’... OK - ‘itanal-in-conquestr.Rmd’ using ‘UTF-8’... OK - ‘plotting.Rmd’ using ‘UTF-8’... failed - ‘responseProbs.Rmd’ using ‘UTF-8’... OK - ‘test_item_review_sheet_markdown.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘data-cleaning-functions-in-conquestr.Rmd’ using rmarkdown - --- finished re-building ‘data-cleaning-functions-in-conquestr.Rmd’ - - --- re-building ‘generateResponses.Rmd’ using rmarkdown - ``` - -# CoreMicrobiomeR - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/CoreMicrobiomeR -* Date/Publication: 2024-04-03 20:03:02 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "CoreMicrobiomeR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CoreMicrobiomeR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: group_bar_plots - > ### Title: Grouped Bar Plots Based on Sample Size - > ### Aliases: group_bar_plots - > - > ### ** Examples - > - > #To run input data - ... - + top_percentage = 10 # Adjust the percentage as needed for core/non-core OTUs - + ) - Warning encountered during diversity analysis:you have empty rows: their dissimilarities may be - meaningless in method “bray” - > #To run grouped bar plot function - > plot_group_bar <- group_bar_plots(core_1$final_otu_table_bef_filter, - + core_1$final_otu_aft_filter, 10) - Error in pm[[2]] : subscript out of bounds - Calls: group_bar_plots -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# correlationfunnel - -
- -* Version: 0.2.0 -* GitHub: https://github.com/business-science/correlationfunnel -* Source code: https://github.com/cran/correlationfunnel -* Date/Publication: 2020-06-09 04:40:03 UTC -* Number of recursive dependencies: 116 - -Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info - -
- -## Newly broken - -* checking tests ... ERROR +* checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. @@ -4562,7 +3839,7 @@ Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info * GitHub: NA * Source code: https://github.com/cran/corrViz * Date/Publication: 2023-06-30 11:40:07 UTC -* Number of recursive dependencies: 140 +* Number of recursive dependencies: 128 Run `revdepcheck::cloud_details(, "corrViz")` for more info @@ -4641,125 +3918,6 @@ Run `revdepcheck::cloud_details(, "corrViz")` for more info doc 6.7Mb ``` -# corx - -
- -* Version: 1.0.7.2 -* GitHub: https://github.com/conig/corx -* Source code: https://github.com/cran/corx -* Date/Publication: 2023-06-16 04:10:02 UTC -* Number of recursive dependencies: 125 - -Run `revdepcheck::cloud_details(, "corx")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(corx) - > - > test_check("corx") - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 16. └─base::.handleSimpleError(...) - 17. └─purrr (local) h(simpleError(msg, call)) - 18. └─cli::cli_abort(...) - 19. └─rlang::abort(...) - - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] - Error: Test failures - Execution halted - ``` - -# cosinor2 - -
- -* Version: 0.2.1 -* GitHub: https://github.com/amutak/cosinor2 -* Source code: https://github.com/cran/cosinor2 -* Date/Publication: 2018-10-15 16:10:03 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "cosinor2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cosinor2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cosinor.PR - > ### Title: Percent Rhythm - > ### Aliases: cosinor.PR - > - > ### ** Examples - > - > fit.temperature<-cosinor.lm(Temperature~time(Time), period = 24, data = temperature_zg) - ... - 1 0.9838823 0.9680243 0 - > - > fit.november<-population.cosinor.lm(data = PANAS_november, time = PANAS_time, - + period = 7) - MESOR Amplitude Acrophase - 1 1.435419 0.2662682 -5.544496 - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: population.cosinor.lm ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘cosinor2.Rmd’ - ... - Loading required package: cosinor - - > fit.panas.cosinor <- population.cosinor.lm(data = PANAS_november, - + time = PANAS_time, period = 7) - MESOR Amplitude Acrophase - 1 1.435419 0.2662682 -5.544496 - - When sourcing ‘cosinor2.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘cosinor2.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘cosinor2.Rmd’ using rmarkdown - - Quitting from lines 47-48 [unnamed-chunk-2] (cosinor2.Rmd) - Error: processing vignette 'cosinor2.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘cosinor2.Rmd’ - - SUMMARY: processing the following file failed: - ‘cosinor2.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - # CoSMoS
@@ -4768,7 +3926,7 @@ Run `revdepcheck::cloud_details(, "cosinor2")` for more info * GitHub: https://github.com/TycheLab/CoSMoS * Source code: https://github.com/cran/CoSMoS * Date/Publication: 2021-05-29 23:20:08 UTC -* Number of recursive dependencies: 81 +* Number of recursive dependencies: 80 Run `revdepcheck::cloud_details(, "CoSMoS")` for more info @@ -4781,15 +3939,15 @@ Run `revdepcheck::cloud_details(, "CoSMoS")` for more info Errors in running code in vignettes: when running code in ‘vignette.Rmd’ ... - `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. - - > precip_ggamma <- analyzeTS(TS = precip, season = "month", - + dist = "ggamma", acsID = "weibull", lag.max = 12) - > reportTS(aTS = precip_ggamma, method = "dist") + theme_light() + > ggplot(data = dta, mapping = aes(x = time, y = value)) + + + geom_line() + facet_grid(facets = variable ~ ., scales = "free_y") + + + theme_li .... [TRUNCATED] When sourcing ‘vignette.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `rows` argument instead. Execution halted ‘vignette.Rmd’ using ‘UTF-8’... failed @@ -4809,7 +3967,7 @@ Run `revdepcheck::cloud_details(, "CoSMoS")` for more info * GitHub: https://github.com/BioGenies/countfitteR * Source code: https://github.com/cran/countfitteR * Date/Publication: 2020-09-30 21:30:02 UTC -* Number of recursive dependencies: 93 +* Number of recursive dependencies: 90 Run `revdepcheck::cloud_details(, "countfitteR")` for more info @@ -4827,80 +3985,17 @@ Run `revdepcheck::cloud_details(, "countfitteR")` for more info > library(countfitteR) > > test_check("countfitteR") - [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('testing.R:45:3'): plot_fit ──────────────────────────────────────── - p$labels[[1]] not equal to "x". - target is NULL, current is character + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 32 ] - [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] - Error: Test failures - Execution halted - ``` - -# coursekata - -
- -* Version: 0.18.0 -* GitHub: https://github.com/coursekata/coursekata-r -* Source code: https://github.com/cran/coursekata -* Date/Publication: 2024-08-16 20:20:02 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "coursekata")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘coursekata-Ex.R’ failed - The error most likely occurred in: - - > ### Name: middle - > ### Title: Find a percentage of a distribution - > ### Aliases: middle tails lower upper - > - > ### ** Examples - > - > ... - > tails(1:10, .5) - [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE - > - > sampling_distribution <- do(1000) * mean(rnorm(100, 5, 10)) - > sampling_distribution %>% - + gf_histogram(~mean, data = sampling_distribution, fill = ~ middle(mean, .68)) %>% - + gf_refine(scale_fill_manual(values = c("blue", "coral"))) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(coursekata) - Loading required package: dslabs - Loading required package: fivethirtyeight - Some larger datasets need to be installed separately, like senators and - house_district_forecast. To install these, we recommend you install the - fivethirtyeightdata package by running: - ... - • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-color.svg - • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-facet.svg - • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-color.svg - • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-facet.svg - • gf_model-visual/gf-violin-cond-mod-y-on-y.svg - • gf_model-visual/gf-violin-horizontal-mull-mod-y-on-x.svg - • gf_model-visual/gf-violin-mull-mod-y-on-x-2.svg - • gf_model-visual/gf-violin-null-mod-y-on-y.svg + Error in `p$labels[[1]]`: subscript out of bounds + Backtrace: + ▆ + 1. └─testthat::expect_equal(p$labels[[1]], "x") at testing.R:45:3 + 2. └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. └─rlang::eval_bare(expr, quo_get_env(quo)) + + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 32 ] Error: Test failures Execution halted ``` @@ -4913,7 +4008,7 @@ Run `revdepcheck::cloud_details(, "coursekata")` for more info * GitHub: https://github.com/cmu-delphi/covidcast * Source code: https://github.com/cran/covidcast * Date/Publication: 2023-07-12 23:40:06 UTC -* Number of recursive dependencies: 93 +* Number of recursive dependencies: 92 Run `revdepcheck::cloud_details(, "covidcast")` for more info @@ -4949,24 +4044,22 @@ Run `revdepcheck::cloud_details(, "covidcast")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘external-data.Rmd’ + when running code in ‘plotting-signals.Rmd’ ... - Warning: Metadata for signal mean and standard deviation not available; defaulting to observed mean and standard deviation to set plot range. - Warning in ggplot2::guide_colorbar(title = NULL, horizontal = TRUE, barheight = legend_height, : - Arguments in `...` must be used. - ✖ Problematic argument: • horizontal = TRUE ℹ Did you misspell an argument name? - ... - Error: Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. - ℹ Message from server: - ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form + When sourcing ‘plotting-signals.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 5th layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (3078). + ✖ Fix the following mappings: `fill`. Execution halted ‘correlation-utils.Rmd’ using ‘UTF-8’... OK ‘covidcast.Rmd’ using ‘UTF-8’... OK - ‘external-data.Rmd’ using ‘UTF-8’... failed + ‘external-data.Rmd’ using ‘UTF-8’... OK ‘multi-signals.Rmd’ using ‘UTF-8’... OK ‘plotting-signals.Rmd’ using ‘UTF-8’... failed ``` @@ -4978,22 +4071,6 @@ Run `revdepcheck::cloud_details(, "covidcast")` for more info --- finished re-building ‘correlation-utils.Rmd’ --- re-building ‘covidcast.Rmd’ using rmarkdown - - Quitting from lines 38-45 [unnamed-chunk-1] (covidcast.Rmd) - Error: processing vignette 'covidcast.Rmd' failed with diagnostics: - Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. - ℹ Message from server: - ... - ℹ Message from server: - ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form - --- failed re-building ‘plotting-signals.Rmd’ - - SUMMARY: processing the following files failed: - ‘covidcast.Rmd’ ‘external-data.Rmd’ ‘multi-signals.Rmd’ - ‘plotting-signals.Rmd’ - - Error: Vignette re-building failed. - Execution halted ``` ## In both @@ -5003,17 +4080,17 @@ Run `revdepcheck::cloud_details(, "covidcast")` for more info Note: found 20 marked UTF-8 strings ``` -# Coxmos +# creditmodel
-* Version: 1.0.2 -* GitHub: https://github.com/BiostatOmics/Coxmos -* Source code: https://github.com/cran/Coxmos -* Date/Publication: 2024-03-25 20:32:38 UTC -* Number of recursive dependencies: 194 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/creditmodel +* Date/Publication: 2022-01-07 11:32:41 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "Coxmos")` for more info +Run `revdepcheck::cloud_details(, "creditmodel")` for more info
@@ -5021,316 +4098,186 @@ Run `revdepcheck::cloud_details(, "Coxmos")` for more info * checking examples ... ERROR ``` - Running examples in ‘Coxmos-Ex.R’ failed + Running examples in ‘creditmodel-Ex.R’ failed The error most likely occurred in: - > ### Name: getAutoKM - > ### Title: getAutoKM - > ### Aliases: getAutoKM + > ### Name: char_to_num + > ### Title: character to number + > ### Aliases: char_to_num > > ### ** Examples > - > data("X_proteomic") - ... - > X_train <- X_proteomic[index_train,1:50] - > Y_train <- Y_proteomic[index_train,] - > X_test <- X_proteomic[-index_train,1:50] - > Y_test <- Y_proteomic[-index_train,] - > splsicox.model <- splsicox(X_train, Y_train, n.comp = 2, penalty = 0.5, x.center = TRUE, - + x.scale = TRUE) - > getAutoKM(type = "LP", model = splsicox.model) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: getAutoKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > dat_sub = lendingclub[c('dti_joint', 'emp_length')] + > str(dat_sub) + 'data.frame': 31766 obs. of 2 variables: + $ dti_joint : chr "Missing" "Missing" "9.02" "Missing" ... + $ emp_length: chr "3 years" "2 years" "2 years" "10+ years" ... + > #variables that are converted to numbers containing strings + > dat_sub = char_to_num(dat_sub) + Error in is.element(class(x), types) : unused argument (types) + Calls: char_to_num -> get_names -> unique -> sapply -> lapply -> FUN Execution halted ``` -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Coxmos-MO-pipeline.Rmd’ + when running code in ‘introduction.Rmd’ ... + > library(creditmodel) + Package 'creditmodel' version 1.3.1 - $proteomic + > B_model = training_model(dat = UCICreditCard, model_name = "UCICreditCard", + + target = "default.payment.next.month", x_list = NULL, occur_time .... [TRUNCATED] + ── Building ─────────────────────────────────────────────────── UCICreditCard ── + When sourcing ‘introduction.R’: + Error: unused argument (c("LR", "XGB", "GBM", "RF")) + Execution halted - > LST_KM_RES_LP <- getAutoKM(type = "LP", model = lst_models$`SB.sPLS-DRCOX`, - + comp = 1:4, top = 10, ori_data = T, BREAKTIME = NULL, only_sig = .... [TRUNCATED] + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking whether package ‘creditmodel’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(x, names(mat_nas_shadow))': unused argument (names(mat_nas_shadow)) + Note: possible error in 'is.element(x, names(corr_random_num))': unused argument (names(corr_random_num)) + Note: possible error in 'is.element(x, colnames(corr_random_char))': unused argument (colnames(corr_random_char)) + Note: possible error in 'is.element(class(dm_x), ': unused argument (c("Date", "numeric", "integer", "double")) + Note: possible error in 'is.element(x, c("cyan", ': unused argument (c("cyan", "grey", "green", "red", "blue", "purple")) + Note: possible error in 'is.element(class(dat), ': unused argument (c("data.table", "list", "tbl_df", "tbl", "matrix")) + Note: possible error in 'is.element(occur_time, ': unused argument (names(dat)) + Note: possible error in 'is.element(class(dat_x), ': unused argument (c("integer", "numeric", "double")) + Note: possible error in 'is.element(class(dat_x), ': unused argument (c("Date")) + ... + Note: possible error in 'is.element("mins", unit)': unused argument (unit) + Note: possible error in 'is.element("hours", unit)': unused argument (unit) + Note: possible error in 'is.element("weeks", unit)': unused argument (unit) + Note: possible error in 'is.element(split_type, ': unused argument (c("OOT", "Random", "byRow")) + Note: possible error in 'is.element(algorithm, ': unused argument (c("LR", "XGB", "GBM", "RF")) + Note: possible error in 'is.element(feature_filter[["filter"]], ': unused argument (c("IV", "PSI", "XGB", "COR")) + See ‘/tmp/workdir/creditmodel/new/creditmodel.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + analysis_nas : : possible error in is.element(x, + names(mat_nas_shadow)): unused argument (names(mat_nas_shadow)) + analysis_nas : : possible error in is.element(x, + names(corr_random_num)): unused argument (names(corr_random_num)) + analysis_nas : : possible error in is.element(x, + colnames(corr_random_char)): unused argument + (colnames(corr_random_char)) + analysis_outliers: possible error in is.element(class(dm_x), c("Date", + "numeric", "integer", "double")): unused argument (c("Date", + "numeric", "integer", "double")) + ... + "GBM", "RF")): unused argument (c("LR", "XGB", "GBM", "RF")) + training_model: possible error in is.element(missing_proc, c("median", + "avg_dist", "default")): unused argument (c("median", "avg_dist", + "default")) + training_model: possible error in + is.element(feature_filter[["filter"]], c("IV", "PSI", "XGB", "COR")): + unused argument (c("IV", "PSI", "XGB", "COR")) + xgb_params_search: possible error in is.element(method, + c("random_search", "grid_search", "local_search")): unused argument + (c("random_search", "grid_search", "local_search")) + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘introduction.Rmd’ using rmarkdown - ... - Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found + Quitting from lines 31-79 [unnamed-chunk-1] (introduction.Rmd) + Error: processing vignette 'introduction.Rmd' failed with diagnostics: + unused argument (c("LR", "XGB", "GBM", "RF")) + --- failed re-building ‘introduction.Rmd’ - > X <- X_proteomic + SUMMARY: processing the following file failed: + ‘introduction.Rmd’ - When sourcing ‘Coxmos-pipeline.R’: - Error: object 'X_proteomic' not found + Error: Vignette re-building failed. Execution halted - - ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... failed - ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed ``` +## In both + * checking installed package size ... NOTE ``` - installed size is 7.4Mb + installed size is 7.6Mb sub-directories of 1Mb or more: R 1.5Mb - data 2.5Mb - doc 2.9Mb + data 5.5Mb ``` -# cpr +# cricketr
-* Version: 0.4.0 -* GitHub: https://github.com/dewittpe/cpr -* Source code: https://github.com/cran/cpr -* Date/Publication: 2024-02-15 15:40:02 UTC -* Number of recursive dependencies: 95 +* Version: 0.0.26 +* GitHub: https://github.com/tvganesh/cricketr +* Source code: https://github.com/cran/cricketr +* Date/Publication: 2021-03-23 05:30:15 UTC +* Number of recursive dependencies: 58 -Run `revdepcheck::cloud_details(, "cpr")` for more info +Run `revdepcheck::cloud_details(, "cricketr")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘cpr.Rmd’ - ... - Warning: Removed 25 rows containing missing values or values outside the scale range - (`geom_rug()`). - Warning: Removed 26 rows containing missing values or values outside the scale range - (`geom_rug()`). - Warning: Removed 38 rows containing missing values or values outside the scale range - (`geom_rug()`). - - When sourcing ‘cpr.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘cnr.Rmd’ using ‘UTF-8’... OK - ‘cpr.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘cricketr’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘cnr.Rmd’ using rmarkdown + Found the following significant warnings: + Note: possible error in 'is.element(1, homeOrAway)': unused argument (homeOrAway) + Note: possible error in 'is.element(2, homeOrAway)': unused argument (homeOrAway) + Note: possible error in 'is.element(3, homeOrAway)': unused argument (homeOrAway) + Note: possible error in 'is.element(1, result)': unused argument (result) + Note: possible error in 'is.element(2, result)': unused argument (result) + Note: possible error in 'is.element(3, result)': unused argument (result) + Note: possible error in 'is.element(4, result)': unused argument (result) + Note: possible error in 'is.element(5, result)': unused argument (result) + See ‘/tmp/workdir/cricketr/new/cricketr.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + getTeamData: possible error in is.element(1, homeOrAway): unused + argument (homeOrAway) + getTeamData: possible error in is.element(2, homeOrAway): unused + argument (homeOrAway) + getTeamData: possible error in is.element(3, homeOrAway): unused + argument (homeOrAway) + getTeamData: possible error in is.element(1, result): unused argument + (result) + getTeamData: possible error in is.element(2, result): unused argument + (result) + getTeamData: possible error in is.element(3, result): unused argument + (result) + getTeamData: possible error in is.element(4, result): unused argument + (result) + getTeamData: possible error in is.element(5, result): unused argument + (result) ``` -## In both +# crosshap -* checking tests ... ERROR - ``` - Running ‘test-bsplineD.R’ - Running ‘test-bsplines.R’ - Running ‘test-btensor.R’ - Running ‘test-build_tensor.R’ - Running ‘test-cn.R’ - Running ‘test-cnr.R’ - Running ‘test-coef_vcov.R’ - Running the tests in ‘tests/test-coef_vcov.R’ failed. - Complete output: - > # Tests for extracting coefficients and vcov matrix from regression fits - ... - + stopifnot(identical(names(COEF_VCOV), c("theta", "coef", "vcov_theta", "vcov"))) - + stopifnot(identical(COEF_VCOV$theta, numeric(0))) - + stopifnot(identical(COEF_VCOV$coef, fixef(fit))) - + stopifnot(identical(COEF_VCOV$vcov_theta, matrix(0)[FALSE, FALSE])) - + stopifnot(identical(COEF_VCOV$vcov, as.matrix(vcov(fit)))) - + }) - Error in initializePtr() : - function 'cholmod_factor_ldetA' not provided by package 'Matrix' - Calls: with ... initialize -> -> initializePtr -> .Call - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.6Mb - sub-directories of 1Mb or more: - doc 1.6Mb - libs 4.1Mb - ``` - -# cpsvote - -
- -* Version: 0.1.0 -* GitHub: https://github.com/Reed-EVIC/cpsvote -* Source code: https://github.com/cran/cpsvote -* Date/Publication: 2020-11-05 16:00:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "cpsvote")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘voting.Rmd’ - ... - + .... [TRUNCATED] - - > library(usmap) - - > cps16 %>% as_survey_design(weights = turnout_weight) %>% - + mutate(state = STATE) %>% group_by(state) %>% summarize(turnout = survey_mean(hurach .... [TRUNCATED] - - When sourcing ‘voting.R’: - Error: argument is of length zero - Execution halted - - ‘add-variables.Rmd’ using ‘UTF-8’... OK - ‘background.Rmd’ using ‘UTF-8’... OK - ‘basics.Rmd’ using ‘UTF-8’... OK - ‘voting.Rmd’ using ‘UTF-8’... failed - ``` - -# crimeutils - -
- -* Version: 0.5.1 -* GitHub: https://github.com/jacobkap/crimeutils -* Source code: https://github.com/cran/crimeutils -* Date/Publication: 2022-12-07 15:10:07 UTC -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "crimeutils")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘crimeutils-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scale_linetype_crim - > ### Title: A set of linetypes - > ### Aliases: scale_linetype_crim - > - > ### ** Examples - > - > ggplot2::ggplot(mtcars, ggplot2::aes(x = mpg, y = hp, linetype = as.character(cyl))) + - + ggplot2::geom_line(size = 1) + - + scale_linetype_crim() + - + theme_crim() - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -# crmPack - -
- -* Version: 1.0.6 -* GitHub: https://github.com/openpharma/crmPack -* Source code: https://github.com/cran/crmPack -* Date/Publication: 2024-06-26 15:00:14 UTC -* Number of recursive dependencies: 70 - -Run `revdepcheck::cloud_details(, "crmPack")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘crmPack-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DataMixture-class - > ### Title: Class for the data with mixture sharing - > ### Aliases: DataMixture-class .DataMixture - > ### Keywords: classes - > - > ### ** Examples - > - ... - + refDose = 50) - > - > nodata <- Data(doseGrid=doseGrid) - > - > priorSamples <- mcmc(nodata, model, options) - > plot(priorSamples, model, nodata) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘example.Rnw’ - ... - [1] -5.070681 - - > newDLTmodel@phi2 - [1] 1.125107 - - > print(plot(samples, model, data)) - - When sourcing ‘example.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘guidelines.Rmd’ using ‘UTF-8’... OK - ‘example.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘guidelines.Rmd’ using rmarkdown - --- finished re-building ‘guidelines.Rmd’ - - --- re-building ‘example.Rnw’ using Sweave - Loading required package: ggplot2 - Registered S3 method overwritten by 'crmPack': - method from - print.gtable gtable - Type crmPackHelp() to open help browser - ... - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - - --- failed re-building ‘example.Rnw’ - - SUMMARY: processing the following file failed: - ‘example.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# crosshap - -
+
* Version: 1.4.0 * GitHub: https://github.com/jacobimarsh/crosshap * Source code: https://github.com/cran/crosshap * Date/Publication: 2024-03-31 15:40:02 UTC -* Number of recursive dependencies: 117 +* Number of recursive dependencies: 116 Run `revdepcheck::cloud_details(, "crosshap")` for more info @@ -5363,6 +4310,38 @@ Run `revdepcheck::cloud_details(, "crosshap")` for more info Execution halted ``` +# CRTgeeDR + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/CRTgeeDR +* Date/Publication: 2022-09-06 07:28:24 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "CRTgeeDR")` for more info + +
+ +## Newly broken + +* checking whether package ‘CRTgeeDR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(id, dropid)': unused argument (dropid) + See ‘/tmp/workdir/CRTgeeDR/new/CRTgeeDR.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + geeDREstimation: possible error in is.element(id, dropid): unused + argument (dropid) + ``` + # ctrialsgov
@@ -5371,7 +4350,7 @@ Run `revdepcheck::cloud_details(, "crosshap")` for more info * GitHub: NA * Source code: https://github.com/cran/ctrialsgov * Date/Publication: 2021-10-18 16:00:02 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info @@ -5419,7 +4398,7 @@ Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info * GitHub: https://github.com/huizezhang-sherry/cubble * Source code: https://github.com/cran/cubble * Date/Publication: 2024-08-27 15:20:02 UTC -* Number of recursive dependencies: 145 +* Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "cubble")` for more info @@ -5430,14 +4409,14 @@ Run `revdepcheck::cloud_details(, "cubble")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘cb5match.Rmd’ + when running code in ‘cb6interactive.Rmd’ ... - > p2 <- ggplot(res_tm_long, aes(x = date, y = matched, - + group = type, color = type)) + geom_line() + facet_wrap(vars(group)) + - + scale_colo .... [TRUNCATED] + + ymax .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. - > (p1 | p2) + patchwork::plot_layout(guides = "collect") + - + plot_annotation(tag_levels = "a") & theme(legend.position = "bottom") + > ts_interactive <- highlight(ggplotly(ts_static, width = 600, + + height = 300), on = "plotly_selected", opacityDim = 0.012) ... Error: subscript out of bounds @@ -5447,7 +4426,7 @@ Run `revdepcheck::cloud_details(, "cubble")` for more info ‘cb2create.Rmd’ using ‘UTF-8’... OK ‘cb3tsibblesf.Rmd’ using ‘UTF-8’... OK ‘cb4glyph.Rmd’ using ‘UTF-8’... OK - ‘cb5match.Rmd’ using ‘UTF-8’... failed + ‘cb5match.Rmd’ using ‘UTF-8’... OK ‘cb6interactive.Rmd’ using ‘UTF-8’... failed ‘cb7misc.Rmd’ using ‘UTF-8’... OK ``` @@ -5477,17 +4456,17 @@ Run `revdepcheck::cloud_details(, "cubble")` for more info doc 1.4Mb ``` -# curtailment +# DAISIE
-* Version: 0.2.6 -* GitHub: https://github.com/martinlaw/curtailment -* Source code: https://github.com/cran/curtailment -* Date/Publication: 2023-10-25 15:50:04 UTC -* Number of recursive dependencies: 36 +* Version: 4.4.1 +* GitHub: https://github.com/rsetienne/DAISIE +* Source code: https://github.com/cran/DAISIE +* Date/Publication: 2023-10-21 23:10:10 UTC +* Number of recursive dependencies: 118 -Run `revdepcheck::cloud_details(, "curtailment")` for more info +Run `revdepcheck::cloud_details(, "DAISIE")` for more info
@@ -5495,88 +4474,52 @@ Run `revdepcheck::cloud_details(, "curtailment")` for more info * checking examples ... ERROR ``` - Running examples in ‘curtailment-Ex.R’ failed + Running examples in ‘DAISIE-Ex.R’ failed The error most likely occurred in: - > ### Name: drawDiagramGeneric - > ### Title: drawDiagramGeneric - > ### Aliases: drawDiagramGeneric + > ### Name: DAISIE_plot_input + > ### Title: DAISIE tree plot + > ### Aliases: DAISIE_plot_input > > ### ** Examples > - > go <- cbind(6:8, rep(8,3)) + > ... - 4. └─ggplot2:::ggplot_build.ggplot(x) - 5. └─layout$setup(data, plot$data, plot$plot_env) - 6. └─ggplot2 (local) setup(..., self = self) - 7. └─self$coord$setup_params(data) - 8. └─ggplot2 (local) setup_params(..., self = self) - 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) - 10. └─ggplot2:::check_logical(expand) - 11. └─ggplot2:::stop_input_type(...) - 12. └─rlang::abort(message, ..., call = call, arg = arg) + ℹ Did you misspell an argument name? + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Joining with `by = join_by(label)` + Warning: Removed 1 row containing missing values or values outside the scale range + (`geom_point()`). + Error in grid.Call.graphics(C_rect, x$x, x$y, x$width, x$height, resolveHJust(x$just, : + invalid hex digit in 'color' or 'lty' + Calls: ... drawDetails -> drawDetails.rect -> grid.Call.graphics Execution halted ``` -# dabestr - -
- -* Version: 2023.9.12 -* GitHub: https://github.com/ACCLAB/dabestr -* Source code: https://github.com/cran/dabestr -* Date/Publication: 2023-10-13 11:50:06 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "dabestr")` for more info - -
- -## Newly broken +## In both -* checking running R code from vignettes ... ERROR +* checking package dependencies ... NOTE ``` - Errors in running code in vignettes: - when running code in ‘tutorial_deltadelta.Rmd’ - ... - > paired_delta2.mean_diff <- load(df, x = Treatment, - + y = Measurement, experiment = Genotype, colour = Rep, delta2 = TRUE, - + idx = list(c(" ..." ... [TRUNCATED] - - > dabest_plot(paired_delta2.mean_diff, raw_marker_size = 0.5, - + raw_marker_alpha = 0.3) - - ... - Error: argument is of length zero - Execution halted - - ‘datasets.Rmd’ using ‘UTF-8’... OK - ‘plot_aesthetics.Rmd’ using ‘UTF-8’... OK - ‘tutorial_basics.Rmd’ using ‘UTF-8’... OK - ‘tutorial_deltadelta.Rmd’ using ‘UTF-8’... failed - ‘tutorial_minimeta.Rmd’ using ‘UTF-8’... failed - ‘tutorial_proportion_plots.Rmd’ using ‘UTF-8’... OK - ‘tutorial_repeated_measures.Rmd’ using ‘UTF-8’... failed + Package which this enhances but not available for checking: ‘doMC’ ``` -* checking re-building of vignette outputs ... NOTE +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘datasets.Rmd’ using rmarkdown - --- finished re-building ‘datasets.Rmd’ - - --- re-building ‘plot_aesthetics.Rmd’ using rmarkdown + installed size is 37.6Mb + sub-directories of 1Mb or more: + libs 35.5Mb ``` # DAISIEprep
-* Version: 0.4.0 +* Version: 1.0.0 * GitHub: https://github.com/joshwlambert/DAISIEprep * Source code: https://github.com/cran/DAISIEprep -* Date/Publication: 2024-04-02 11:30:06 UTC -* Number of recursive dependencies: 149 +* Date/Publication: 2024-12-18 00:20:02 UTC +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info @@ -5593,7 +4536,7 @@ Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info > library(DAISIEprep) > > test_check("DAISIEprep") - [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + [ FAIL 4 | WARN 4 | SKIP 14 | PASS 2235 ] ══ Skipped tests (14) ══════════════════════════════════════════════════════════ ... @@ -5604,22 +4547,22 @@ Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info ── Failure ('test-plot_phylod.R:18:3'): plot_phylod runs silent without error ── `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings. - [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + [ FAIL 4 | WARN 4 | SKIP 14 | PASS 2235 ] Error: Test failures Execution halted ``` -# dbmss +# daltoolbox
-* Version: 2.9-2 -* GitHub: https://github.com/EricMarcon/dbmss -* Source code: https://github.com/cran/dbmss -* Date/Publication: 2024-08-24 11:00:02 UTC -* Number of recursive dependencies: 96 +* Version: 1.1.727 +* GitHub: https://github.com/cefet-rj-dal/daltoolbox +* Source code: https://github.com/cran/daltoolbox +* Date/Publication: 2024-11-25 05:10:02 UTC +* Number of recursive dependencies: 108 -Run `revdepcheck::cloud_details(, "dbmss")` for more info +Run `revdepcheck::cloud_details(, "daltoolbox")` for more info
@@ -5627,148 +4570,221 @@ Run `revdepcheck::cloud_details(, "dbmss")` for more info * checking examples ... ERROR ``` - Running examples in ‘dbmss-Ex.R’ failed + Running examples in ‘daltoolbox-Ex.R’ failed The error most likely occurred in: - > ### Name: DEnvelope - > ### Title: Estimation of the confidence envelope of the D function under - > ### its null hypothesis - > ### Aliases: DEnvelope + > ### Name: plot_ts_pred + > ### Title: Plot a time series chart with predictions + > ### Aliases: plot_ts_pred > > ### ** Examples > + > data(sin_data) ... - > r <- 0:30 - > NumberOfSimulations <- 20 - > Alpha <- .05 - > # Plot the envelope (after normalization by pi.r^2) - > autoplot(DEnvelope(X, r, NumberOfSimulations, Alpha, - + "V. Americana", "Q. Rosea", Intertype = TRUE), ./(pi*r^2) ~ r) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + > samp <- ts_sample(ts, test_size= 5) + > io_train <- ts_projection(samp$train) + > io_test <- ts_projection(samp$test) + > + > model <- ts_arima() + > model <- fit(model, x=io_train$input, y=io_train$output) + Error in is.element("drift", names(obj$model$coef)) : + unused argument (names(obj$model$coef)) + Calls: fit -> fit.ts_arima Execution halted ``` -* checking running R code from vignettes ... ERROR +* checking whether package ‘daltoolbox’ can be installed ... WARNING ``` - Errors in running code in vignettes: - when running code in ‘dbmss.Rmd’ - ... - - > autoplot(paracou16, labelSize = expression("Basal area (" ~ - + cm^2 ~ ")"), labelColor = "Species") - - > autoplot(Mhat(paracou16, ReferenceType = "V. Americana", - + NeighborType = "Q. Rosea"), main = "") - - When sourcing ‘dbmss.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘dbmss.Rmd’ using ‘UTF-8’... failed + Found the following significant warnings: + Note: possible error in 'is.element("drift", names(obj$model$coef))': unused argument (names(obj$model$coef)) + See ‘/tmp/workdir/daltoolbox/new/daltoolbox.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -* checking re-building of vignette outputs ... NOTE +* checking R code for possible problems ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘dbmss.Rmd’ using rmarkdown + fit.ts_arima: possible error in is.element("drift", + names(obj$model$coef)): unused argument (names(obj$model$coef)) ``` -# deeptime +# dawaR
-* Version: 2.0.0 -* GitHub: https://github.com/willgearty/deeptime -* Source code: https://github.com/cran/deeptime -* Date/Publication: 2024-08-19 07:00:43 UTC -* Number of recursive dependencies: 197 +* Version: 0.2.7 +* GitHub: https://github.com/aleksanderbl29/dawaR +* Source code: https://github.com/cran/dawaR +* Date/Publication: 2024-12-08 00:00:06 UTC +* Number of recursive dependencies: 150 -Run `revdepcheck::cloud_details(, "deeptime")` for more info +Run `revdepcheck::cloud_details(, "dawaR")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘dawaR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_data + > ### Title: Get data from section + > ### Aliases: get_data + > + > ### ** Examples + > + > if (connection_check()) { + ... + + x <- get_data("regioner") + + head(x) + + } + ✖ Request failed: HTTP 504 Gateway Timeout. + ✖ The API returned a error. + ✖ No content will be returned + Error in do.call(rbind.data.frame, response) : + second argument must be a list + Calls: get_data -> do.call + Execution halted + ``` + +## Newly fixed + * checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: - > library(testthat) - > library(deeptime) - > - > test_check("deeptime") - Scale for y is already present. - Adding another scale for y, which will replace the existing scale. - Scale for y is already present. + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html ... - • patterns/geo-pattern2-new.svg - • patterns/scale-fill-geopattern-labels-new.svg - • patterns/scale-fill-geopattern-limits-new.svg - • patterns/scale-fill-geopattern-na-new.svg - • patterns/scale-fill-geopattern-na2-new.svg - • points_range/geom-points-range-aes-new.svg - • points_range/geom-points-range-bg-new.svg - • points_range/geom-points-range-h-new.svg + ── Error ('test-get_data.R:55:5'): get_data(section = 'regioner') snapshot ───── + Error in `do.call(rbind.data.frame, response)`: second argument must be a list + Backtrace: + ▆ + 1. └─testthat::expect_snapshot(get_data(section = "regioner")) at test-get_data.R:55:5 + 2. └─rlang::cnd_signal(state$error) + + [ FAIL 1 | WARN 0 | SKIP 48 | PASS 10 ] Error: Test failures Execution halted ``` -* checking running R code from vignettes ... ERROR +## In both + +* checking re-building of vignette outputs ... NOTE ``` - Errors in running code in vignettes: - when running code in ‘coord_geo.Rmd’ + Error(s) in re-building vignettes: ... - + y = n)) + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + - + coord_geo(xlim = .... [TRUNCATED] - - > ggplot(coral_div) + geom_line(aes(x = stage_age, y = n)) + - + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + coord_geo(dat = "periods", - + .... [TRUNCATED] + --- re-building ‘dawaR.Rmd’ using rmarkdown + Quitting from lines 62-70 [municipality_map] (dawaR.Rmd) + Error: processing vignette 'dawaR.Rmd' failed with diagnostics: + Problem while computing aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error: + ! object 'regionsnavn' not found ... - Error: argument is of length zero - Execution halted + --- finished re-building ‘renv-issues.Rmd’ + + --- re-building ‘status.Rmd’ using rmarkdown + --- finished re-building ‘status.Rmd’ + + SUMMARY: processing the following file failed: + ‘dawaR.Rmd’ - ‘coord.Rmd’ using ‘UTF-8’... OK - ‘coord_geo.Rmd’ using ‘UTF-8’... failed - ‘geo.Rmd’ using ‘UTF-8’... OK - ‘ggarrange2.Rmd’ using ‘UTF-8’... OK - ‘phylogenies.Rmd’ using ‘UTF-8’... OK - ‘time.Rmd’ using ‘UTF-8’... failed - ‘traits.Rmd’ using ‘UTF-8’... OK + Error: Vignette re-building failed. + Execution halted ``` -* checking re-building of vignette outputs ... NOTE +# DDPNA + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/liukf10/DDPNA +* Source code: https://github.com/cran/DDPNA +* Date/Publication: 2024-03-14 03:20:15 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "DDPNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR ``` - Error(s) in re-building vignettes: - --- re-building ‘coord.Rmd’ using rmarkdown + Running examples in ‘DDPNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MaxQprotein + > ### Title: read proteomic quantification data and seperate the protein + > ### information and quantification information. + > ### Aliases: MaxQprotein + > + > ### ** Examples + > + > data(ProteomicData) + > # example for MaxQ Data + > MaxQdata <- MaxQprotein(ProteomicData$MaxQ) + Error in is.element("Potential.contaminant", colnames(infile)) : + unused argument (colnames(infile)) + Calls: MaxQprotein -> removeConRev + Execution halted ``` -## In both +* checking whether package ‘DDPNA’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element("Potential.contaminant", ': unused argument (colnames(infile)) + Note: possible error in 'is.element("+", unique(infile$Potential.contaminant))': unused argument (unique(infile$Potential.contaminant)) + Note: possible error in 'is.element("Reverse", ': unused argument (colnames(infile)) + Note: possible error in 'is.element("+", unique(infile$Reverse))': unused argument (unique(infile$Reverse)) + Note: possible error in 'is.element(IDname, colname)': unused argument (colname) + Note: possible error in 'is.element(QuanCol, colname)': unused argument (colname) + See ‘/tmp/workdir/DDPNA/new/DDPNA.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` -* checking installed package size ... NOTE +* checking R code for possible problems ... NOTE ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - R 2.8Mb - doc 1.8Mb - help 1.1Mb + MaxQprotein : removeConRev: possible error in + is.element("Potential.contaminant", colnames(infile)): unused + argument (colnames(infile)) + MaxQprotein : removeConRev: possible error in is.element("+", + unique(infile$Potential.contaminant)): unused argument + (unique(infile$Potential.contaminant)) + MaxQprotein : removeConRev: possible error in is.element("Reverse", + colnames(infile)): unused argument (colnames(infile)) + MaxQprotein : removeConRev: possible error in is.element("+", + unique(infile$Reverse)): unused argument (unique(infile$Reverse)) + MaxQprotein: possible error in is.element(IDname, colname): unused + argument (colname) + MaxQprotein: possible error in is.element(QuanCol, colname): unused + argument (colname) ``` -# descriptio +# Deducer
-* Version: 1.3 -* GitHub: https://github.com/nicolas-robette/descriptio -* Source code: https://github.com/cran/descriptio -* Date/Publication: 2024-03-07 11:00:02 UTC -* Number of recursive dependencies: 98 +* Version: 0.7-9 +* GitHub: NA +* Source code: https://github.com/cran/Deducer +* Date/Publication: 2015-12-29 22:16:31 +* Number of recursive dependencies: 118 -Run `revdepcheck::cloud_details(, "descriptio")` for more info +Run `revdepcheck::cloud_details(, "Deducer")` for more info
@@ -5776,82 +4792,239 @@ Run `revdepcheck::cloud_details(, "descriptio")` for more info * checking examples ... ERROR ``` - Running examples in ‘descriptio-Ex.R’ failed + Running examples in ‘Deducer-Ex.R’ failed The error most likely occurred in: - > ### Name: ggassoc_crosstab - > ### Title: Proportional area plot - > ### Aliases: ggassoc_crosstab - > ### Keywords: multivariate aplot + > ### Name: sort.data.frame + > ### Title: Sort Data + > ### Aliases: sort.data.frame > > ### ** Examples > - > data(Movies) - > ggassoc_crosstab(data=Movies, mapping=ggplot2::aes(Genre, Country)) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggassoc_crosstab ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > data(mtcars) + > + > #sort by the number of cylenders + > sort(mtcars, by= ~cyl) + Error in is.element(substring(formc, 1, 1), c("+", "-")) : + unused argument (c("+", "-")) + Calls: sort -> sort -> sort.data.frame Execution halted ``` -## In both +* checking whether package ‘Deducer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(substring(formc, ': unused argument (c("+", "-")) + See ‘/tmp/workdir/Deducer/new/Deducer.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` -* checking Rd cross-references ... NOTE +* checking R code for possible problems ... NOTE ``` - Packages unavailable to check Rd xrefs: ‘FactoMineR’, ‘vcd’ + sort.data.frame: possible error in is.element(substring(formc, 1, 1), + c("+", "-")): unused argument (c("+", "-")) ``` -# directlabels +# deeptime
-* Version: 2024.1.21 -* GitHub: https://github.com/tdhock/directlabels -* Source code: https://github.com/cran/directlabels -* Date/Publication: 2024-01-24 19:20:07 UTC -* Number of recursive dependencies: 82 +* Version: 2.1.0 +* GitHub: https://github.com/willgearty/deeptime +* Source code: https://github.com/cran/deeptime +* Date/Publication: 2024-10-25 23:30:02 UTC +* Number of recursive dependencies: 197 -Run `revdepcheck::cloud_details(, "directlabels")` for more info +Run `revdepcheck::cloud_details(, "deeptime")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘deeptime-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_wrap_color + > ### Title: Wrap a 1d ribbon of panels into 2d with colored strips + > ### Aliases: facet_wrap_color FacetWrapColor + > ### Keywords: datasets + > + > ### ** Examples + > + ... + is.element + + > df <- data.frame(x = 1:10, y = 1:10, period = c("Permian", "Triassic")) + > ggplot(df) + + + geom_point(aes(x, y)) + + + facet_wrap_color(vars(period), colors = periods) + Error in asNamespace("ggplot2")$wrap_as_facets_list(...) : + attempt to apply non-function + Calls: facet_wrap_color -> wrap_as_facets_list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(deeptime) + > + > test_check("deeptime") + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + ... + • patterns/geo-pattern2-new.svg + • patterns/scale-fill-geopattern-labels-new.svg + • patterns/scale-fill-geopattern-limits-new.svg + • patterns/scale-fill-geopattern-na-new.svg + • patterns/scale-fill-geopattern-na2-new.svg + • points_range/geom-points-range-aes-new.svg + • points_range/geom-points-range-bg-new.svg + • points_range/geom-points-range-h-new.svg + Error: Test failures + Execution halted + ``` + +# desplot + +
+ +* Version: 1.10 +* GitHub: https://github.com/kwstat/desplot +* Source code: https://github.com/cran/desplot +* Date/Publication: 2023-03-09 23:20:06 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "desplot")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘desplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: desplot + > ### Title: Plot the layout/data of a field experiment. + > ### Aliases: desplot ggdesplot + > + > ### ** Examples + > + > if(require(agridat)){ + ... + + desplot(yates.oats, + + block ~ col+row, + + col=nitro, text=gen, cex=1, out1=block, + + out2=gen, out2.gpar=list(col = "gray50", lwd = 1, lty = 1)) + + + + } + Loading required package: agridat + Error in is.element(x, dn) : unused argument (dn) + Calls: desplot -> checkvars + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(desplot) + > + > test_check("desplot") + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 10 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Error ('test_desplot.R:142:1'): (code run outside of `test_that()`) ───────── + Error in `is.element(x, dn)`: unused argument (dn) + Backtrace: + ▆ + 1. └─desplot::desplot(...) at test_desplot.R:142:1 + 2. └─desplot (local) checkvars(col.string, dn) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘examples.Rmd’ + when running code in ‘desplot_examples.Rmd’ ... - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + > if (is.element("x", names(yates.oats))) yates.oats <- transform(yates.oats, + + col = x, row = y) - When sourcing ‘examples.R’: - Error: Problem while computing stat. - ℹ Error occurred in the 3rd layer. - Caused by error in `get()`: - ! object 'last.qp' of mode 'function' was not found + > desplot(yates.oats, block ~ col + row, col = nitro, + + text = gen, cex = 1, out1 = block, out2 = gen, out2.gpar = list(col = "gray50", + + .... [TRUNCATED] + + When sourcing ‘desplot_examples.R’: + Error: unused argument (dn) Execution halted - ‘examples.Rmd’... failed + ‘desplot_examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking whether package ‘desplot’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(x, dn)': unused argument (dn) + See ‘/tmp/workdir/desplot/new/desplot.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + desplot : checkvars: possible error in is.element(x, dn): unused + argument (dn) + ggdesplot : checkvars: possible error in is.element(x, dn): unused + argument (dn) ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘examples.Rmd’ using knitr + ... + --- re-building ‘desplot_examples.Rmd’ using rmarkdown + + Quitting from lines 30-39 [yates] (desplot_examples.Rmd) + Error: processing vignette 'desplot_examples.Rmd' failed with diagnostics: + unused argument (dn) + --- failed re-building ‘desplot_examples.Rmd’ + + SUMMARY: processing the following file failed: + ‘desplot_examples.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# disto +# diceR
-* Version: 0.2.0 -* GitHub: https://github.com/talegari/disto -* Source code: https://github.com/cran/disto -* Date/Publication: 2018-08-02 12:50:02 UTC -* Number of recursive dependencies: 115 +* Version: 2.2.0 +* GitHub: https://github.com/AlineTalhouk/diceR +* Source code: https://github.com/cran/diceR +* Date/Publication: 2024-01-22 21:22:46 UTC +* Number of recursive dependencies: 155 -Run `revdepcheck::cloud_details(, "disto")` for more info +Run `revdepcheck::cloud_details(, "diceR")` for more info
@@ -5859,84 +5032,171 @@ Run `revdepcheck::cloud_details(, "disto")` for more info * checking examples ... ERROR ``` - Running examples in ‘disto-Ex.R’ failed + Running examples in ‘diceR-Ex.R’ failed The error most likely occurred in: - > ### Name: plot.disto - > ### Title: Plot a disto object - > ### Aliases: plot.disto + > ### Name: graphs + > ### Title: Graphical Displays + > ### Aliases: graphs graph_cdf graph_delta_area graph_heatmap graph_tracking + > ### graph_all > > ### ** Examples > - > temp <- stats::dist(iris[,1:4]) ... - > dio <- disto(objectname = "temp") - > plot(dio, type = "heatmap") - > plot(dio, type = "dendrogram") - Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as - of ggplot2 3.3.4. - ℹ The deprecated feature was likely used in the factoextra package. - Please report the issue at . - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─diceR (local) .f(...) + 9. ├─base::loadNamespace(x) + 10. │ └─base (local) runHook(".onLoad", env, package.lib, package) + 11. │ └─base::stop(...) + 12. └─base::.handleSimpleError(...) + 13. └─purrr (local) h(simpleError(msg, call)) + 14. └─cli::cli_abort(...) + 15. └─rlang::abort(...) Execution halted ``` +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(diceR) + > + > test_check("diceR") + Selecting k and imputing non-clustered cases + Computing consensus functions + Evaluating output with consensus function results + ... + 18. │ └─base (local) runHook(".onLoad", env, package.lib, package) + 19. │ └─base::stop(...) + 20. └─base::.handleSimpleError(...) + 21. └─purrr (local) h(simpleError(msg, call)) + 22. └─cli::cli_abort(...) + 23. └─rlang::abort(...) + + [ FAIL 9 | WARN 7 | SKIP 0 | PASS 91 ] + Error: Test failures + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘vignette_disto.Rmd’ + when running code in ‘overview.Rmd’ ... + > hm <- graph_heatmap(pam.4) - > plot(dio, type = "dendrogram") - Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as - of ggplot2 3.3.4. - ℹ The deprecated feature was likely used in the factoextra package. - Please report the issue at . - - When sourcing ‘vignette_disto.R’: - Error: argument is of length zero + When sourcing ‘overview.R’: + Error: ℹ In index: 1. + ℹ With name: PAM_Euclidean k=4. + Caused by error: + ! .onLoad failed in loadNamespace() for 'NMF', details: + call: is.element(models, models.wraps) + error: unused argument (models.wraps) Execution halted - ‘vignette_disto.Rmd’ using ‘UTF-8’... failed + ‘overview.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... - --- re-building ‘vignette_disto.Rmd’ using rmarkdown + --- re-building ‘overview.Rmd’ using rmarkdown - Quitting from lines 42-72 [unnamed-chunk-1] (vignette_disto.Rmd) - Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘vignette_disto.Rmd’ + Quitting from lines 169-170 [graph_heatmap] (overview.Rmd) + Error: processing vignette 'overview.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: PAM_Euclidean k=4. + Caused by error: + ! .onLoad failed in loadNamespace() for 'NMF', details: + call: is.element(models, models.wraps) + error: unused argument (models.wraps) + --- failed re-building ‘overview.Rmd’ SUMMARY: processing the following file failed: - ‘vignette_disto.Rmd’ + ‘overview.Rmd’ Error: Vignette re-building failed. Execution halted ``` -## In both +# directlabels -* checking dependencies in R code ... NOTE +
+ +* Version: 2024.1.21 +* GitHub: https://github.com/tdhock/directlabels +* Source code: https://github.com/cran/directlabels +* Date/Publication: 2024-01-24 19:20:07 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "directlabels")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR ``` - Namespaces in Imports field not imported from: - ‘dplyr’ ‘proxy’ - All declared Imports should be used. + Running examples in ‘directlabels-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qp.labels + > ### Title: Make a Positioning Method for non-overlapping lineplot labels + > ### Aliases: qp.labels + > + > ### ** Examples + > + > SegCost$error <- factor(SegCost$error,c("FP","FN","E","I")) + ... + ! The `panel.margin` argument of `theme()` was deprecated in ggplot2 + 2.2.0 and is now defunct. + ℹ Please use the `panel.spacing` argument instead. + Backtrace: + ▆ + 1. └─ggplot2::theme(panel.margin = grid::unit(0, "lines")) + 2. └─lifecycle::deprecate_stop("2.2.0", "theme(panel.margin)", "theme(panel.spacing)") + 3. └─lifecycle:::deprecate_stop0(msg) + 4. └─rlang::cnd_signal(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘examples.Rmd’ + ... + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + + When sourcing ‘examples.R’: + Error: Problem while computing stat. + ℹ Error occurred in the 3rd layer. + Caused by error in `get()`: + ! object 'last.qp' of mode 'function' was not found + Execution halted + + ‘examples.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘examples.Rmd’ using knitr ``` # distributional
-* Version: 0.4.0 +* Version: 0.5.0 * GitHub: https://github.com/mitchelloharawild/distributional * Source code: https://github.com/cran/distributional -* Date/Publication: 2024-02-07 13:30:02 UTC -* Number of recursive dependencies: 64 +* Date/Publication: 2024-09-17 06:20:02 UTC +* Number of recursive dependencies: 120 Run `revdepcheck::cloud_details(, "distributional")` for more info @@ -5977,7 +5237,7 @@ Run `revdepcheck::cloud_details(, "distributional")` for more info * GitHub: https://github.com/dtm2451/dittoViz * Source code: https://github.com/cran/dittoViz * Date/Publication: 2024-02-02 00:00:12 UTC -* Number of recursive dependencies: 99 +* Number of recursive dependencies: 98 Run `revdepcheck::cloud_details(, "dittoViz")` for more info @@ -6018,34 +5278,34 @@ Run `revdepcheck::cloud_details(, "dittoViz")` for more info > library(testthat) > library(dittoViz) Loading required package: ggplot2 - > test_check("dittoViz") - [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] - ══ Failed tests ════════════════════════════════════════════════════════════════ + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': ... - 6. └─dittoViz:::.yPlot_add_data_y_direction(...) - 7. └─ggplot2:::`+.gg`(p, do.call(geom_boxplot, boxplot.args)) - 8. └─ggplot2:::add_ggplot(e1, e2, e2name) - 9. ├─ggplot2::ggplot_add(object, p, objectname) - 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 2. └─dittoViz::freqPlot(...) + 3. └─dittoViz::yPlot(...) + 4. └─dittoViz:::.warn_or_apply_plotly(p, plots) + 5. ├─plotly::ggplotly(p, tooltip = "text") + 6. └─plotly:::ggplotly.ggplot(p, tooltip = "text") + 7. └─plotly::gg2list(...) - [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] + [ FAIL 29 | WARN 0 | SKIP 0 | PASS 252 ] Error: Test failures Execution halted ``` -# dotwhisker +# divent
-* Version: 0.8.2 -* GitHub: https://github.com/fsolt/dotwhisker -* Source code: https://github.com/cran/dotwhisker -* Date/Publication: 2024-06-07 12:20:06 UTC -* Number of recursive dependencies: 72 +* Version: 0.4-4 +* GitHub: https://github.com/EricMarcon/divent +* Source code: https://github.com/cran/divent +* Date/Publication: 2024-11-06 16:10:08 UTC +* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "dotwhisker")` for more info +Run `revdepcheck::cloud_details(, "divent")` for more info
@@ -6053,253 +5313,392 @@ Run `revdepcheck::cloud_details(, "dotwhisker")` for more info * checking examples ... ERROR ``` - Running examples in ‘dotwhisker-Ex.R’ failed + Running examples in ‘divent-Ex.R’ failed The error most likely occurred in: - > ### Name: small_multiple - > ### Title: Generate a 'Small Multiple' Plot of Regression Results - > ### Aliases: small_multiple + > ### Name: accum_div_phylo + > ### Title: Phylogenetic Diversity Accumulation of a Community + > ### Aliases: accum_div_phylo accum_ent_phylo accum_ent_phylo.numeric + > ### accum_ent_phylo.abundances accum_div_phylo.numeric + > ### accum_div_phylo.abundances > > ### ** Examples - > - > library(broom) ... - + m[[i]] <- update(m[[i-1]], paste(". ~ . +", ordered_vars[i])) - + m123456_df <- rbind(m123456_df, m[[i]] %>% tidy %>% by_2sd(mtcars) %>% - + mutate(model = paste("Model", i))) - + } - > - > # Generate a 'small multiple' plot - > small_multiple(m123456_df) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: small_multiple ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + 11. │ └─base::withCallingHandlers(...) + 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. └─l$compute_geom_2(d, theme = plot$theme) + 14. └─ggplot2 (local) compute_geom_2(..., self = self) + 15. └─self$geom$use_defaults(...) + 16. └─ggplot2 (local) use_defaults(..., self = self) + 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘dotwhisker-vignette.Rmd’ + when running code in ‘divent.Rmd’ ... - + wt = "Weight", cyl = "Cylinders", disp = "Displacement", - + .... [TRUNCATED] - > small_multiple(m123456_df) + theme_bw(base_size = 4) + - + ylab("Coefficient Estimate") + geom_hline(yintercept = 0, - + colour = "grey60", li .... [TRUNCATED] + > autoplot(paracou_6_abd[1, ]) - ... - - > small_multiple(results_df, show_stats = FALSE) + scale_x_discrete(limits = model_names) + - + theme_bw() + ylab("Coefficient Estimate") + geom_hl .... [TRUNCATED] - - When sourcing ‘kl2007_examples.R’: - Error: argument is of length zero + When sourcing ‘divent.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (189). + ✖ Fix the following mappings: `shape` and `size`. Execution halted - ‘dotwhisker-vignette.Rmd’ using ‘UTF-8’... failed - ‘kl2007_examples.Rmd’ using ‘ASCII’... failed + ‘divent.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown + ... + --- re-building ‘divent.Rmd’ using rmarkdown + + Quitting from lines 59-60 [plot_paracou6] (divent.Rmd) + Error: processing vignette 'divent.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (189). + ✖ Fix the following mappings: `shape` and `size`. + --- failed re-building ‘divent.Rmd’ + + SUMMARY: processing the following file failed: + ‘divent.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# DRomics +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘dbmss’ + ``` + +# doBy
-* Version: 2.5-2 -* GitHub: https://github.com/aursiber/DRomics -* Source code: https://github.com/cran/DRomics -* Date/Publication: 2024-01-31 09:30:02 UTC -* Number of recursive dependencies: 153 +* Version: 4.6.24 +* GitHub: https://github.com/hojsgaard/doBy +* Source code: https://github.com/cran/doBy +* Date/Publication: 2024-10-07 23:20:12 UTC +* Number of recursive dependencies: 84 -Run `revdepcheck::cloud_details(, "DRomics")` for more info +Run `revdepcheck::cloud_details(, "doBy")` for more info
## Newly broken +* checking whether package ‘doBy’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(substring(formc, ': unused argument (c("+", "-")) + See ‘/tmp/workdir/doBy/new/doBy.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + orderBy: possible error in is.element(substring(formc, 1, 1), c("+", + "-")): unused argument (c("+", "-")) + ``` + +## In both + * checking examples ... ERROR ``` - Running examples in ‘DRomics-Ex.R’ failed + Running examples in ‘doBy-Ex.R’ failed The error most likely occurred in: - > ### Name: PCAdataplot - > ### Title: Performs and plots the results of a PCA on omic data - > ### Aliases: PCAdataplot + > ### Name: by-order + > ### Title: Ordering (sorting) rows of a data frame + > ### Aliases: by-order order_by orderBy + > ### Keywords: utilities > > ### ** Examples > > - ... - Number of items: 100 - Identifiers of the first 20 items: - [1] "1" "2" "3" "4" "5.1" "6.1" "7.1" "8.1" "9.1" "10.1" - [11] "11.1" "12.1" "13.1" "14.1" "15" "16.1" "17.1" "18.1" "19.1" "20.1" - Data were normalized between arrays using the following method: cyclicloess - > plot(o) - > PCAdataplot(o) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: PCAdataplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > orderBy(~ conc + Treatment, CO2) + Error in is.element(substring(formc, 1, 1), c("+", "-")) : + unused argument (c("+", "-")) + Calls: orderBy Execution halted ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘DRomics_vignette.Rmd’ using rmarkdown - ``` - -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘DRomics_vignette.Rmd’ + when running code in ‘doby.rmd’ ... - [16] "ENSDARG00000100660" "ENSDARG00000113107" "ENSDARG00000099787" - [19] "ENSDARG00000112451" "ENSDARG00000070546" - Data were normalized with respect to library size and tranformed using - the following method: rlog + > myfun1 <- function(x) { + + c(m = mean(x), s = sd(x)) + + } - > PCAdataplot(o, batch = zebraf$batch) + theme_bw() + > summaryBy(cbind(mpg, cyl, lh = log(hp)) ~ vs, data = mtcars, + + FUN = myfun1) - When sourcing ‘DRomics_vignette.R’: - Error: argument is of length zero + ... + > fm.mix <- lmer(uptake ~ conc + Treatment + Type + + + (1 | Plant), data = CO2.ubal) + + When sourcing ‘linest_lsmeans.R’: + Error: function 'cholmod_factor_ldetA' not provided by package 'Matrix' Execution halted - ‘DRomics_vignette.Rmd’ using ‘UTF-8’... failed + ‘doby.rmd’ using ‘UTF-8’... failed + ‘linest_lsmeans.rnw’ using ‘UTF-8’... failed + ‘section_fun.rmd’ using ‘UTF-8’... OK ``` * checking installed package size ... NOTE ``` - installed size is 6.2Mb + installed size is 8.2Mb sub-directories of 1Mb or more: - doc 2.9Mb + data 7.0Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘doby.rmd’ using knitr + + Quitting from lines 70-75 [unnamed-chunk-4] (doby.rmd) + Error: processing vignette 'doby.rmd' failed with diagnostics: + unused argument (c("+", "-")) + --- failed re-building ‘doby.rmd’ + + --- re-building ‘linest_lsmeans.rnw’ using knitr + ... + --- failed re-building ‘linest_lsmeans.rnw’ + + --- re-building ‘section_fun.rmd’ using knitr + --- finished re-building ‘section_fun.rmd’ + + SUMMARY: processing the following files failed: + ‘doby.rmd’ ‘linest_lsmeans.rnw’ + + Error: Vignette re-building failed. + Execution halted ``` -# dtwclust +# DoseFinding
-* Version: 6.0.0 -* GitHub: https://github.com/asardaes/dtwclust -* Source code: https://github.com/cran/dtwclust -* Date/Publication: 2024-07-23 08:50:02 UTC -* Number of recursive dependencies: 96 +* Version: 1.2-1 +* GitHub: https://github.com/openpharma/DoseFinding +* Source code: https://github.com/cran/DoseFinding +* Date/Publication: 2024-08-23 16:20:09 UTC +* Number of recursive dependencies: 103 -Run `revdepcheck::cloud_details(, "dtwclust")` for more info +Run `revdepcheck::cloud_details(, "DoseFinding")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘DoseFinding-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DoseFinding-package + > ### Title: DoseFinding: Planning and Analyzing Dose Finding Experiments + > ### Aliases: DoseFinding DoseFinding-package + > ### Keywords: internal + > + > ### ** Examples + > + ... + > data(IBScovars) + > + > ## perform (model based) multiple contrast test + > ## define candidate dose-response shapes + > models <- Mods(linear = NULL, emax = 0.2, quadratic = -0.17, + + doses = c(0, 1, 2, 3, 4)) + Error in is.element(x, c("emax", "quadratic", "exponential")) : + unused argument (c("emax", "quadratic", "exponential")) + Calls: Mods -> fullMod -> modCount -> lapply -> FUN + Execution halted + ``` + * checking tests ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. + Running ‘testgFit.R’ + Running the tests in ‘tests/testgFit.R’ failed. Complete output: - > library(dtwclust) - Loading required package: proxy - - Attaching package: 'proxy' - - The following objects are masked from 'package:stats': - - ... - 7. └─dtwclust (local) .local(x, y = y, ...) - 8. └─ggplot2:::`+.gg`(gg, do_call(ggrepel::geom_label_repel, labels)) - 9. └─ggplot2:::add_ggplot(e1, e2, e2name) - 10. ├─ggplot2::ggplot_add(object, p, objectname) - 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 0 | SKIP 15 | PASS 1930 ] - Error: Test failures + > require("DoseFinding") + Loading required package: DoseFinding + > data(IBScovars) + > lmfit <- lm(resp~factor(dose)+gender, data=IBScovars) + > cf <- coef(lmfit)[-c(6)] + > vcv <- vcov(lmfit)[-c(6), -c(6)] + > lmfit2 <- lm(resp~as.factor(dose)-1+gender, data=IBScovars) + > cf2 <- coef(lmfit2)[-c(6)] + > vcv2 <- vcov(lmfit2)[-c(6), -c(6)] + > dose <- c(0:4) + > + > ## test fitting all available models + > fitMod(dose[-1], cf[-1], S=vcv[-1,-1], model="linear", placAdj=TRUE,type="general") + Error in is.element(modelNum, 1:4) : unused argument (1:4) + Calls: fitMod -> fitMod.raw Execution halted ``` -## In both - -* checking re-building of vignette outputs ... WARNING +* checking running R code from vignettes ... ERROR ``` - Error(s) in re-building vignettes: - --- re-building ‘parallelization-considerations.Rmd’ using rmarkdown_notangle - --- finished re-building ‘parallelization-considerations.Rmd’ + Errors in running code in vignettes: + when running code in ‘analysis_normal.Rmd’ + ... + + > doses <- c(0, 12.5, 25, 50, 100) + + > mods <- Mods(emax = c(2.6, 12.5), sigEmax = c(30.5, + + 3.5), quadratic = -0.00776, placEff = 1.25, maxEff = 0.15, + + doses = doses) + + ... + When sourcing ‘sample_size.R’: + Error: unused argument (c("emax", "quadratic", "exponential")) + Execution halted - --- re-building ‘timing-experiments.Rmd’ using rmarkdown_notangle + ‘analysis_normal.Rmd’ using ‘UTF-8’... failed + ‘binary_data.Rmd’ using ‘UTF-8’... failed + ‘faq.Rmd’ using ‘UTF-8’... OK + ‘mult_regimen.Rmd’ using ‘UTF-8’... failed + ‘overview.Rmd’ using ‘UTF-8’... failed + ‘sample_size.Rmd’ using ‘UTF-8’... failed ``` -* checking installed package size ... NOTE +* checking whether package ‘DoseFinding’ can be installed ... WARNING ``` - installed size is 15.5Mb - sub-directories of 1Mb or more: - R 1.5Mb - doc 2.1Mb - libs 11.1Mb + Found the following significant warnings: + Note: possible error in 'is.element(modelNum, ': unused argument (1:4) + Note: possible error in 'is.element(names(data), ': unused argument (usedVars) + Note: possible error in 'is.element(nm, c("emax", ': unused argument (c("emax", "exponential", "quadratic")) + Note: possible error in 'is.element(nm, c("logistic", ': unused argument (c("logistic", "betaMod", "sigEmax")) + Note: possible error in 'is.element(type, c("TD", ': unused argument (c("TD", "ED")) + Note: possible error in 'is.element(x, c("emax", ': unused argument (c("emax", "quadratic", "exponential")) + Note: possible error in 'is.element(x, c("sigEmax", ': unused argument (c("sigEmax", "logistic", "betaMod")) + Note: possible error in 'is.element(optimizer, ': unused argument (c("Nelder-Mead", "nlminb")) + Note: possible error in 'is.element(model, "linInt")': unused argument ("linInt") + ... + Note: possible error in 'is.element("S", namargs)': unused argument (namargs) + Note: possible error in 'is.element("df", namargs)': unused argument (namargs) + Note: possible error in 'is.element("n", namargs)': unused argument (namargs) + Note: possible error in 'is.element("sigma", namargs)': unused argument (namargs) + Note: possible error in 'is.element(tms, names(newdata))': unused argument (names(newdata)) + Note: possible error in 'is.element(model, c("logistic", ': unused argument (c("logistic", "linlog")) + See ‘/tmp/workdir/DoseFinding/new/DoseFinding.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + fitMod.raw: possible error in is.element(modelNum, 1:4): unused + argument (1:4) + fitMod.raw: possible error in is.element(names(data), usedVars): unused + argument (usedVars) + fullMod: possible error in is.element(nm, c("emax", "exponential", + "quadratic")): unused argument (c("emax", "exponential", + "quadratic")) + fullMod: possible error in is.element(nm, c("logistic", "betaMod", + "sigEmax")): unused argument (c("logistic", "betaMod", "sigEmax")) + getSimEst: possible error in is.element(type, c("TD", "ED")): unused + ... + sampSizeMCT: possible error in is.element("placAdj", namargs): unused + argument (namargs) + sampSizeMCT: possible error in is.element("S", namargs): unused + argument (namargs) + sampSizeMCT: possible error in is.element("df", namargs): unused + argument (namargs) + sampSizeMCT: possible error in is.element("n", namargs): unused + argument (namargs) + sampSizeMCT: possible error in is.element("sigma", namargs): unused + argument (namargs) ``` -* checking for GNU extensions in Makefiles ... NOTE +* checking re-building of vignette outputs ... NOTE ``` - GNU make is a SystemRequirements. + Error(s) in re-building vignettes: + --- re-building ‘analysis_normal.Rmd’ using rmarkdown ``` -# duke +# dotsViolin
-* Version: 0.0.3 -* GitHub: https://github.com/aidangildea/duke -* Source code: https://github.com/cran/duke -* Date/Publication: 2023-12-15 21:50:16 UTC -* Number of recursive dependencies: 89 +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/dotsViolin +* Date/Publication: 2023-10-30 13:20:02 UTC +* Number of recursive dependencies: 39 -Run `revdepcheck::cloud_details(, "duke")` for more info +Run `revdepcheck::cloud_details(, "dotsViolin")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files + Running examples in ‘dotsViolin-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dots_and_violin + > ### Title: Makes a composite dot-plot and violin-plot + > ### Aliases: dots_and_violin + > ### Keywords: dot-plot violin-plot + > + > ### ** Examples + > ... - 2. │ └─testthat:::expect_condition_matching(...) - 3. │ └─testthat:::quasi_capture(...) - 4. │ ├─testthat (local) .capture(...) - 5. │ │ └─base::withCallingHandlers(...) - 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 7. └─testthat::expect_equal(ggplot2::layer_data(p3)$fill[9], "#B5B5B5") - - [ FAIL 1 | WARN 9 | SKIP 0 | PASS 27 ] - Error: Test failures - Execution halted + 29. │ └─ggplot2 (local) draw_group(...) + 30. │ ├─ggplot2:::ggname(...) + 31. │ │ └─grid::grobName(grob, prefix) + 32. │ └─ggplot2:::dotstackGrob(...) + 33. └─base::.handleSimpleError(...) + 34. └─rlang (local) h(simpleError(msg, call)) + 35. └─handlers[[1L]](cnd) + 36. └─cli::cli_abort(...) + 37. └─rlang::abort(...) + Execution halted ``` -# easysurv +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# dr4pl
-* Version: 2.0.1 -* GitHub: https://github.com/Maple-Health-Group/easysurv -* Source code: https://github.com/cran/easysurv -* Date/Publication: 2024-06-21 10:30:06 UTC -* Number of recursive dependencies: 156 +* Version: 2.0.0 +* GitHub: NA +* Source code: https://github.com/cran/dr4pl +* Date/Publication: 2021-08-17 16:10:18 UTC +* Number of recursive dependencies: 149 -Run `revdepcheck::cloud_details(, "easysurv")` for more info +Run `revdepcheck::cloud_details(, "dr4pl")` for more info
@@ -6307,77 +5706,106 @@ Run `revdepcheck::cloud_details(, "easysurv")` for more info * checking examples ... ERROR ``` - Running examples in ‘easysurv-Ex.R’ failed + Running examples in ‘dr4pl-Ex.R’ failed The error most likely occurred in: - > ### Name: get_km - > ### Title: Generate Kaplan-Meier estimates - > ### Aliases: get_km + > ### Name: IC + > ### Title: Obtain Inhibitory Concentrations (IC) of a dose-response curve + > ### Aliases: IC > > ### ** Examples > - > km_results <- get_km( - ... - Poor Poor 228 145 3.101736 0.1772520 2.183562 1.978082 2.619178 - Median follow-up - Good 4.452055 - Medium 4.712329 - Poor 4.115068 - - Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = "{n.risk}", : - argument "risktable_height" is missing, with no default - Calls: ... ggsurvfit_build -> -> .construct_risktable + > data.test <- data.frame(x = c(0.0001, 0.001, 0.01, 0.1, 1), + + y = c(10, 9, 5, 1, 0)) + > obj.dr4pl <- dr4pl(y ~ x, + + data = data.test) + Error in is.element(method.init, types.method.init) : + unused argument (types.method.init) + Calls: dr4pl -> dr4pl.formula -> dr4pl.default Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘easysurv.Rmd’ + when running code in ‘walk_through_in_R.Rmd’ ... - Median follow-up - Tab+Vis 2.217659 - Tab->Vis 2.220397 - Tab 2.308008 - Vis 2.198494 + + }, warning = function(war) { + + print(paste(sep = " ", war)) + + }, error .... [TRUNCATED] + [1] "simpleWarning in log(dose/parmMat[, 4]): NaNs produced\n" + > dr4pl.error.1 <- dr4pl(Response ~ Dose, data = drc_error_1) - When sourcing ‘easysurv.R’: - Error: argument "risktable_height" is missing, with no default + When sourcing ‘walk_through_in_R.R’: + Error: unused argument (types.method.init) Execution halted - ‘easysurv.Rmd’ using ‘UTF-8’... failed + ‘dr4pl_derivatives.Rmd’ using ‘UTF-8’... OK + ‘walk_through_in_R.Rmd’ using ‘UTF-8’... failed + ``` + +* checking whether package ‘dr4pl’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(trend, types.trend)': unused argument (types.trend) + Note: possible error in 'is.element(method.init, ': unused argument (types.method.init) + Note: possible error in 'is.element(method.robust, ': unused argument (types.method.robust) + Note: possible error in 'is.element(method.optim, ': unused argument (types.method.optim) + Note: possible error in 'is.element(method.robust, ': unused argument (c("absolute", "Huber")) + See ‘/tmp/workdir/dr4pl/new/dr4pl.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + FindInitialParms: possible error in is.element(trend, types.trend): + unused argument (types.trend) + FindInitialParms: possible error in is.element(method.init, + types.method.init): unused argument (types.method.init) + FindInitialParms: possible error in is.element(method.robust, + types.method.robust): unused argument (types.method.robust) + dr4pl.default: possible error in is.element(method.init, + types.method.init): unused argument (types.method.init) + dr4pl.default: possible error in is.element(method.optim, + types.method.optim): unused argument (types.method.optim) + dr4pl.default: possible error in is.element(trend, types.trend): unused + argument (types.trend) + dr4pl.default: possible error in is.element(method.robust, + c("absolute", "Huber")): unused argument (c("absolute", "Huber")) ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘easysurv.Rmd’ using rmarkdown - - Quitting from lines 149-157 [km] (easysurv.Rmd) - Error: processing vignette 'easysurv.Rmd' failed with diagnostics: - argument "risktable_height" is missing, with no default - --- failed re-building ‘easysurv.Rmd’ - - SUMMARY: processing the following file failed: - ‘easysurv.Rmd’ + --- re-building ‘dr4pl_derivatives.Rmd’ using rmarkdown + --- finished re-building ‘dr4pl_derivatives.Rmd’ - Error: Vignette re-building failed. - Execution halted + --- re-building ‘walk_through_in_R.Rmd’ using rmarkdown + ``` + +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \& + checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \& + checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \& ``` -# EGAnet +# DRomics
-* Version: 2.0.7 -* GitHub: https://github.com/hfgolino/EGAnet -* Source code: https://github.com/cran/EGAnet -* Date/Publication: 2024-09-02 20:00:01 UTC -* Number of recursive dependencies: 190 +* Version: 2.6-2 +* GitHub: https://github.com/lbbe-software/DRomics +* Source code: https://github.com/cran/DRomics +* Date/Publication: 2024-10-16 09:50:02 UTC +* Number of recursive dependencies: 151 -Run `revdepcheck::cloud_details(, "EGAnet")` for more info +Run `revdepcheck::cloud_details(, "DRomics")` for more info
@@ -6385,50 +5813,156 @@ Run `revdepcheck::cloud_details(, "EGAnet")` for more info * checking examples ... ERROR ``` - Running examples in ‘EGAnet-Ex.R’ failed + Running examples in ‘DRomics-Ex.R’ failed The error most likely occurred in: - > ### Name: dimensionStability - > ### Title: Dimension Stability Statistics from 'bootEGA' - > ### Aliases: dimensionStability + > ### Name: bmdfilter + > ### Title: Filtering BMDs according to estimation quality + > ### Aliases: bmdfilter > > ### ** Examples > - > # Load data + > ... - 16. │ └─e1 %+% e2 - 17. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 18. │ ├─ggplot2::ggplot_add(object, p, objectname) - 19. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 20. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 21. └─base::.handleSimpleError(...) - 22. └─purrr (local) h(simpleError(msg, call)) - 23. └─cli::cli_abort(...) - 24. └─rlang::abort(...) + > + > ### (1.a) Examples on BMD.xfold (with some undefined BMD.xfold values) + > + > # Plot of BMDs with no filtering + > subres <- bmdfilter(b$res, BMDfilter = "none") + > bmdplot(subres, BMDtype = "xfold", point.size = 3, add.CI = TRUE) + Error in is.element(c("id", "BMD.xfold"), cnames) : + unused argument (cnames) + Calls: bmdplot Execution halted ``` +* checking whether package ‘DRomics’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(c("BMD.zSD"), ': unused argument (cnames) + Note: possible error in 'is.element(c("BMD.zSD.upper", ': unused argument (cnames) + Note: possible error in 'is.element(c("BMD.xfold"), ': unused argument (cnames) + Note: possible error in 'is.element(c("BMD.xfold.upper", ': unused argument (cnames) + Note: possible error in 'is.element(c("id", "BMD.zSD"), ': unused argument (cnames) + Note: possible error in 'is.element(c("id", "BMD.xfold"), ': unused argument (cnames) + Note: possible error in 'is.element(shapeby, cnames)': unused argument (cnames) + Note: possible error in 'is.element(colorby, cnames)': unused argument (cnames) + Note: possible error in 'is.element(facetby, cnames)': unused argument (cnames) + ... + Note: possible error in 'is.element(c("id", "model", ': unused argument (cnames) + Note: possible error in 'is.element(c("BMD.zSD", ': unused argument (cnames) + Note: possible error in 'is.element(c("BMD.xfold", ': unused argument (cnames) + Note: possible error in 'is.element(group, cnames)': unused argument (cnames) + Note: possible error in 'is.element(explev, cnames)': unused argument (cnames) + Note: possible error in 'is.element(c("trend"), ': unused argument (cnames) + See ‘/tmp/workdir/DRomics/new/DRomics.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + bmdfilter: possible error in is.element(c("BMD.zSD"), cnames): unused + argument (cnames) + bmdfilter: possible error in is.element(c("BMD.zSD.upper", + "BMD.zSD.lower"), cnames): unused argument (cnames) + bmdfilter: possible error in is.element(c("BMD.xfold"), cnames): unused + argument (cnames) + bmdfilter: possible error in is.element(c("BMD.xfold.upper", + "BMD.xfold.lower"), cnames): unused argument (cnames) + bmdplot: possible error in is.element(c("id", "BMD.zSD"), cnames): + unused argument (cnames) + ... + sensitivityplot: possible error in is.element(group, cnames): unused + argument (cnames) + sensitivityplot: possible error in is.element(colorby, cnames): unused + argument (cnames) + trendplot: possible error in is.element(group, cnames): unused argument + (cnames) + trendplot: possible error in is.element(c("trend"), cnames): unused + argument (cnames) + trendplot: possible error in is.element(facetby, cnames): unused + argument (cnames) + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘DRomics_vignette.Rmd’ using rmarkdown + ``` + ## In both +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘DRomics_vignette.Rmd’ + ... + 6 8.90 5.47 8.19 + + > plot(r, BMDtype = "zSD", plottype = "ecdf") + theme_bw() + + > bmdplotwithgradient(r$res, BMDtype = "zSD", facetby = "trend", + + shapeby = "model", line.size = 1.2, scaling = TRUE) + + When sourcing ‘DRomics_vignette.R’: + Error: unused argument (cnames) + Execution halted + + ‘DRomics_vignette.Rmd’ using ‘UTF-8’... failed + ``` + * checking installed package size ... NOTE ``` - installed size is 5.6Mb + installed size is 5.8Mb sub-directories of 1Mb or more: - R 1.5Mb - data 3.5Mb + doc 2.5Mb ``` -# EGM +# drpop
-* Version: 0.1.0 -* GitHub: https://github.com/shah-in-boots/EGM -* Source code: https://github.com/cran/EGM -* Date/Publication: 2024-05-23 16:10:05 UTC -* Number of recursive dependencies: 77 +* Version: 0.0.3 +* GitHub: NA +* Source code: https://github.com/cran/drpop +* Date/Publication: 2021-11-05 21:10:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "EGM")` for more info +Run `revdepcheck::cloud_details(, "drpop")` for more info + +
+ +## Newly broken + +* checking whether package ‘drpop’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(condvar, colnames(data))': unused argument (colnames(data)) + See ‘/tmp/workdir/drpop/new/drpop.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + popsize_cond: possible error in is.element(condvar, colnames(data)): + unused argument (colnames(data)) + ``` + +# duke + +
+ +* Version: 0.0.3 +* GitHub: https://github.com/aidangildea/duke +* Source code: https://github.com/cran/duke +* Date/Publication: 2023-12-15 21:50:16 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "duke")` for more info
@@ -6439,128 +5973,136 @@ Run `revdepcheck::cloud_details(, "EGM")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: - > library(testthat) - > library(EGM) - Loading required package: vctrs - Loading required package: data.table - > EGM::set_wfdb_path("/usr/local/bin") - > - > test_check("EGM") + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-ggm.R:63:2'): theming works ────────────────────────────────── - g$labels$x (`actual`) not equal to "sample" (`expected`). - - `actual` is NULL - `expected` is a character vector ('sample') + 2. │ └─testthat:::expect_condition_matching(...) + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─testthat::expect_equal(ggplot2::layer_data(p3)$fill[9], "#B5B5B5") - [ FAIL 1 | WARN 0 | SKIP 19 | PASS 43 ] + [ FAIL 1 | WARN 9 | SKIP 0 | PASS 27 ] Error: Test failures Execution halted ``` -# emmeans +# dymo
-* Version: 1.10.4 -* GitHub: https://github.com/rvlenth/emmeans -* Source code: https://github.com/cran/emmeans -* Date/Publication: 2024-08-21 03:00:01 UTC -* Number of recursive dependencies: 159 +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/dymo +* Date/Publication: 2022-05-05 08:00:02 UTC +* Number of recursive dependencies: 147 -Run `revdepcheck::cloud_details(, "emmeans")` for more info +Run `revdepcheck::cloud_details(, "dymo")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘dymo’ can be installed ... WARNING ``` - Running examples in ‘emmeans-Ex.R’ failed - The error most likely occurred in: - - > ### Name: auto.noise - > ### Title: Auto Pollution Filter Noise - > ### Aliases: auto.noise - > ### Keywords: datasets - > - > ### ** Examples - > - > # (Based on belief that noise/10 is in decibel units) - > noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise) - > - > # Interaction plot of predictions - > emmip(noise.lm, type ~ size | side) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: emmip ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::is.scale’ by ‘greybox::is.scale’ when loading ‘dymo’ + See ‘/tmp/workdir/dymo/new/dymo.Rcheck/00install.out’ for details. + ``` + +# dynr + +
+ +* Version: 0.1.16-105 +* GitHub: https://github.com/mhunter1/dynr +* Source code: https://github.com/cran/dynr +* Date/Publication: 2023-11-28 05:20:05 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "dynr")` for more info + +
+ +## Newly broken + +* checking whether package ‘dynr’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(id, id_toplot)': unused argument (id_toplot) + See ‘/tmp/workdir/dynr/new/dynr.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + autoplot.dynrTaste: possible error in is.element(id, id_toplot): unused + argument (id_toplot) ``` ## In both -* checking running R code from vignettes ... ERROR +* checking Rd files ... WARNING ``` - Errors in running code in vignettes: - when running code in ‘basics.Rmd’ - ... - 'emmGrid' object with variables: - source = fish, soy, skim - percent = 9, 12, 15, 18 - Transformation: “inverse” - - > emmip(RG4, source ~ percent, style = "factor") - - ... - ‘messy-data.Rmd’ using ‘UTF-8’... failed - ‘models.Rmd’ using ‘UTF-8’... OK - ‘predictions.Rmd’ using ‘UTF-8’... failed - ‘re-engineering-clds.rmd’ using ‘UTF-8’... OK - ‘sophisticated.Rmd’ using ‘UTF-8’... failed - ‘transformations.Rmd’ using ‘UTF-8’... failed - ‘utilities.Rmd’ using ‘UTF-8’... OK - ‘vignette-topics.Rmd’ using ‘UTF-8’... OK - ‘xplanations.Rmd’ using ‘UTF-8’... failed - ‘xtending.Rmd’ using ‘UTF-8’... OK + prepare_Rd: ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original ‘Matrix’ package ``` -* checking package dependencies ... NOTE +* checking installed package size ... NOTE ``` - Packages which this enhances but not available for checking: - 'CARBayes', 'coxme', 'gee', 'geepack', 'MCMCglmm', 'MCMCpack', - 'mice', 'pscl', 'rstanarm', 'sommer' + installed size is 10.1Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 6.0Mb + doc 1.4Mb ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘AQuickStart.Rmd’ using rmarkdown - --- finished re-building ‘AQuickStart.Rmd’ + --- re-building ‘linearSDE.Rmd’ using rmarkdown + --- finished re-building ‘linearSDE.Rmd’ - --- re-building ‘FAQs.Rmd’ using rmarkdown - --- finished re-building ‘FAQs.Rmd’ + --- re-building ‘InstallationForDevelopers.Rnw’ using Sweave + Error: processing vignette 'InstallationForDevelopers.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'InstallationForDevelopers.tex' failed. + LaTeX errors: + ! LaTeX Error: File `menukeys.sty' not found. - --- re-building ‘basics.Rmd’ using rmarkdown + ... + {bm}%bm^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘NonlinearContinuousTimeModels.Rnw’ - Quitting from lines 260-262 [unnamed-chunk-13] (basics.Rmd) - Error: processing vignette 'basics.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘basics.Rmd’ + SUMMARY: processing the following files failed: + ‘InstallationForDevelopers.Rnw’ ‘InstallationForUsers.Rnw’ + ‘LinearDiscreteTimeModels.Rnw’ ‘NonlinearContinuousTimeModels.Rnw’ - --- re-building ‘comparisons.Rmd’ using rmarkdown + Error: Vignette re-building failed. + Execution halted ``` -# EMMIXmfa +# easysurv
-* Version: 2.0.14 -* GitHub: https://github.com/suren-rathnayake/EMMIXmfa -* Source code: https://github.com/cran/EMMIXmfa -* Date/Publication: 2024-01-25 20:30:02 UTC -* Number of recursive dependencies: 59 +* Version: 2.0.1 +* GitHub: https://github.com/Maple-Health-Group/easysurv +* Source code: https://github.com/cran/easysurv +* Date/Publication: 2024-06-21 10:30:06 UTC +* Number of recursive dependencies: 155 -Run `revdepcheck::cloud_details(, "EMMIXmfa")` for more info +Run `revdepcheck::cloud_details(, "easysurv")` for more info
@@ -6568,29 +6110,107 @@ Run `revdepcheck::cloud_details(, "EMMIXmfa")` for more info * checking examples ... ERROR ``` - Running examples in ‘EMMIXmfa-Ex.R’ failed + Running examples in ‘easysurv-Ex.R’ failed The error most likely occurred in: - > ### Name: factor_scores - > ### Title: Computes Factor Scores - > ### Aliases: factor_scores factor_scores.mcfa factor_scores.mctfa - > ### plot.emmix - > ### Keywords: cluster multivariate models + > ### Name: get_km + > ### Title: Generate Kaplan-Meier estimates + > ### Aliases: get_km > > ### ** Examples - ... - > Y <- iris[-c(sel_subset), -5] - > Y <- as.matrix(Y) - > clust <- predict(model, Y) > - > fa_scores <- factor_scores(model, Y) - > # Visualizing new data in factor space - > plot_factors(fa_scores, type = "Umean", clust = clust) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot_factors ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > km_results <- get_km( + ... + Poor Poor 228 145 3.101736 0.1772520 2.183562 1.978082 2.619178 + Median follow-up + Good 4.452055 + Medium 4.712329 + Poor 4.115068 + + Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = "{n.risk}", : + argument "risktable_height" is missing, with no default + Calls: ... ggsurvfit_build -> -> .construct_risktable + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘easysurv.Rmd’ + ... + Median follow-up + Tab+Vis 2.217659 + Tab->Vis 2.220397 + Tab 2.308008 + Vis 2.198494 + + + When sourcing ‘easysurv.R’: + Error: argument "risktable_height" is missing, with no default + Execution halted + + ‘easysurv.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘easysurv.Rmd’ using rmarkdown + + Quitting from lines 149-157 [km] (easysurv.Rmd) + Error: processing vignette 'easysurv.Rmd' failed with diagnostics: + argument "risktable_height" is missing, with no default + --- failed re-building ‘easysurv.Rmd’ + + SUMMARY: processing the following file failed: + ‘easysurv.Rmd’ + + Error: Vignette re-building failed. Execution halted ``` +# EGM + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/shah-in-boots/EGM +* Source code: https://github.com/cran/EGM +* Date/Publication: 2024-05-23 16:10:05 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "EGM")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(EGM) + Loading required package: vctrs + Loading required package: data.table + > EGM::set_wfdb_path("/usr/local/bin") + > + > test_check("EGM") + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-ggm.R:63:2'): theming works ────────────────────────────────── + g$labels$x (`actual`) not equal to "sample" (`expected`). + + `actual` is NULL + `expected` is a character vector ('sample') + + [ FAIL 1 | WARN 0 | SKIP 19 | PASS 43 ] + Error: Test failures + Execution halted + ``` + # entropart
@@ -6599,7 +6219,7 @@ Run `revdepcheck::cloud_details(, "EMMIXmfa")` for more info * GitHub: https://github.com/EricMarcon/entropart * Source code: https://github.com/cran/entropart * Date/Publication: 2024-08-26 19:30:09 UTC -* Number of recursive dependencies: 125 +* Number of recursive dependencies: 128 Run `revdepcheck::cloud_details(, "entropart")` for more info @@ -6673,57 +6293,6 @@ Run `revdepcheck::cloud_details(, "entropart")` for more info Execution halted ``` -# EnvStats - -
- -* Version: 3.0.0 -* GitHub: https://github.com/alexkowa/EnvStats -* Source code: https://github.com/cran/EnvStats -* Date/Publication: 2024-08-24 23:10:05 UTC -* Number of recursive dependencies: 79 - -Run `revdepcheck::cloud_details(, "EnvStats")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EnvStats-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_stripchart - > ### Title: 1-D Scatter Plots with Confidence Intervals Using ggplot2 - > ### Aliases: geom_stripchart - > ### Keywords: hplot htest - > - > ### ** Examples - > - ... - > - > p + geom_stripchart() + - + labs(x = "Number of Cylinders", y = "Miles per Gallon") - Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0. - ℹ Please use the `fun` argument instead. - ℹ The deprecated feature was likely used in the EnvStats package. - Please report the issue to the authors. - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.8Mb - sub-directories of 1Mb or more: - R 3.5Mb - help 3.5Mb - ``` - # epiCleanr
@@ -6732,7 +6301,7 @@ Run `revdepcheck::cloud_details(, "EnvStats")` for more info * GitHub: https://github.com/truenomad/epiCleanr * Source code: https://github.com/cran/epiCleanr * Date/Publication: 2023-09-28 12:20:05 UTC -* Number of recursive dependencies: 130 +* Number of recursive dependencies: 129 Run `revdepcheck::cloud_details(, "epiCleanr")` for more info @@ -6820,11 +6389,11 @@ Run `revdepcheck::cloud_details(, "epiphy")` for more info
-* Version: 0.4.0 +* Version: 0.5.0 * GitHub: NA * Source code: https://github.com/cran/EQUALSTATS -* Date/Publication: 2024-09-06 16:10:15 UTC -* Number of recursive dependencies: 120 +* Date/Publication: 2024-09-23 08:30:02 UTC +* Number of recursive dependencies: 131 Run `revdepcheck::cloud_details(, "EQUALSTATS")` for more info @@ -6864,17 +6433,17 @@ Run `revdepcheck::cloud_details(, "EQUALSTATS")` for more info Package unavailable to check Rd xrefs: ‘lmerTest’ ``` -# ergm.multi +# esci
-* Version: 0.2.1 -* GitHub: https://github.com/statnet/ergm.multi -* Source code: https://github.com/cran/ergm.multi -* Date/Publication: 2024-02-20 23:20:05 UTC -* Number of recursive dependencies: 82 +* Version: 1.0.6 +* GitHub: https://github.com/rcalinjageman/esci +* Source code: https://github.com/cran/esci +* Date/Publication: 2024-12-21 16:00:02 UTC +* Number of recursive dependencies: 92 -Run `revdepcheck::cloud_details(, "ergm.multi")` for more info +Run `revdepcheck::cloud_details(, "esci")` for more info
@@ -6882,91 +6451,13 @@ Run `revdepcheck::cloud_details(, "ergm.multi")` for more info * checking examples ... ERROR ``` - Running examples in ‘ergm.multi-Ex.R’ failed + Running examples in ‘esci-Ex.R’ failed The error most likely occurred in: - > ### Name: gofN - > ### Title: Linear model diagnostics for multinetwork linear models - > ### Aliases: gofN [.gofN augment.gofN summary.gofN - > - > ### ** Examples - > - > data(samplk) - ... - > - > ### If 'ggplot2' and 'ggrepel' are installed, illustrate the autoplot() method. - > if(require("ggplot2") && requireNamespace("ggrepel")){ - + autoplot(fit.gof) - + } - Loading required package: ggplot2 - Loading required namespace: ggrepel - Error in if (new_name %in% existing) { : argument is of length zero - Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Goeyvaerts_reproduction.Rmd’ - ... - [1] 0.9763295 - - - - > autoplot(gof.wd) - Loading required namespace: ggrepel - - When sourcing ‘Goeyvaerts_reproduction.R’: - Error: argument is of length zero - Execution halted - - ‘Goeyvaerts_reproduction.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Goeyvaerts_reproduction.Rmd’ using rmarkdown - - Quitting from lines 157-158 [unnamed-chunk-16] (Goeyvaerts_reproduction.Rmd) - Error: processing vignette 'Goeyvaerts_reproduction.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Goeyvaerts_reproduction.Rmd’ - - SUMMARY: processing the following file failed: - ‘Goeyvaerts_reproduction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# esci - -
- -* Version: 1.0.3 -* GitHub: https://github.com/rcalinjageman/esci -* Source code: https://github.com/cran/esci -* Date/Publication: 2024-07-08 21:40:10 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "esci")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘esci-Ex.R’ failed - The error most likely occurred in: - - > ### Name: estimate_mdiff_2x2_between - > ### Title: Estimates for a 2x2 between-subjects design with a continuous - > ### outcome variable - > ### Aliases: estimate_mdiff_2x2_between + > ### Name: estimate_mdiff_2x2_between + > ### Title: Estimates for a 2x2 between-subjects design with a continuous + > ### outcome variable + > ### Aliases: estimate_mdiff_2x2_between > > ### ** Examples > @@ -6992,9 +6483,9 @@ Run `revdepcheck::cloud_details(, "esci")` for more info > library(esci) > > test_check("esci") - Loading required package: Matrix - Loading required package: metadat - Loading required package: numDeriv + [1] "WARNING: ratio-scale scores cannot be negative" + [1] "WARNING: ratio-scale scores cannot be negative" + [1] "WARNING: ratio-scale scores cannot be negative" ... 17. │ └─self$geom$use_defaults(...) 18. └─base::.handleSimpleError(...) @@ -7003,7 +6494,7 @@ Run `revdepcheck::cloud_details(, "esci")` for more info 21. └─cli::cli_abort(...) 22. └─rlang::abort(...) - [ FAIL 14 | WARN 0 | SKIP 0 | PASS 3182 ] + [ FAIL 3 | WARN 0 | SKIP 52 | PASS 2889 ] Error: Test failures Execution halted ``` @@ -7016,7 +6507,7 @@ Run `revdepcheck::cloud_details(, "esci")` for more info * GitHub: https://github.com/MichaelLLi/evalITR * Source code: https://github.com/cran/evalITR * Date/Publication: 2023-08-25 23:10:06 UTC -* Number of recursive dependencies: 167 +* Number of recursive dependencies: 166 Run `revdepcheck::cloud_details(, "evalITR")` for more info @@ -7072,7 +6563,7 @@ Run `revdepcheck::cloud_details(, "evalITR")` for more info * GitHub: https://github.com/JMSLab/eventstudyr * Source code: https://github.com/cran/eventstudyr * Date/Publication: 2024-03-04 15:00:02 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 100 Run `revdepcheck::cloud_details(, "eventstudyr")` for more info @@ -7105,89 +6596,6 @@ Run `revdepcheck::cloud_details(, "eventstudyr")` for more info Execution halted ``` -# EvoPhylo - -
- -* Version: 0.3.2 -* GitHub: https://github.com/tiago-simoes/EvoPhylo -* Source code: https://github.com/cran/EvoPhylo -* Date/Publication: 2022-11-03 17:00:02 UTC -* Number of recursive dependencies: 145 - -Run `revdepcheck::cloud_details(, "EvoPhylo")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EvoPhylo-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_clusters - > ### Title: Estimate and plot character partitions - > ### Aliases: make_clusters plot.cluster_df - > - > ### ** Examples - > - > # See vignette("char-part") for how to use this - ... - > # tSNE (3 dimensions; default is 2) - > cluster_df_tsne <- make_clusters(Dmatrix, k = 3, tsne = TRUE, - + tsne_dim = 2) - > - > # Plot clusters, plots divided into 2 rows, and increasing - > # overlap of text labels (default = 10) - > plot(cluster_df_tsne, nrow = 2, max.overlaps = 20) - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits - Execution halted - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘char-part.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘char-part.Rmd’ - ... - + collapse = TRUE, dpi = 300) - - > devtools::load_all(".") - - When sourcing ‘char-part.R’: - Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in - '/tmp/Rtmp6FtfyP/file1a7972246c9b/vignettes'. - ... - ℹ Are you in your project directory and does your project have a 'DESCRIPTION' - file? - Execution halted - - ‘char-part.Rmd’ using ‘UTF-8’... failed - ‘data_treatment.Rmd’ using ‘UTF-8’... OK - ‘fbd-params.Rmd’ using ‘UTF-8’... failed - ‘offset_handling.Rmd’ using ‘UTF-8’... failed - ‘rates-selection_BEAST2.Rmd’ using ‘UTF-8’... failed - ‘rates-selection_MrBayes.Rmd’ using ‘UTF-8’... failed - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - data 2.5Mb - doc 1.6Mb - extdata 2.4Mb - ``` - # expirest
@@ -7196,7 +6604,7 @@ Run `revdepcheck::cloud_details(, "EvoPhylo")` for more info * GitHub: https://github.com/piusdahinden/expirest * Source code: https://github.com/cran/expirest * Date/Publication: 2024-03-25 16:30:02 UTC -* Number of recursive dependencies: 46 +* Number of recursive dependencies: 45 Run `revdepcheck::cloud_details(, "expirest")` for more info @@ -7233,11 +6641,11 @@ Run `revdepcheck::cloud_details(, "expirest")` for more info
-* Version: 1.0.1 +* Version: 1.0.2 * GitHub: https://github.com/PERSIMUNE/explainer * Source code: https://github.com/cran/explainer -* Date/Publication: 2024-04-18 09:00:02 UTC -* Number of recursive dependencies: 183 +* Date/Publication: 2024-09-30 17:30:02 UTC +* Number of recursive dependencies: 186 Run `revdepcheck::cloud_details(, "explainer")` for more info @@ -7278,67 +6686,6 @@ Run `revdepcheck::cloud_details(, "explainer")` for more info All declared Imports should be used. ``` -# exuber - -
- -* Version: 1.0.2 -* GitHub: https://github.com/kvasilopoulos/exuber -* Source code: https://github.com/cran/exuber -* Date/Publication: 2023-03-22 23:10:02 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "exuber")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘exuber.Rmd’ - ... - 370 1 1 1 0 - 371 1 1 0 0 - 372 1 1 0 0 - - > autoplot(est_stocks) - Using `radf_crit` for `cv`. - - ... - - > autoplot(estimation, crit_values) - - When sourcing ‘plotting.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘exuber.Rmd’ using ‘UTF-8’... failed - ‘plotting.Rmd’ using ‘UTF-8’... failed - ‘simulation.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘exuber.Rmd’ using rmarkdown - - Quitting from lines 73-74 [plot-radf] (exuber.Rmd) - Error: processing vignette 'exuber.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘exuber.Rmd’ - - --- re-building ‘plotting.Rmd’ using rmarkdown - - Quitting from lines 58-59 [autoplot-basic] (plotting.Rmd) - Error: processing vignette 'plotting.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘plotting.Rmd’ - - --- re-building ‘simulation.Rmd’ using rmarkdown - ``` - # ezEDA
@@ -7347,7 +6694,7 @@ Run `revdepcheck::cloud_details(, "exuber")` for more info * GitHub: https://github.com/kviswana/ezEDA * Source code: https://github.com/cran/ezEDA * Date/Publication: 2021-06-29 04:40:10 UTC -* Number of recursive dependencies: 92 +* Number of recursive dependencies: 79 Run `revdepcheck::cloud_details(, "ezEDA")` for more info @@ -7380,42 +6727,6 @@ Run `revdepcheck::cloud_details(, "ezEDA")` for more info Execution halted ``` -# ezplot - -
- -* Version: 0.7.13 -* GitHub: NA -* Source code: https://github.com/cran/ezplot -* Date/Publication: 2024-01-28 11:30:05 UTC -* Number of recursive dependencies: 109 - -Run `revdepcheck::cloud_details(, "ezplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ezplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: model_plot - > ### Title: model_plot - > ### Aliases: model_plot - > - > ### ** Examples - > - > y = rnorm(26) - > df = data.frame(ID = 1:26, actual = y + rnorm(26), fitted = y, id = letters) - > model_plot(df, "ID", "actual", "fitted") - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - # fable.prophet
@@ -7424,7 +6735,7 @@ Run `revdepcheck::cloud_details(, "ezplot")` for more info * GitHub: https://github.com/mitchelloharawild/fable.prophet * Source code: https://github.com/cran/fable.prophet * Date/Publication: 2020-08-20 09:30:03 UTC -* Number of recursive dependencies: 114 +* Number of recursive dependencies: 113 Run `revdepcheck::cloud_details(, "fable.prophet")` for more info @@ -7437,15 +6748,15 @@ Run `revdepcheck::cloud_details(, "fable.prophet")` for more info Errors in running code in vignettes: when running code in ‘intro.Rmd’ ... - 9 Domestic mdl 2019 Dec sample[5000] 5338093. - 10 Domestic mdl 2020 Jan sample[5000] 4888643. + 9 Domestic mdl 2019 Dec sample[5000] 5336974. + 10 Domestic mdl 2020 Jan sample[5000] 4886604. # ℹ 62 more rows > fc %>% autoplot(lax_passengers) When sourcing ‘intro.R’: Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, N Execution halted ‘intro.Rmd’ using ‘UTF-8’... failed @@ -7468,11 +6779,11 @@ Run `revdepcheck::cloud_details(, "fable.prophet")` for more info
-* Version: 0.4.2 +* Version: 0.5.0 * GitHub: https://github.com/tidyverts/fabletools * Source code: https://github.com/cran/fabletools -* Date/Publication: 2024-04-22 11:22:41 UTC -* Number of recursive dependencies: 106 +* Date/Publication: 2024-09-17 07:30:02 UTC +* Number of recursive dependencies: 107 Run `revdepcheck::cloud_details(, "fabletools")` for more info @@ -7500,7 +6811,7 @@ Run `revdepcheck::cloud_details(, "fabletools")` for more info > fc %>% autoplot(aus_production) Error in use_defaults(..., self = self) : unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, Calls: ... -> -> compute_geom_2 -> Execution halted ``` @@ -7525,52 +6836,11 @@ Run `revdepcheck::cloud_details(, "fabletools")` for more info ── Failure ('test-graphics.R:346:3'): autoplot_dcmp_ts() ─────────────────────── `print(p)` produced warnings. - [ FAIL 4 | WARN 5 | SKIP 1 | PASS 267 ] + [ FAIL 4 | WARN 5 | SKIP 1 | PASS 266 ] Error: Test failures Execution halted ``` -# factoextra - -
- -* Version: 1.0.7 -* GitHub: https://github.com/kassambara/factoextra -* Source code: https://github.com/cran/factoextra -* Date/Publication: 2020-04-01 21:20:02 UTC -* Number of recursive dependencies: 116 - -Run `revdepcheck::cloud_details(, "factoextra")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘factoextra-Ex.R’ failed - The error most likely occurred in: - - > ### Name: eclust - > ### Title: Visual enhancement of clustering analysis - > ### Aliases: eclust - > - > ### ** Examples - > - > # Load and scale data - ... - 12. │ └─ggplot2:::`+.gg`(...) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - Execution halted - ``` - # fairmodels
@@ -7579,7 +6849,7 @@ Run `revdepcheck::cloud_details(, "factoextra")` for more info * GitHub: https://github.com/ModelOriented/fairmodels * Source code: https://github.com/cran/fairmodels * Date/Publication: 2022-08-23 19:50:06 UTC -* Number of recursive dependencies: 87 +* Number of recursive dependencies: 86 Run `revdepcheck::cloud_details(, "fairmodels")` for more info @@ -7600,29 +6870,29 @@ Run `revdepcheck::cloud_details(, "fairmodels")` for more info Welcome to DALEX (version: 2.4.3). Find examples and detailed introduction at: http://ema.drwhy.ai/ ... - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 312 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plot_density.R:14:3'): Test plot_density ───────────────────── plt$labels$x not equal to "probability". target is NULL, current is character - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 312 ] Error: Test failures Execution halted ``` -# fastR2 +# FCPS
-* Version: 1.2.4 -* GitHub: https://github.com/rpruim/fastR2 -* Source code: https://github.com/cran/fastR2 -* Date/Publication: 2023-11-09 06:30:03 UTC -* Number of recursive dependencies: 165 +* Version: 1.3.4 +* GitHub: https://github.com/Mthrun/FCPS +* Source code: https://github.com/cran/FCPS +* Date/Publication: 2023-10-19 13:20:02 UTC +* Number of recursive dependencies: 269 -Run `revdepcheck::cloud_details(, "fastR2")` for more info +Run `revdepcheck::cloud_details(, "FCPS")` for more info
@@ -7630,134 +6900,92 @@ Run `revdepcheck::cloud_details(, "fastR2")` for more info * checking examples ... ERROR ``` - Running examples in ‘fastR2-Ex.R’ failed + Running examples in ‘FCPS-Ex.R’ failed The error most likely occurred in: - > ### Name: ACTgpa - > ### Title: ACT scores and GPA - > ### Aliases: ACTgpa - > ### Keywords: datasets + > ### Name: SOTAclustering + > ### Title: SOTA Clustering + > ### Aliases: SOTAclustering sotaClustering + > ### Keywords: SOTAclustering > > ### ** Examples > - > - > gf_point(GPA ~ ACT, data = ACTgpa) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > #Does Work + > data('Hepta') + > out=SOTAclustering(Hepta$Data,ClusterNo=7) + Error in is.element(i, clust) : unused argument (clust) + Calls: SOTAclustering -> sota -> trainLeaves Execution halted ``` +* checking whether package ‘FCPS’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(i, clust)': unused argument (clust) + See ‘/tmp/workdir/FCPS/new/FCPS.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + trainLeaves: possible error in is.element(i, clust): unused argument + (clust) + ``` + ## In both * checking installed package size ... NOTE ``` - installed size is 6.1Mb + installed size is 11.1Mb sub-directories of 1Mb or more: - data 2.0Mb - snippet 3.7Mb + data 6.5Mb + doc 3.9Mb ``` -# faux +# fdANOVA
-* Version: 1.2.1 -* GitHub: https://github.com/debruine/faux -* Source code: https://github.com/cran/faux -* Date/Publication: 2023-04-20 07:00:11 UTC -* Number of recursive dependencies: 132 +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/fdANOVA +* Date/Publication: 2018-08-29 19:54:26 UTC +* Number of recursive dependencies: 70 -Run `revdepcheck::cloud_details(, "faux")` for more info +Run `revdepcheck::cloud_details(, "fdANOVA")` for more info
## Newly broken -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘codebook.Rmd’ using rmarkdown - --- finished re-building ‘codebook.Rmd’ - - --- re-building ‘continuous.Rmd’ using rmarkdown - ``` - -## In both - * checking examples ... ERROR ``` - Running examples in ‘faux-Ex.R’ failed + Running examples in ‘fdANOVA-Ex.R’ failed The error most likely occurred in: - > ### Name: beta2norm - > ### Title: Convert beta to normal - > ### Aliases: beta2norm + > ### Name: fanova.tests + > ### Title: Tests for FANOVA Problem + > ### Aliases: fanova.tests + > ### Keywords: Multivariate Test > > ### ** Examples > + ... + + own.basis = own.basis, + + own.cross.prod.mat = own.cross.prod.mat))) > - > x <- rbeta(10000, 2, 3) - > y <- beta2norm(x) - shape1 was set to 1.96704823352025 - shape2 was set to 2.94110338061547 - > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y)) - > ggExtra::ggMarginal(g, type = "histogram") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > # the tests based on random projections with the Gaussian white noise generated for projections + > fanova4 <- fanova.tests(x.gait, group.label.gait, test = "TRP", + + params = list(paramTRP = list(k = c(1, 2), B.TRP = 2))) + Error in is.element(substring(formc, 1, 1), c("+", "-")) : + unused argument (c("+", "-")) + Calls: fanova.tests ... pf -> anova.statistic.quick -> -> orderBy Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(faux) - - ************ - Welcome to faux. For support and examples visit: - https://debruine.github.io/faux/ - - Get and set global package options with: faux_options() - ... - 6. └─methods (local) ``(...) - 7. └─methods::new(def, ...) - 8. ├─methods::initialize(value, ...) - 9. └─methods::initialize(value, ...) - 10. └─.Object$initialize(...) - 11. └─lme4 (local) initializePtr() - - [ FAIL 20 | WARN 6 | SKIP 14 | PASS 1331 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘norta.Rmd’ - ... - - > p <- ggplot(dat, aes(uniform_var, poisson_var)) + - + geom_point() + geom_smooth() - - > ggMarginal(p, type = "histogram") - `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")' - - ... - Error: argument is of length zero - Execution halted - - ‘codebook.Rmd’ using ‘UTF-8’... OK - ‘continuous.Rmd’ using ‘UTF-8’... OK - ‘contrasts.Rmd’ using ‘UTF-8’... OK - ‘norta.Rmd’ using ‘UTF-8’... failed - ‘rnorm_multi.Rmd’ using ‘UTF-8’... OK - ‘sim_design.Rmd’ using ‘UTF-8’... OK - ‘sim_df.Rmd’ using ‘UTF-8’... OK - ``` - -# fddm +# fddm
@@ -7765,7 +6993,7 @@ Run `revdepcheck::cloud_details(, "faux")` for more info * GitHub: https://github.com/rtdists/fddm * Source code: https://github.com/cran/fddm * Date/Publication: 2024-07-02 16:00:07 UTC -* Number of recursive dependencies: 93 +* Number of recursive dependencies: 92 Run `revdepcheck::cloud_details(, "fddm")` for more info @@ -7812,11 +7040,11 @@ Run `revdepcheck::cloud_details(, "fddm")` for more info
-* Version: 0.3.2 +* Version: 0.4.1 * GitHub: https://github.com/tidyverts/feasts * Source code: https://github.com/cran/feasts -* Date/Publication: 2024-03-15 09:10:02 UTC -* Number of recursive dependencies: 101 +* Date/Publication: 2024-09-25 23:40:02 UTC +* Number of recursive dependencies: 100 Run `revdepcheck::cloud_details(, "feasts")` for more info @@ -7834,7 +7062,7 @@ Run `revdepcheck::cloud_details(, "feasts")` for more info Loading required package: fabletools > > test_check("feasts") - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 100 ] ... ── Error ('test-graphics.R:192:3'): gg_tsdisplay() plots ─────────────────────── @@ -7844,52 +7072,11 @@ Run `revdepcheck::cloud_details(, "feasts")` for more info Component "x": 1 string mismatch Component "y": 1 string mismatch - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 100 ] Error: Test failures Execution halted ``` -# fergm - -
- -* Version: 1.1.4 -* GitHub: https://github.com/benjamin-w-campbell/fergm -* Source code: https://github.com/cran/fergm -* Date/Publication: 2018-10-17 22:20:11 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "fergm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fergm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: coef_posterior_density - > ### Title: Plots the posterior density for FERGM model terms. - > ### Aliases: coef_posterior_density - > ### Keywords: FERGM interpret summary - > - > ### ** Examples - > - ... - > data("ergm.fit") - > data("fergm.fit") - > data("mesa") - > - > # rstan functions - > # Histogram of the posterior - > rstan::stan_hist(fergm.fit$stan.fit, par = "beta") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - # ffp
@@ -7898,7 +7085,7 @@ Run `revdepcheck::cloud_details(, "fergm")` for more info * GitHub: https://github.com/Reckziegel/FFP * Source code: https://github.com/cran/ffp * Date/Publication: 2022-09-29 15:10:06 UTC -* Number of recursive dependencies: 107 +* Number of recursive dependencies: 106 Run `revdepcheck::cloud_details(, "ffp")` for more info @@ -7923,85 +7110,11 @@ Run `revdepcheck::cloud_details(, "ffp")` for more info > scenario_density(x, p, 500) Error in use_defaults(..., self = self) : unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NU Calls: ... -> -> compute_geom_2 -> Execution halted ``` -# fic - -
- -* Version: 1.0.0 -* GitHub: https://github.com/chjackson/fic -* Source code: https://github.com/cran/fic -* Date/Publication: 2019-04-13 08:32:39 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "fic")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘linear.Rnw’ - ... - - > library(ggplot2) - - > if (requireNamespace("GGally", quietly = TRUE)) { - + GGally::ggpairs(mtcars[, c("mpg", "am", "wt", "qsec", "disp", - + "hp")], aes(colour .... [TRUNCATED] - - ... - When sourcing 'linear.R': - Error: argument is of length zero - Execution halted - - ‘fic.Rnw’ using ‘UTF-8’... OK - ‘linear.Rnw’ using ‘UTF-8’... failed - ‘loss.Rnw’ using ‘UTF-8’... OK - ‘multistate.Rnw’ using ‘UTF-8’... OK - ‘skewnormal.Rnw’ using ‘UTF-8’... OK - ‘survival.Rnw’ using ‘UTF-8’... OK - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘numDeriv’ - All declared Imports should be used. - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘fic.Rnw’ using knitr - Error: processing vignette 'fic.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'fic.tex' failed. - LaTeX errors: - ! LaTeX Error: File `grfext.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - - ... - --- finished re-building ‘skewnormal.Rnw’ - - --- re-building ‘survival.Rnw’ using knitr - --- finished re-building ‘survival.Rnw’ - - SUMMARY: processing the following files failed: - ‘fic.Rnw’ ‘linear.Rnw’ ‘multistate.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - # fido
@@ -8010,7 +7123,7 @@ Run `revdepcheck::cloud_details(, "fic")` for more info * GitHub: https://github.com/jsilve24/fido * Source code: https://github.com/cran/fido * Date/Publication: 2024-06-05 21:30:06 UTC -* Number of recursive dependencies: 134 +* Number of recursive dependencies: 133 Run `revdepcheck::cloud_details(, "fido")` for more info @@ -8036,7 +7149,7 @@ Run `revdepcheck::cloud_details(, "fido")` for more info Adding another scale for colour, which will replace the existing scale. Error in use_defaults(..., self = self) : unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), N Calls: ... -> -> compute_geom_2 -> Execution halted ``` @@ -8093,10 +7206,10 @@ Run `revdepcheck::cloud_details(, "fido")` for more info * checking installed package size ... NOTE ``` - installed size is 106.5Mb + installed size is 106.6Mb sub-directories of 1Mb or more: data 4.0Mb - libs 100.6Mb + libs 100.8Mb ``` * checking re-building of vignette outputs ... NOTE @@ -8111,111 +7224,94 @@ Run `revdepcheck::cloud_details(, "fido")` for more info --- re-building ‘non-linear-models.Rmd’ using rmarkdown ``` -# fitdistrplus +# FielDHub
-* Version: 1.2-1 -* GitHub: https://github.com/lbbe-software/fitdistrplus -* Source code: https://github.com/cran/fitdistrplus -* Date/Publication: 2024-07-12 12:20:02 UTC -* Number of recursive dependencies: 108 +* Version: 1.4.2 +* GitHub: https://github.com/DidierMurilloF/FielDHub +* Source code: https://github.com/cran/FielDHub +* Date/Publication: 2024-07-26 20:20:06 UTC +* Number of recursive dependencies: 113 -Run `revdepcheck::cloud_details(, "fitdistrplus")` for more info +Run `revdepcheck::cloud_details(, "FielDHub")` for more info
## Newly broken -* checking examples ... ERROR +* checking running R code from vignettes ... ERROR ``` - Running examples in ‘fitdistrplus-Ex.R’ failed - The error most likely occurred in: + Errors in running code in vignettes: + when running code in ‘RCBD_augmented.Rmd’ + ... + 7 7 Cassava_2022 FARGO 2025 1007 1 7 1 1 4 CH4 + 8 8 Cassava_2022 FARGO 2025 1008 1 8 0 1 44 G44 + 9 9 Cassava_2022 FARGO 2025 1009 1 9 0 1 23 G23 + 10 10 Cassava_2022 FARGO 2025 1010 1 10 0 1 113 G113 + + > plot(aug_RCBD) - > ### Name: CIcdfplot - > ### Title: Empirical cumulative distribution function with pointwise - > ### confidence intervals on probabilities or on quantiles - > ### Aliases: CIcdfplot - > ### Keywords: distribution - > - > ### ** Examples - ... - > f1 <- fitdist(s1, "exp") - > b1 <- bootdist(f1, niter= 11) #voluntarily low to decrease computation time - > - > # plot 95 percent bilateral confidence intervals on y values (probabilities) - > CIcdfplot(b1, CI.level= 95/100, CI.output = "probability") - > if (ggplotEx) CIcdfplot(b1, CI.level= 95/100, CI.output = "probability", plotstyle = "ggplot") - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘t-CIcdfplot.R’ - Running the tests in ‘tests/t-CIcdfplot.R’ failed. - Complete output: - > library(fitdistrplus) - Loading required package: MASS - Loading required package: survival - > - > nbboot <- 201 - > nbboot <- 10 - > ggplotEx <- requireNamespace("ggplot2", quietly = TRUE) ... - 97.5 % 2.152084 2.778622 - > - > par(mfrow=c(1,2)) - > CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black") - > CIcdfplot(b1, CI.level=95/100, CI.output = "quantile", datacol="blue") - > if(ggplotEx) CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black", plotstyle = "ggplot") - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted + + ‘RCBD_augmented.Rmd’ using ‘UTF-8’... failed + ‘alpha_lattice.Rmd’ using ‘UTF-8’... failed + ‘diagonal_arrangement.Rmd’ using ‘UTF-8’... failed + ‘full_factorial.Rmd’ using ‘UTF-8’... failed + ‘multi_location_prep.Rmd’ using ‘UTF-8’... failed + ‘partially_replicated.Rmd’ using ‘UTF-8’... failed + ‘rcbd.Rmd’ using ‘UTF-8’... failed + ‘row_column.Rmd’ using ‘UTF-8’... failed + ‘split_plot.Rmd’ using ‘UTF-8’... failed ``` -* checking running R code from vignettes ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Errors in running code in vignettes: - when running code in ‘FAQ.Rmd’ - ... + Error(s) in re-building vignettes: + --- re-building ‘RCBD_augmented.Rmd’ using rmarkdown - > dcomp <- denscomp(list(fitW, fitln, fitg), legendtext = c("Weibull", - + "lognormal", "gamma"), xlab = "serving sizes (g)", xlim = c(0, - + 25 .... [TRUNCATED] + Quitting from lines 210-211 [unnamed-chunk-12] (RCBD_augmented.Rmd) + Error: processing vignette 'RCBD_augmented.Rmd' failed with diagnostics: + unused argument (dn) + --- failed re-building ‘RCBD_augmented.Rmd’ - > dcomp + ggplot2::theme_minimal() + ggplot2::ggtitle("Ground beef fits") + --- re-building ‘alpha_lattice.Rmd’ using rmarkdown - When sourcing ‘FAQ.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted + ... + --- failed re-building ‘split_plot.Rmd’ + + SUMMARY: processing the following files failed: + ‘RCBD_augmented.Rmd’ ‘alpha_lattice.Rmd’ ‘diagonal_arrangement.Rmd’ + ‘full_factorial.Rmd’ ‘multi_location_prep.Rmd’ + ‘partially_replicated.Rmd’ ‘rcbd.Rmd’ ‘row_column.Rmd’ + ‘split_plot.Rmd’ - ‘FAQ.Rmd’ using ‘UTF-8’... failed - ‘Optimalgo.Rmd’ using ‘UTF-8’... OK - ‘fitdistrplus_vignette.Rmd’ using ‘UTF-8’... OK - ‘starting-values.Rmd’ using ‘UTF-8’... OK + Error: Vignette re-building failed. + Execution halted ``` -* checking re-building of vignette outputs ... NOTE +## In both + +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘FAQ.Rmd’ using rmarkdown + installed size is 5.3Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.8Mb + help 1.1Mb ``` -# fitlandr +# figuRes2
-* Version: 0.1.0 -* GitHub: https://github.com/Sciurus365/fitlandr -* Source code: https://github.com/cran/fitlandr -* Date/Publication: 2023-02-10 10:40:02 UTC -* Number of recursive dependencies: 123 +* Version: 1.0.0 +* GitHub: https://github.com/gcicc/figures2 +* Source code: https://github.com/cran/figuRes2 +* Date/Publication: 2022-09-09 08:02:55 UTC +* Number of recursive dependencies: 112 -Run `revdepcheck::cloud_details(, "fitlandr")` for more info +Run `revdepcheck::cloud_details(, "figuRes2")` for more info
@@ -8223,23 +7319,49 @@ Run `revdepcheck::cloud_details(, "fitlandr")` for more info * checking examples ... ERROR ``` - Running examples in ‘fitlandr-Ex.R’ failed + Running examples in ‘figuRes2-Ex.R’ failed The error most likely occurred in: - > ### Name: fit_2d_vf - > ### Title: Estimate a 2D vector field - > ### Aliases: fit_2d_vf + > ### Name: theme_grey2_nomargins + > ### Title: figuRes2 themes + > ### Aliases: theme_grey2_nomargins theme_grey2_default_margins + > ### theme_bw2_nomargins theme_bw2_default_margins theme_table_nomargins > > ### ** Examples > - > # generate data - > single_output_grad <- simlandr::sim_fun_grad(length = 200, seed = 1614) - > # fit the vector field - > v2 <- fit_2d_vf(single_output_grad, x = "x", y = "y", method = "MVKE") - > plot(v2) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + ... + ▆ + 1. ├─ggplot2::theme_set(theme_grey2_nomargins()) + 2. │ └─ggplot2:::check_object(new, is.theme, "a {.cls theme} object") + 3. │ └─ggplot2 (local) check_fun(x) + 4. └─figuRes2::theme_grey2_nomargins() + 5. └─ggplot2::theme(...) + 6. └─lifecycle::deprecate_stop(...) + 7. └─lifecycle:::deprecate_stop0(msg) + 8. └─rlang::cnd_signal(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basics.Rmd’ + ... + Your page setup allocates: 0.1 inches to the bottom margin. + Your page setup allocates: a rectangle, 10.8 inches wide by 8.3 inches tall for graphics/tables. + + > theme_set(theme_grey2_nomargins()) + + When sourcing ‘basics.R’: + Error: The `axis.ticks.margin` argument of `theme()` was deprecated in ggplot2 + 2.0.0 and is now defunct. + ℹ Please set `margin` property of `axis.text` instead Execution halted + + ‘basics.Rmd’ using ‘UTF-8’... failed + ‘forest-plots.Rmd’ using ‘UTF-8’... OK + ‘km.Rmd’ using ‘UTF-8’... OK + ‘large-scale.Rmd’ using ‘UTF-8’... OK ``` # flexsurv @@ -8250,7 +7372,7 @@ Run `revdepcheck::cloud_details(, "fitlandr")` for more info * GitHub: https://github.com/chjackson/flexsurv * Source code: https://github.com/cran/flexsurv * Date/Publication: 2024-08-17 05:50:02 UTC -* Number of recursive dependencies: 147 +* Number of recursive dependencies: 150 Run `revdepcheck::cloud_details(, "flexsurv")` for more info @@ -8258,20 +7380,45 @@ Run `revdepcheck::cloud_details(, "flexsurv")` for more info ## Newly broken +* checking tests ... ERROR + ``` + Running ‘test_base.R’ + Running the tests in ‘tests/test_base.R’ failed. + Complete output: + > test_partial <- FALSE + > + > if (test_partial) + + options( + + warnPartialMatchArgs = TRUE, + + warnPartialMatchAttr = TRUE, + + warnPartialMatchDollar = TRUE + ... + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + • On CRAN (1): 'test_standsurv.R:276:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_custom.R:14:1'): (code run outside of `test_that()`) ─────────── + Error in `is.element("eha", installed.packages()[, 1])`: unused argument (installed.packages()[, 1]) + + [ FAIL 1 | WARN 0 | SKIP 1 | PASS 705 ] + Error: Test failures + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: when running code in ‘standsurv.Rmd’ ... - 5 0 967 Good 2.649315 68.74975 25110 1986-05-18 female Good - 6 0 629 Good 1.723288 64.53328 23570 1987-03-07 female Good - - > km <- survfit(Surv(recyrs, censrec) ~ group2, data = bc) > kmsurvplot <- ggsurvplot(km) + > kmsurvplot + xlab("Time from diagnosis (years)") + Warning in eval(ei, envir) : + Incompatible methods ("+.ggsurv", "+.gg") for "+" + When sourcing ‘standsurv.R’: - Error: argument is of length zero + Error: non-numeric argument to binary operator Execution halted ‘standsurv.Rmd’ using ‘UTF-8’... failed @@ -8299,7 +7446,7 @@ Run `revdepcheck::cloud_details(, "flexsurv")` for more info Quitting from lines 113-116 [unnamed-chunk-4] (standsurv.Rmd) Error: processing vignette 'standsurv.Rmd' failed with diagnostics: - argument is of length zero + non-numeric argument to binary operator --- failed re-building ‘standsurv.Rmd’ --- re-building ‘flexsurv.Rnw’ using knitr @@ -8325,7 +7472,7 @@ Run `revdepcheck::cloud_details(, "flexsurv")` for more info * GitHub: https://github.com/LMJL-Alea/flipr * Source code: https://github.com/cran/flipr * Date/Publication: 2023-08-23 09:00:02 UTC -* Number of recursive dependencies: 107 +* Number of recursive dependencies: 106 Run `revdepcheck::cloud_details(, "flipr")` for more info @@ -8384,58 +7531,17 @@ Run `revdepcheck::cloud_details(, "flipr")` for more info libs 1.4Mb ``` -# FLOPART +# forestmodel
-* Version: 2024.6.19 +* Version: 0.6.2 * GitHub: NA -* Source code: https://github.com/cran/FLOPART -* Date/Publication: 2024-06-20 21:30:10 UTC -* Number of recursive dependencies: 55 - -Run `revdepcheck::cloud_details(, "FLOPART")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘comparison.Rmd’ - ... - - > if (require("ggplot2")) { - + ggplot() + ggtitle("Models with label constraints (FLOPART) and without (penalty values)") + - + scale_fill_m .... [TRUNCATED] - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - When sourcing ‘comparison.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘comparison.Rmd’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘comparison.Rmd’ using knitr - ``` - -# fmesher - -
- -* Version: 0.1.7 -* GitHub: https://github.com/inlabru-org/fmesher -* Source code: https://github.com/cran/fmesher -* Date/Publication: 2024-07-01 13:00:02 UTC -* Number of recursive dependencies: 93 +* Source code: https://github.com/cran/forestmodel +* Date/Publication: 2020-07-19 11:50:03 UTC +* Number of recursive dependencies: 57 -Run `revdepcheck::cloud_details(, "fmesher")` for more info +Run `revdepcheck::cloud_details(, "forestmodel")` for more info
@@ -8443,76 +7549,74 @@ Run `revdepcheck::cloud_details(, "fmesher")` for more info * checking examples ... ERROR ``` - Running examples in ‘fmesher-Ex.R’ failed + Running examples in ‘forestmodel-Ex.R’ failed The error most likely occurred in: - > ### Name: fm_mesh_1d - > ### Title: Make a 1D mesh object - > ### Aliases: fm_mesh_1d + > ### Name: forest_rma + > ### Title: Generate a forest plot from a meta-analysis + > ### Aliases: forest_rma > > ### ** Examples > - > if (require("ggplot2")) { + > if (require("metafor")) { ... - + boundary = c("neumann", "free"), - + degree = 2 - + ) - + ggplot() + - + geom_fm(data = m, xlim = c(0.5, 10.5)) - + } - Loading required package: ggplot2 - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘basic_use.Rmd’ - ... - - > plot(mesh2) + Loading required package: metadat + Loading required package: numDeriv - > suppressPackageStartupMessages(library(ggplot2)) + Loading the 'metafor' package (version 4.6-0). For an + introduction to the package please type: help(metafor) - > ggplot() + geom_fm(data = mesh2) - - When sourcing ‘basic_use.R’: - Error: argument is of length zero + Error in h(simpleError(msg, call)) : + error in evaluating the argument 'x' in selecting a method for function 'print': unused argument (c("OR", "PETO", "D2OR", "D2ORN", "D2ORL")) + Calls: print ... default_forest_panels -> %||% -> rma_setlab -> .handleSimpleError -> h Execution halted - - ‘basic_use.Rmd’ using ‘UTF-8’... failed - ‘fmesher_library.Rmd’ using ‘UTF-8’... OK - ‘inla_conversion.Rmd’ using ‘UTF-8’... OK ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘forestmodel’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘basic_use.Rmd’ using rmarkdown + Found the following significant warnings: + Note: possible error in 'is.element(measure, c("OR", ': unused argument (c("OR", "PETO", "D2OR", "D2ORN", "D2ORL")) + Note: possible error in 'is.element(measure, c("SMD", ': unused argument (c("SMD", "SMDH", "PBIT", "OR2D", "OR2DN", "OR2DL")) + Note: possible error in 'is.element(measure, c("COR", ': unused argument (c("COR", "UCOR", "RTET", "RBIS")) + Note: possible error in 'is.element(measure, c("SMCC", ': unused argument (c("SMCC", "SMCR", "SMCRH")) + See ‘/tmp/workdir/forestmodel/new/forestmodel.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + rma_setlab: possible error in is.element(measure, c("OR", "PETO", + "D2OR", "D2ORN", "D2ORL")): unused argument (c("OR", "PETO", "D2OR", + "D2ORN", "D2ORL")) + rma_setlab: possible error in is.element(measure, c("SMD", "SMDH", + "PBIT", "OR2D", "OR2DN", "OR2DL")): unused argument (c("SMD", "SMDH", + "PBIT", "OR2D", "OR2DN", "OR2DL")) + rma_setlab: possible error in is.element(measure, c("COR", "UCOR", + "RTET", "RBIS")): unused argument (c("COR", "UCOR", "RTET", "RBIS")) + rma_setlab: possible error in is.element(measure, c("SMCC", "SMCR", + "SMCRH")): unused argument (c("SMCC", "SMCR", "SMCRH")) ``` ## In both -* checking installed package size ... NOTE +* checking LazyData ... NOTE ``` - installed size is 12.5Mb - sub-directories of 1Mb or more: - libs 10.5Mb + 'LazyData' is specified without a 'data' directory ``` -# fmf +# frailtyEM
-* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/fmf -* Date/Publication: 2020-09-03 07:32:12 UTC -* Number of recursive dependencies: 175 +* Version: 1.0.1 +* GitHub: https://github.com/tbalan/frailtyEM +* Source code: https://github.com/cran/frailtyEM +* Date/Publication: 2019-09-22 13:00:10 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "fmf")` for more info +Run `revdepcheck::cloud_details(, "frailtyEM")` for more info
@@ -8520,124 +7624,72 @@ Run `revdepcheck::cloud_details(, "fmf")` for more info * checking examples ... ERROR ``` - Running examples in ‘fmf-Ex.R’ failed + Running examples in ‘frailtyEM-Ex.R’ failed The error most likely occurred in: - > ### Name: plot - > ### Title: PCA Plot of the Noise Score of Each Individual - > ### Aliases: plot + > ### Name: summary.emfrail + > ### Title: Summary for 'emfrail' objects + > ### Aliases: summary.emfrail > > ### ** Examples > - > + > data("bladder") ... - 17. │ └─ggplot2:::`+.gg`(...) - 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 19. │ ├─ggplot2::ggplot_add(object, p, objectname) - 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 22. └─base::.handleSimpleError(...) - 23. └─purrr (local) h(simpleError(msg, call)) - 24. └─cli::cli_abort(...) - 25. └─rlang::abort(...) + filter + + The following object is masked from ‘package:graphics’: + + layout + + > ggplotly(pl2) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` ## In both -* checking C++ specification ... NOTE +* checking LazyData ... NOTE ``` - Specified C++11: please drop specification unless essential - ``` - -# forestly - -
- -* Version: 0.1.1 -* GitHub: https://github.com/Merck/forestly -* Source code: https://github.com/cran/forestly -* Date/Publication: 2024-07-08 19:40:02 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "forestly")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘forest-plot-static.Rmd’ - ... - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <86> - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <92> - - When sourcing ‘forest-plot-static.R’: - Error: object is not a unit - Execution halted - - ‘forest-plot-static.Rmd’ using ‘UTF-8’... failed - ‘forestly-cran.Rmd’ using ‘UTF-8’... OK + 'LazyData' is specified without a 'data' directory ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘forest-plot-static.Rmd’ using rmarkdown - ``` - -# FossilSim - -
- -* Version: 2.4.0 -* GitHub: NA -* Source code: https://github.com/cran/FossilSim -* Date/Publication: 2024-09-05 19:40:02 UTC -* Number of recursive dependencies: 155 - -Run `revdepcheck::cloud_details(, "FossilSim")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FossilSim-Ex.R’ failed - The error most likely occurred in: + --- re-building ‘frailtyEM_manual.Rnw’ using Sweave + Loading required package: survival - > ### Name: plot.fbdrange - > ### Title: Plot oriented tree with stratigraphic ranges - > ### Aliases: plot.fbdrange - > - > ### ** Examples - > - > tree_file <- system.file("extdata", "fbdrange.trees", package = "FossilSim") - > fbdr <- get_fbdrange_from_file(tree_file) - > p <- plot(fbdr, smart.labels = TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Attaching package: ‘ggplot2’ + + The following object is masked from ‘package:base’: + + is.element + + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘frailtyEM_manual.Rnw’ + + SUMMARY: processing the following file failed: + ‘frailtyEM_manual.Rnw’ + + Error: Vignette re-building failed. Execution halted ``` -# FPDclustering +# gapmap
-* Version: 2.3.1 -* GitHub: NA -* Source code: https://github.com/cran/FPDclustering -* Date/Publication: 2024-01-30 00:10:06 UTC -* Number of recursive dependencies: 104 +* Version: 1.0.0 +* GitHub: https://github.com/evanbiederstedt/gapmap +* Source code: https://github.com/cran/gapmap +* Date/Publication: 2024-01-22 20:50:02 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "FPDclustering")` for more info +Run `revdepcheck::cloud_details(, "gapmap")` for more info
@@ -8645,149 +7697,90 @@ Run `revdepcheck::cloud_details(, "FPDclustering")` for more info * checking examples ... ERROR ``` - Running examples in ‘FPDclustering-Ex.R’ failed + Running examples in ‘gapmap-Ex.R’ failed The error most likely occurred in: - > ### Name: GPDC - > ### Title: Gaussian PD-Clustering - > ### Aliases: GPDC + > ### Name: gapmap + > ### Title: Function to draw a gapped cluster heatmap + > ### Aliases: gapmap > > ### ** Examples > - > #Load the data + > set.seed(1234) ... - > #Results - > table(res$label,ais$sex) - - f m - 1 95 1 - 2 5 101 - > plot(res) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + ℹ Please use the `panel.spacing` argument instead. + Backtrace: + ▆ + 1. └─gapmap::gapmap(m = as.matrix(distxy), d_row = rev(dend), d_col = dend) + 2. └─gapmap::gap_dendrogram(...) + 3. └─ggplot2::theme(...) + 4. └─lifecycle::deprecate_stop("2.2.0", "theme(panel.margin)", "theme(panel.spacing)") + 5. └─lifecycle:::deprecate_stop0(msg) + 6. └─rlang::cnd_signal(...) Execution halted ``` -# frailtyEM - -
- -* Version: 1.0.1 -* GitHub: https://github.com/tbalan/frailtyEM -* Source code: https://github.com/cran/frailtyEM -* Date/Publication: 2019-09-22 13:00:10 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "frailtyEM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR +* checking running R code from vignettes ... ERROR ``` - Running examples in ‘frailtyEM-Ex.R’ failed - The error most likely occurred in: + Errors in running code in vignettes: + when running code in ‘simple_example.Rmd’ + ... + ℹ See also `vignette("ggplot2-in-packages")` for more information. + ℹ The deprecated feature was likely used in the gapmap package. + Please report the issue at + . - > ### Name: summary.emfrail - > ### Title: Summary for 'emfrail' objects - > ### Aliases: summary.emfrail - > - > ### ** Examples - > - > data("bladder") + When sourcing ‘simple_example.R’: + Error: The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 ... - filter + . - The following object is masked from ‘package:graphics’: - - layout - - > ggplotly(pl2) - Error in pm[[2]] : subscript out of bounds - Calls: ggplotly -> ggplotly.ggplot -> gg2list + When sourcing ‘tcga_example.R’: + Error: The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `panel.spacing` argument instead. Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory + + ‘simple_example.Rmd’ using ‘UTF-8’... failed + ‘tcga_example.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘frailtyEM_manual.Rnw’ using Sweave - Loading required package: survival - Loading required package: gridExtra - Warning: The `` argument of `guides()` cannot be `FALSE`. Use - "none" instead as of ggplot2 3.3.4. - Warning: Removed 2 rows containing missing values or values outside - the scale range (`geom_path()`). - Warning in data("kidney") : data set ‘kidney’ not found - Warning in emfrail(Surv(time, status) ~ age + sex + cluster(id), data = kidney, : + ... + --- re-building ‘simple_example.Rmd’ using rmarkdown + + Quitting from lines 36-38 [unnamed-chunk-3] (simple_example.Rmd) + Error: processing vignette 'simple_example.Rmd' failed with diagnostics: + The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `panel.spacing` argument instead. + --- failed re-building ‘simple_example.Rmd’ ... - l.179 \RequirePackage{grfext}\relax - ^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘frailtyEM_manual.Rnw’ + The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `panel.spacing` argument instead. + --- failed re-building ‘tcga_example.Rmd’ - SUMMARY: processing the following file failed: - ‘frailtyEM_manual.Rnw’ + SUMMARY: processing the following files failed: + ‘simple_example.Rmd’ ‘tcga_example.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# funcharts - -
- -* Version: 1.5.0 -* GitHub: https://github.com/unina-sfere/funcharts -* Source code: https://github.com/cran/funcharts -* Date/Publication: 2024-07-19 12:00:31 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "funcharts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘funcharts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: pca_mfd - > ### Title: Multivariate functional principal components analysis - > ### Aliases: pca_mfd - > - > ### ** Examples - > - > library(funcharts) - > mfdobj <- data_sim_mfd() - > pca_obj <- pca_mfd(mfdobj) - > plot_pca_mfd(pca_obj) - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits - Execution halted - ``` - -# FunnelPlotR +# gapminder
-* Version: 0.5.0 -* GitHub: https://github.com/nhs-r-community/FunnelPlotR -* Source code: https://github.com/cran/FunnelPlotR -* Date/Publication: 2024-04-12 08:40:02 UTC -* Number of recursive dependencies: 85 +* Version: 1.0.0 +* GitHub: https://github.com/jennybc/gapminder +* Source code: https://github.com/cran/gapminder +* Date/Publication: 2023-03-10 09:50:08 UTC +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "FunnelPlotR")` for more info +Run `revdepcheck::cloud_details(, "gapminder")` for more info
@@ -8795,108 +7788,128 @@ Run `revdepcheck::cloud_details(, "FunnelPlotR")` for more info * checking examples ... ERROR ``` - Running examples in ‘FunnelPlotR-Ex.R’ failed + Running examples in ‘gapminder-Ex.R’ failed The error most likely occurred in: - > ### Name: funnel_plot - > ### Title: Funnel plots for comparing institutional performance - > ### Aliases: funnel_plot + > ### Name: country_colors + > ### Title: Gapminder color schemes. + > ### Aliases: country_colors continent_colors + > ### Keywords: datasets > > ### ** Examples > - > # We will use the 'medpar' dataset from the 'COUNT' package. ... - > # Draw plot, returning just the plot object - > fp<-funnel_plot(medpar, denominator=prds, numerator=los, - + group = provnum, limit=95, title="An example funnel plot") - > - > # Methods for viewing/extracting - > print(fp) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + and is now defunct. + ℹ Please use the `show.legend` argument instead. + Backtrace: + ▆ + 1. └─ggplot2::geom_line(lwd = 1, show_guide = FALSE) + 2. └─ggplot2::layer(...) + 3. └─lifecycle::deprecate_stop("2.0.0", "layer(show_guide)", "layer(show.legend)") + 4. └─lifecycle:::deprecate_stop0(msg) + 5. └─rlang::cnd_signal(...) Execution halted ``` +## In both + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘changing_funnel_plot_options.Rmd’ + when running code in ‘gapminder.Rmd’ ... - + family = "poisson", data = medpar) - > medpar$prds <- predict(mod, newdata = medpar, type = "response") + > head(continent_colors) + Africa Americas Asia Europe Oceania + "#7F3B08" "#A50026" "#40004B" "#276419" "#313695" - > funnel_plot(medpar, denominator = prds, numerator = los, - + group = provnum, limit = 99, label = "outlier", draw_unadjusted = TRUE) + > knitr::include_graphics("../man/figures/gapminder-color-scheme-ggplot2.png") - ... - + group = provnum, title = "Length of Stay Funnel plot for `medpar` data", - + draw .... [TRUNCATED] - Plotting using unadjusted limits - - When sourcing ‘funnel_plots.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + When sourcing ‘gapminder.R’: + Error: Cannot find the file(s): "../man/figures/gapminder-color-scheme-ggplot2.png" Execution halted - ‘changing_funnel_plot_options.Rmd’ using ‘UTF-8’... failed - ‘funnel_plots.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘changing_funnel_plot_options.Rmd’ using rmarkdown - - Quitting from lines 33-49 [dtsetup] (changing_funnel_plot_options.Rmd) - Error: processing vignette 'changing_funnel_plot_options.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘changing_funnel_plot_options.Rmd’ - - --- re-building ‘funnel_plots.Rmd’ using rmarkdown + ‘gapminder.Rmd’ using ‘UTF-8’... failed ``` -# genekitr +# GEInter
-* Version: 1.2.8 -* GitHub: https://github.com/GangLiLab/genekitr -* Source code: https://github.com/cran/genekitr -* Date/Publication: 2024-09-06 13:00:06 UTC -* Number of recursive dependencies: 202 +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/GEInter +* Date/Publication: 2022-05-19 06:50:19 UTC +* Number of recursive dependencies: 74 -Run `revdepcheck::cloud_details(, "genekitr")` for more info +Run `revdepcheck::cloud_details(, "GEInter")` for more info
## Newly broken +* checking whether package ‘GEInter’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(variable[t], ': unused argument (variable[1:(t - 1)]) + Note: possible error in 'is.element(E_type[1:q], ': unused argument (c("ED")) + Note: possible error in 'is.element(fit$v_type[1:q], ': unused argument (c("ED")) + Note: possible error in 'is.element(b[, 1], a[1])': unused argument (a[1]) + Note: possible error in 'is.element(b[, 2], a[2])': unused argument (a[2]) + See ‘/tmp/workdir/GEInter/new/GEInter.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + RobSBoosting: possible error in is.element(variable[t], variable[1:(t - + 1)]): unused argument (variable[1:(t - 1)]) + plot.Miss.boosting: possible error in is.element(E_type[1:q], c("ED")): + unused argument (c("ED")) + plot.RobSBoosting: possible error in is.element(fit$v_type[1:q], + c("ED")): unused argument (c("ED")) + which.column: possible error in is.element(b[, 1], a[1]): unused + argument (a[1]) + which.column: possible error in is.element(b[, 2], a[2]): unused + argument (a[2]) + ``` + +## In both + * checking examples ... ERROR ``` - Running examples in ‘genekitr-Ex.R’ failed + Running examples in ‘GEInter-Ex.R’ failed The error most likely occurred in: - > ### Name: plotVenn - > ### Title: Venn plot for groups of genes - > ### Aliases: plotVenn + > ### Name: Miss.boosting + > ### Title: Robust gene-environment interaction analysis approach via sparse + > ### boosting, where the missingness in environmental measurements is + > ### effectively accommodated using multiple imputation approach + > ### Aliases: Miss.boosting > > ### ** Examples - > - > k1 = requireNamespace("ComplexUpset",quietly = TRUE) ... - + use_venn = FALSE, - + main_text_size = 15, - + legend_text_size = 8, - + legend_position = 'left' - + ) - + } - Color length should be same with venn_list, auto assign colors... - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plotVenn ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > + > ##continuous + > E1[7,1]=NA + > fit1<-Miss.boosting(G,E1,Y,im_time=1,loop_time=100,num.knots=c(2),Boundary.knots, + + degree=c(2),v=0.1,tau=0.3,family="continuous",knots=knots,E_type=c("EC","EC","ED","ED")) + [1] "The 1 th impute" + Error in is.element(variable[t], variable[1:(t - 1)]) : + unused argument (variable[1:(t - 1)]) + Calls: Miss.boosting -> RobSBoosting Execution halted ``` +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + data 7.0Mb + ``` + # geoheatmap
@@ -8905,7 +7918,7 @@ Run `revdepcheck::cloud_details(, "genekitr")` for more info * GitHub: NA * Source code: https://github.com/cran/geoheatmap * Date/Publication: 2024-09-05 15:40:02 UTC -* Number of recursive dependencies: 106 +* Number of recursive dependencies: 105 Run `revdepcheck::cloud_details(, "geoheatmap")` for more info @@ -8942,11 +7955,11 @@ Run `revdepcheck::cloud_details(, "geoheatmap")` for more info
-* Version: 0.1.4 +* Version: 0.1.5 * GitHub: https://github.com/AllanCameron/geomtextpath * Source code: https://github.com/cran/geomtextpath -* Date/Publication: 2024-06-13 06:40:02 UTC -* Number of recursive dependencies: 94 +* Date/Publication: 2025-01-14 17:40:02 UTC +* Number of recursive dependencies: 93 Run `revdepcheck::cloud_details(, "geomtextpath")` for more info @@ -8968,7 +7981,7 @@ Run `revdepcheck::cloud_details(, "geomtextpath")` for more info > ggplot(waterways) + ... 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) - 20. │ └─self$draw_panel(data, panel_params, coord, na.rm = FALSE, legend = "other") + 20. │ └─self$draw_panel(...) 21. │ └─geomtextpath (local) draw_panel(...) 22. │ └─geomtextpath:::sf_textgrob(...) 23. └─base::.handleSimpleError(...) @@ -8987,10 +8000,10 @@ Run `revdepcheck::cloud_details(, "geomtextpath")` for more info > library(testthat) > library(geomtextpath) Loading required package: ggplot2 - > - > test_check("geomtextpath") - [ FAIL 1 | WARN 0 | SKIP 4 | PASS 463 ] + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': ... ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-sf.R:91:3'): We can make grobs from sf features ──────────────── @@ -9004,66 +8017,52 @@ Run `revdepcheck::cloud_details(, "geomtextpath")` for more info Execution halted ``` -# geostan +# ggalign
-* Version: 0.6.2 -* GitHub: https://github.com/ConnorDonegan/geostan -* Source code: https://github.com/cran/geostan -* Date/Publication: 2024-06-04 09:45:37 UTC -* Number of recursive dependencies: 108 +* Version: 0.0.5 +* GitHub: https://github.com/Yunuuuu/ggalign +* Source code: https://github.com/cran/ggalign +* Date/Publication: 2024-11-14 08:00:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "geostan")` for more info +Run `revdepcheck::cloud_details(, "ggalign")` for more info
## Newly broken -* checking examples ... ERROR +* checking for code/documentation mismatches ... WARNING ``` - Running examples in ‘geostan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: print.geostan_fit - > ### Title: print or plot a fitted geostan model - > ### Aliases: print.geostan_fit plot.geostan_fit - > - > ### ** Examples - > - > data(georgia) - ... - log(income) -1.013 0.001 0.019 -1.049 -1.029 -1.014 -0.998 -0.974 188 1.003 - - Samples were drawn using NUTS(diag_e) at Tue Sep 10 09:34:29 2024. - For each parameter, n_eff is a crude measure of effective sample size, - and Rhat is the potential scale reduction factor on split chains (at - convergence, Rhat=1). - > plot(fit) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted + Codoc mismatches from documentation object 'plot_theme': + plot_theme + Code: function(..., line, rect, text, title, geom, spacing, margins, + aspect.ratio, axis.title, axis.title.x, + axis.title.x.top, axis.title.x.bottom, axis.title.y, + axis.title.y.left, axis.title.y.right, axis.text, + axis.text.x, axis.text.x.top, axis.text.x.bottom, + axis.text.y, axis.text.y.left, axis.text.y.right, + axis.text.theta, axis.text.r, axis.ticks, + axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, + ... + strip.text.x.top, strip.text.y, strip.text.y.left, + strip.text.y.right, strip.switch.pad.grid, + strip.switch.pad.wrap, complete = FALSE, validate = + TRUE) + Argument names in code not in docs: + geom spacing margins + Mismatches in argument names (first 3): + Position: 6 Code: geom Docs: aspect.ratio + Position: 7 Code: spacing Docs: axis.title + Position: 8 Code: margins Docs: axis.title.x ``` ## In both -* checking installed package size ... NOTE - ``` - installed size is 129.8Mb - sub-directories of 1Mb or more: - libs 127.7Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE +* checking Rd cross-references ... NOTE ``` - GNU make is a SystemRequirements. + Packages unavailable to check Rd xrefs: ‘ComplexHeatmap’, ‘pheatmap’ ``` # GGally @@ -9074,7 +8073,7 @@ Run `revdepcheck::cloud_details(, "geostan")` for more info * GitHub: https://github.com/ggobi/ggally * Source code: https://github.com/cran/GGally * Date/Publication: 2024-02-14 00:53:32 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "GGally")` for more info @@ -9082,31 +8081,6 @@ Run `revdepcheck::cloud_details(, "GGally")` for more info ## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘GGally-Ex.R’ failed - The error most likely occurred in: - - > ### Name: +.gg - > ### Title: Modify a 'ggmatrix' object by adding an 'ggplot2' object to all - > ### plots - > ### Aliases: +.gg add_to_ggmatrix - > - > ### ** Examples - > - ... - > p_ <- GGally::print_if_interactive - > data(tips) - > - > pm <- ggpairs(tips[, 2:4], ggplot2::aes(color = sex)) - > ## change to black and white theme - > pm + ggplot2::theme_bw() - `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - * checking tests ... ERROR ``` Running ‘spelling.R’ @@ -9120,14 +8094,14 @@ Run `revdepcheck::cloud_details(, "GGally")` for more info + test_check("GGally") + } ... - 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) - 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) - 22. └─grid:::drawGrob(x) - 23. ├─grid::drawDetails(x, recording = FALSE) - 24. └─grid:::drawDetails.polyline(x, recording = FALSE) - 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + `expected` is a character vector ('tip') + ── Failure ('test-ggsurv.R:26:3'): multiple ──────────────────────────────────── + !is.null(a$labels$group) is not TRUE - [ FAIL 20 | WARN 1 | SKIP 22 | PASS 426 ] + `actual`: FALSE + `expected`: TRUE + + [ FAIL 3 | WARN 1 | SKIP 26 | PASS 477 ] Error: Test failures Execution halted ``` @@ -9140,7 +8114,7 @@ Run `revdepcheck::cloud_details(, "GGally")` for more info * GitHub: https://github.com/thomasp85/gganimate * Source code: https://github.com/cran/gganimate * Date/Publication: 2024-02-27 14:00:03 UTC -* Number of recursive dependencies: 97 +* Number of recursive dependencies: 96 Run `revdepcheck::cloud_details(, "gganimate")` for more info @@ -9156,10 +8130,10 @@ Run `revdepcheck::cloud_details(, "gganimate")` for more info > library(testthat) > library(gganimate) Loading required package: ggplot2 - > - > test_check("gganimate") - [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': ... 3. ├─gganimate::animate(p, nframes = 2) at test-anim_save.R:14:5 4. └─gganimate:::animate.gganim(p, nframes = 2) @@ -9185,7 +8159,7 @@ Run `revdepcheck::cloud_details(, "gganimate")` for more info ! no applicable method for 'element_grob' applied to an object of class "NULL" When sourcing ‘gganimate.R’: - Error: Provided file (/tmp/RtmpPBufaF/165c2292cd97/gganim_plot0001.png) does + Error: Provided file (/tmp/Rtmp2TPR8x/1a1142709f90/gganim_plot0001.png) does not exist Execution halted @@ -9198,251 +8172,45 @@ Run `revdepcheck::cloud_details(, "gganimate")` for more info --- re-building ‘gganimate.Rmd’ using rmarkdown ``` -# ggbrain +# ggblanket
-* Version: 0.8.1 -* GitHub: https://github.com/michaelhallquist/ggbrain -* Source code: https://github.com/cran/ggbrain -* Date/Publication: 2023-03-21 18:00:05 UTC -* Number of recursive dependencies: 74 +* Version: 12.1.0 +* GitHub: https://github.com/davidhodge931/ggblanket +* Source code: https://github.com/cran/ggblanket +* Date/Publication: 2025-01-27 09:00:12 UTC +* Number of recursive dependencies: 111 -Run `revdepcheck::cloud_details(, "ggbrain")` for more info +Run `revdepcheck::cloud_details(, "ggblanket")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking examples ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘ggbrain_introduction.Rmd’ - ... - - > gg_obj <- gg_base + geom_brain(definition = "underlay", - + fill_scale = scale_fill_gradient(low = "grey8", high = "grey62"), - + show_legend .... [TRUNCATED] - - > gg_obj$render() + Running examples in ‘ggblanket-Ex.R’ failed + The error most likely occurred in: + > ### Name: annotate_axis_line + > ### Title: Replace a axis line with an annotated segment + > ### Aliases: annotate_axis_line + > + > ### ** Examples + > + > library(dplyr) ... - - > plot(gg_obj) - - When sourcing ‘ggbrain_labels.R’: - Error: argument is of length zero + 25. │ │ └─rlang::list2(...) + 26. │ └─scales::alpha(coord$colour, coord$alpha) + 27. │ └─farver::decode_colour(colour, alpha = TRUE) + 28. │ └─farver:::decode_c(...) + 29. └─base::.handleSimpleError(``, "Unknown colour name: ~", base::quote(NULL)) + 30. └─rlang (local) h(simpleError(msg, call)) + 31. └─handlers[[1L]](cnd) + 32. └─cli::cli_abort(...) + 33. └─rlang::abort(...) Execution halted - - ‘ggbrain_aesthetics.Rmd’ using ‘UTF-8’... OK - ‘ggbrain_introduction.Rmd’ using ‘UTF-8’... failed - ‘ggbrain_labels.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ggbrain_aesthetics.Rmd’ using rmarkdown - --- finished re-building ‘ggbrain_aesthetics.Rmd’ - - --- re-building ‘ggbrain_introduction.Rmd’ using rmarkdown - - Quitting from lines 238-239 [unnamed-chunk-16] (ggbrain_introduction.Rmd) - Error: processing vignette 'ggbrain_introduction.Rmd' failed with diagnostics: - argument is of length zero - ... - Quitting from lines 47-54 [unnamed-chunk-2] (ggbrain_labels.Rmd) - Error: processing vignette 'ggbrain_labels.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggbrain_labels.Rmd’ - - SUMMARY: processing the following files failed: - ‘ggbrain_introduction.Rmd’ ‘ggbrain_labels.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.8Mb - sub-directories of 1Mb or more: - doc 3.0Mb - extdata 1.6Mb - libs 5.5Mb - ``` - -# ggbreak - -
- -* Version: 0.1.2 -* GitHub: https://github.com/YuLab-SMU/ggbreak -* Source code: https://github.com/cran/ggbreak -* Date/Publication: 2023-06-26 05:40:02 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "ggbreak")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggbreak-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scale_wrap - > ### Title: scale-wrap - > ### Aliases: scale_wrap - > - > ### ** Examples - > - > library(ggplot2) - > library(ggbreak) - > p <- ggplot(economics, aes(x=date, y = unemploy, colour = uempmed)) + - + geom_line() - > p + scale_wrap(n=4) - Error in identicalUnits(x) : object is not a unit - Calls: -> print.ggwrap - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggbreak.Rmd’ - ... - > p1 + p2 - - > p2 + scale_x_break(c(18, 21)) - - > p1 + scale_x_break(c(7, 17), scales = 1.5) + scale_x_break(c(18, - + 21), scales = 2) - - When sourcing ‘ggbreak.R’: - Error: second argument must be a list - Execution halted - - ‘ggbreak.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ggbreak.Rmd’ using rmarkdown - ``` - -# ggcharts - -
- -* Version: 0.2.1 -* GitHub: https://github.com/thomas-neitmann/ggcharts -* Source code: https://github.com/cran/ggcharts -* Date/Publication: 2020-05-20 00:40:02 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "ggcharts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggcharts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bar_chart - > ### Title: Bar Chart - > ### Aliases: bar_chart column_chart - > - > ### ** Examples - > - > data(biomedicalrevenue) - > revenue2018 <- biomedicalrevenue[biomedicalrevenue$year == 2018, ] - > revenue_roche <- biomedicalrevenue[biomedicalrevenue$company == "Roche", ] - > - > ## By default bar_chart() creates a horizontal and sorted plot - > bar_chart(revenue2018, company, revenue) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: bar_chart ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggcharts) - Loading required package: ggplot2 - > - > test_check("ggcharts") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] - - ... - 4. └─ggcharts::bar_chart(revenue_2018, company, revenue) - 5. └─ggplot2:::`+.gg`(...) - 6. └─ggplot2:::add_ggplot(e1, e2, e2name) - 7. ├─ggplot2::ggplot_add(object, p, objectname) - 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘customize.Rmd’ - ... - > dreaded_lang <- tibble::tribble(~language, ~pct, "VBA", - + 75.2, "Objective-C", 68.7, "Assembly", 64.4, "C", 57.5, "PHP", - + 54.2, "Erlang", .... [TRUNCATED] - - > (chart <- lollipop_chart(dreaded_lang, language, pct, - + highlight = "R")) - - ... - - > lollipop_chart(diamonds, cut, highlight = "Good") - - When sourcing ‘themes.R’: - Error: argument is of length zero - Execution halted - - ‘customize.Rmd’ using ‘UTF-8’... failed - ‘highlight.Rmd’ using ‘UTF-8’... failed - ‘themes.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘customize.Rmd’ using rmarkdown - - Quitting from lines 25-44 [unnamed-chunk-2] (customize.Rmd) - Error: processing vignette 'customize.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘customize.Rmd’ - - --- re-building ‘highlight.Rmd’ using rmarkdown - - Quitting from lines 37-44 [unnamed-chunk-2] (highlight.Rmd) - Error: processing vignette 'highlight.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘highlight.Rmd’ - - --- re-building ‘themes.Rmd’ using rmarkdown ``` # ggdark @@ -9453,7 +8221,7 @@ Run `revdepcheck::cloud_details(, "ggcharts")` for more info * GitHub: NA * Source code: https://github.com/cran/ggdark * Date/Publication: 2019-01-11 17:30:06 UTC -* Number of recursive dependencies: 46 +* Number of recursive dependencies: 45 Run `revdepcheck::cloud_details(, "ggdark")` for more info @@ -9518,6 +8286,29 @@ Run `revdepcheck::cloud_details(, "ggdark")` for more info 'LazyData' is specified without a 'data' directory ``` +# ggdemetra + +
+ +* Version: 0.2.8 +* GitHub: https://github.com/AQLT/ggdemetra +* Source code: https://github.com/cran/ggdemetra +* Date/Publication: 2024-02-04 14:50:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "ggdemetra")` for more info + +
+ +## Newly broken + +* checking whether package ‘ggdemetra’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: `aes_()` was deprecated in ggplot2 3.0.0. + See ‘/tmp/workdir/ggdemetra/new/ggdemetra.Rcheck/00install.out’ for details. + ``` + # ggdist
@@ -9526,7 +8317,7 @@ Run `revdepcheck::cloud_details(, "ggdark")` for more info * GitHub: https://github.com/mjskay/ggdist * Source code: https://github.com/cran/ggdist * Date/Publication: 2024-03-05 05:30:23 UTC -* Number of recursive dependencies: 127 +* Number of recursive dependencies: 126 Run `revdepcheck::cloud_details(, "ggdist")` for more info @@ -9554,7 +8345,7 @@ Run `revdepcheck::cloud_details(, "ggdist")` for more info + stat_slabinterval(aes(alpha = !!p_(x))) Error in use_defaults(..., self = self) : unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, Calls: ... -> -> compute_geom_2 -> Execution halted ``` @@ -9627,7 +8418,7 @@ Run `revdepcheck::cloud_details(, "ggdist")` for more info ℹ Error occurred in the 1st layer. Caused by error in `use_defaults()`: ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, - 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0 Execution halted ‘dotsinterval.Rmd’ using ‘UTF-8’... failed @@ -9645,98 +8436,6 @@ Run `revdepcheck::cloud_details(, "ggdist")` for more info help 1.5Mb ``` -# ggeasy - -
- -* Version: 0.1.4 -* GitHub: https://github.com/jonocarroll/ggeasy -* Source code: https://github.com/cran/ggeasy -* Date/Publication: 2023-03-12 10:00:23 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "ggeasy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggeasy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: easy_labs - > ### Title: Easily add ggplot labels using label attribute of 'data.frame' - > ### column - > ### Aliases: easy_labs - > - > ### ** Examples - > - ... - + ggplot2::geom_line(ggplot2::aes(colour=Species)) - > - > p - > - > p + easy_labs() - > p + easy_labs(title = "Plot Title", subtitle = 'Plot Subtitle', x = 'x axis label') - Error in utils::modifyList(p_labs, as.list(unlist(man_labs))) : - is.list(x) is not TRUE - Calls: +.gg ... ggplot_add.easy_labs -> easy_update_labs -> -> stopifnot - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggeasy) - > - > test_check("ggeasy") - [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] - - ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ - ... - 1. └─ggeasy (local) expect_eqNe(easy_res$labels[sort(names(easy_res$labels))], hard_res$labels[sort(names(hard_res$labels))]) at test-labs.R:76:3 - 2. └─testthat::expect_equal(..., check.environment = FALSE) at test-labs.R:6:16 - - [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] - Deleting unused snapshots: - • labs/labels-attrib.svg - • labs/labels-manual.svg - • labs/labels-mytitle.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘shortcuts.Rmd’ - ... - - > p1 <- p + labs(title = "default labels") - - > p2 <- p + easy_labs() + labs(title = "Replace titles with column labels") - - > p3 <- p + easy_labs(x = "My x axis") + labs(title = "Manually add x axis label") - - When sourcing ‘shortcuts.R’: - Error: is.list(x) is not TRUE - Execution halted - - ‘shortcuts.Rmd’ using ‘UTF-8’... failed - ‘tests_and_coverage.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘shortcuts.Rmd’ using rmarkdown - ``` - # ggedit
@@ -9745,7 +8444,7 @@ Run `revdepcheck::cloud_details(, "ggeasy")` for more info * GitHub: https://github.com/yonicd/ggedit * Source code: https://github.com/cran/ggedit * Date/Publication: 2024-03-04 14:40:02 UTC -* Number of recursive dependencies: 95 +* Number of recursive dependencies: 94 Run `revdepcheck::cloud_details(, "ggedit")` for more info @@ -9758,19 +8457,19 @@ Run `revdepcheck::cloud_details(, "ggedit")` for more info Running examples in ‘ggedit-Ex.R’ failed The error most likely occurred in: - > ### Name: dput.ggedit - > ### Title: Convert ggplot object to a string call - > ### Aliases: dput.ggedit + > ### Name: compare + > ### Title: compare + > ### Aliases: compare > > ### ** Examples > - > - > pList$pointSmooth #original compiled plot - `geom_smooth()` using formula = 'y ~ x' - Error in compute_geom_2(..., self = self) : - unused arguments (list(6), list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, - Calls: ... get_layer_key -> Map -> mapply -> -> + > compare(ggplot2::theme_bw(),ggplot2::theme_get()) + [1] "theme(panel.background=element_rect(fill='white'),panel.grid=element_line(arrow.fill=''#'*EBEBEBFF',colour=''#'*EBEBEBFF'),strip.background=element_rect(colour=''#'*333333FF'))" + > compare(ggplot2::theme_bw(),ggplot2::theme_get(),verbose=FALSE) + Error in parse(text = out) : :2:0: unexpected end of input + 1: theme(panel.background=element_rect(fill='white'),panel.grid=element_line(arrow.fill=''#'*EBEBEBFF',colour=''#'*EBEBEBFF'),strip.background=element_rect(colour=''#'*333333FF')) + ^ + Calls: compare -> eval -> parse Execution halted ``` @@ -9782,7 +8481,7 @@ Run `revdepcheck::cloud_details(, "ggedit")` for more info * GitHub: https://github.com/kiangkiangkiang/ggESDA * Source code: https://github.com/cran/ggESDA * Date/Publication: 2022-08-19 08:40:10 UTC -* Number of recursive dependencies: 214 +* Number of recursive dependencies: 218 Run `revdepcheck::cloud_details(, "ggESDA")` for more info @@ -9795,162 +8494,43 @@ Run `revdepcheck::cloud_details(, "ggESDA")` for more info Running examples in ‘ggESDA-Ex.R’ failed The error most likely occurred in: - > ### Name: BLOOD - > ### Title: BLOOD data example - > ### Aliases: BLOOD - > ### Keywords: datasets + > ### Name: ggInterval_scatter + > ### Title: scatter plot for two continuous interval data + > ### Aliases: ggInterval_scatter > > ### ** Examples > - > data(BLOOD) - > ggInterval_minmax(BLOOD, aes(x = Hematocrit)) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggInterval_minmax ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggESDA.Rmd’ - ... - [1] "knit_image_paths" "knit_asis" - - > CONCEPT <- rep(c("FRA", "HUS", "INC", "ISA", "JPL", - + "KHA", "LOT", "PHI", "ROM"), each = 3) - - > p <- ggInterval_PCA(facedata, poly = T, concepts_group = CONCEPT) - - When sourcing ‘ggESDA.R’: - Error: argument is of length zero - Execution halted - - ‘ggESDA.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ggESDA.Rmd’ using rmarkdown - - Quitting from lines 390-406 [ggInterval_PCA] (ggESDA.Rmd) - Error: processing vignette 'ggESDA.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggESDA.Rmd’ - - SUMMARY: processing the following file failed: - ‘ggESDA.Rmd’ - - Error: Vignette re-building failed. + > a<-rnorm(1000,0,5) + ... + 11. │ └─base::withCallingHandlers(...) + 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. └─l$compute_geom_2(d, theme = plot$theme) + 14. └─ggplot2 (local) compute_geom_2(..., self = self) + 15. └─self$geom$use_defaults(...) + 16. └─ggplot2 (local) use_defaults(..., self = self) + 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) Execution halted ``` -# ggExtra +# ggfixest
-* Version: 0.10.1 -* GitHub: https://github.com/daattali/ggExtra -* Source code: https://github.com/cran/ggExtra -* Date/Publication: 2023-08-21 14:40:02 UTC -* Number of recursive dependencies: 117 +* Version: 0.2.0 +* GitHub: https://github.com/grantmcdermott/ggfixest +* Source code: https://github.com/cran/ggfixest +* Date/Publication: 2025-01-22 01:00:02 UTC +* Number of recursive dependencies: 78 -Run `revdepcheck::cloud_details(, "ggExtra")` for more info +Run `revdepcheck::cloud_details(, "ggfixest")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggExtra.Rmd’ - ... - - > p1 <- ggplot(df1, aes(x, y)) + geom_point() + theme_bw() - - > p1 - - > ggMarginal(p1) - - When sourcing ‘ggExtra.R’: - Error: argument is of length zero - Execution halted - - ‘ggExtra.Rmd’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ggExtra.Rmd’ using rmarkdown - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘R6’ ‘scales’ ‘utils’ - All declared Imports should be used. - ``` - -# ggfacto - -
- -* Version: 0.3.1 -* GitHub: https://github.com/BriceNocenti/ggfacto -* Source code: https://github.com/cran/ggfacto -* Date/Publication: 2024-08-30 15:00:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "ggfacto")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggfacto-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MCA2 - > ### Title: Multiple Correspondence Analysis - > ### Aliases: MCA2 - > - > ### ** Examples - > - > data(tea, package = "FactoMineR") - > res.mca <- MCA2(tea, active_vars = 1:18) - > - > res.mca %>% - + ggmca(tea, sup_vars = c("SPC"), ylim = c(NA, 1.2), text_repel = TRUE) %>% - + ggi() #to make the graph interactive - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# ggfixest - -
- -* Version: 0.1.0 -* GitHub: https://github.com/grantmcdermott/ggfixest -* Source code: https://github.com/cran/ggfixest -* Date/Publication: 2023-12-14 08:00:06 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "ggfixest")` for more info - -
- -## Newly broken - -* checking tests ... ERROR +* checking tests ... ERROR ``` Running ‘tinytest.R’ Running the tests in ‘tests/tinytest.R’ failed. @@ -9963,7 +8543,6 @@ Run `revdepcheck::cloud_details(, "ggfixest")` for more info + library(fixest) + setFixest_nthreads(1) ... - ----- FAILED[]: test_ggiplot.R<192--192> call| expect_snapshot_plot(p19a, label = "ggiplot_multi_complex_kitchen_iid") diff| 1774 info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png @@ -9971,79 +8550,11 @@ Run `revdepcheck::cloud_details(, "ggfixest")` for more info call| expect_snapshot_plot(p19b, label = "ggiplot_multi_complex_kitchen_iid") diff| 1774 info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png - Error: 16 out of 101 tests failed + Error: 5 out of 103 tests failed + In addition: There were 11 warnings (use warnings() to see them) Execution halted ``` -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggiplot.Rmd’ - ... - > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), - + ref.line = -1, main = "Staggered treatment: Split mutli-sample") - The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. - Note that you can provide the argument `df.t` directly. - - When sourcing ‘ggiplot.R’: - Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: - The 1st element of 'object' raises and error: - Error in nb * sd : non-numeric argument to binary operator - Execution halted - - ‘ggiplot.Rmd’ using ‘UTF-8’... failed - ``` - -# ggfocus - -
- -* Version: 1.0.0 -* GitHub: https://github.com/Freguglia/ggfocus -* Source code: https://github.com/cran/ggfocus -* Date/Publication: 2020-01-23 13:20:02 UTC -* Number of recursive dependencies: 55 - -Run `revdepcheck::cloud_details(, "ggfocus")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘introduction_to_ggfocus.Rmd’ - ... - + geom_point() + scale_alpha_focus(c("A", "B"), alpha_other = 0.5) + - + scale_c .... [TRUNCATED] - - > ggplot(datasets::airquality, aes(x = Day, y = Temp, - + linetype = factor(Month), group = factor(Month))) + geom_line() + - + scale_linetype_f .... [TRUNCATED] - - When sourcing ‘introduction_to_ggfocus.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘introduction_to_ggfocus.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘introduction_to_ggfocus.Rmd’ using rmarkdown - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - # ggforce
@@ -10084,9 +8595,9 @@ Run `revdepcheck::cloud_details(, "ggforce")` for more info * checking installed package size ... NOTE ``` - installed size is 27.8Mb + installed size is 27.3Mb sub-directories of 1Mb or more: - R 1.5Mb + R 1.0Mb help 1.2Mb libs 25.0Mb ``` @@ -10099,7 +8610,7 @@ Run `revdepcheck::cloud_details(, "ggforce")` for more info * GitHub: https://github.com/ProjectMOSAIC/ggformula * Source code: https://github.com/cran/ggformula * Date/Publication: 2023-11-09 12:30:07 UTC -* Number of recursive dependencies: 123 +* Number of recursive dependencies: 122 Run `revdepcheck::cloud_details(, "ggformula")` for more info @@ -10107,68 +8618,6 @@ Run `revdepcheck::cloud_details(, "ggformula")` for more info ## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘ggformula-Ex.R’ failed - The error most likely occurred in: - - > ### Name: discrete_breaks - > ### Title: Discrete Breaks - > ### Aliases: discrete_breaks - > - > ### ** Examples - > - > x <- rbinom(100, 100, 0.4) - > p <- gf_bar( ~ x) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: gf_bar ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggformula) - Loading required package: ggplot2 - Loading required package: scales - Loading required package: ggridges - - New to ggformula? Try the tutorials: - ... - • layer-factory/gf-text1.svg - • layer-factory/gf-text2.svg - • layer-factory/gf-tile1.svg - • layer-factory/proportions-within-all-dodge.svg - • layer-factory/proportions-within-fill-dodge.svg - • layer-factory/proportions-within-fill-facet-grid-and-group.svg - • layer-factory/proportions-within-fill-facet-grid.svg - • layer-factory/proportions-within-group-facet-grid.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggformula.Rmd’ - ... - - > theme_set(theme_light()) - - > library(ggformula) - - > gf_point(mpg ~ hp, data = mtcars) - - When sourcing ‘ggformula.R’: - Error: argument is of length zero - Execution halted - - ‘ggformula.Rmd’ using ‘UTF-8’... failed - ``` - * checking for code/documentation mismatches ... WARNING ``` Codoc mismatches from documentation object 'gf_abline': @@ -10194,24 +8643,6 @@ Run `revdepcheck::cloud_details(, "ggformula")` for more info Position: 17 Code: show.help Docs: inherit ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ggformula.Rmd’ using rmarkdown - - Quitting from lines 106-109 [simple-example] (ggformula.Rmd) - Error: processing vignette 'ggformula.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggformula.Rmd’ - - SUMMARY: processing the following file failed: - ‘ggformula.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - ## In both * checking Rd cross-references ... NOTE @@ -10227,7 +8658,7 @@ Run `revdepcheck::cloud_details(, "ggformula")` for more info * GitHub: https://github.com/sinhrks/ggfortify * Source code: https://github.com/cran/ggfortify * Date/Publication: 2024-04-17 04:30:04 UTC -* Number of recursive dependencies: 125 +* Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "ggfortify")` for more info @@ -10235,25 +8666,6 @@ Run `revdepcheck::cloud_details(, "ggfortify")` for more info ## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘ggfortify-Ex.R’ failed - The error most likely occurred in: - - > ### Name: autoplot.cv.glmnet - > ### Title: Autoplot 'glmnet::cv.glmnet' - > ### Aliases: autoplot.cv.glmnet - > - > ### ** Examples - > - > if (requireNamespace("survival", quietly = TRUE)) { - + autoplot(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3]))) - + } - Error in if (new_name %in% existing) { : argument is of length zero - Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - * checking tests ... ERROR ``` Running ‘test-all.R’ @@ -10267,79 +8679,29 @@ Run `revdepcheck::cloud_details(, "ggfortify")` for more info > test_check('ggfortify') Loading required package: ggfortify ... - 3. └─ggfortify:::autoplot.ts(original.data, columns = "Data", ...) - 4. └─ggplot2:::`+.gg`(p, do.call(geom_factory, args)) - 5. └─ggplot2:::add_ggplot(e1, e2, e2name) - 6. ├─ggplot2::ggplot_add(object, p, objectname) - 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) - [ FAIL 32 | WARN 10 | SKIP 47 | PASS 358 ] + x[3]: "#595959FF" + y[3]: "grey35" + + x[4]: "#595959FF" + y[4]: "grey35" + + [ FAIL 5 | WARN 13 | SKIP 48 | PASS 734 ] Error: Test failures Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘basics.Rmd’ - ... - + warning = FALSE) - - > library(ggfortify) - Loading required package: ggplot2 - - > autoplot(AirPassengers) - - ... - Error: argument is of length zero - Execution halted - - ‘basics.Rmd’ using ‘UTF-8’... failed - ‘plot_dist.Rmd’ using ‘UTF-8’... failed - ‘plot_lm.Rmd’ using ‘UTF-8’... OK - ‘plot_map.Rmd’ using ‘UTF-8’... failed - ‘plot_pca.Rmd’ using ‘UTF-8’... OK - ‘plot_surv.Rmd’ using ‘UTF-8’... failed - ‘plot_ts.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘basics.Rmd’ using knitr - - Attaching package: 'zoo' - - The following objects are masked from 'package:base': - - as.Date, as.Date.numeric - - - ... - - Quitting from lines 20-22 [unnamed-chunk-1] (plot_dist.Rmd) - Error: processing vignette 'plot_dist.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘plot_dist.Rmd’ - - --- re-building ‘plot_lm.Rmd’ using knitr - --- finished re-building ‘plot_lm.Rmd’ - - --- re-building ‘plot_map.Rmd’ using knitr - ``` - -# gggenomes +# ggh4x
-* Version: 1.0.1 -* GitHub: https://github.com/thackl/gggenomes -* Source code: https://github.com/cran/gggenomes -* Date/Publication: 2024-08-30 11:40:02 UTC -* Number of recursive dependencies: 112 +* Version: 0.3.0 +* GitHub: https://github.com/teunbrand/ggh4x +* Source code: https://github.com/cran/ggh4x +* Date/Publication: 2024-12-15 17:20:02 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "gggenomes")` for more info +Run `revdepcheck::cloud_details(, "ggh4x")` for more info
@@ -10347,91 +8709,27 @@ Run `revdepcheck::cloud_details(, "gggenomes")` for more info * checking examples ... ERROR ``` - Running examples in ‘gggenomes-Ex.R’ failed + Running examples in ‘ggh4x-Ex.R’ failed The error most likely occurred in: - > ### Name: flip - > ### Title: Flip bins and sequences - > ### Aliases: flip flip_seqs sync + > ### Name: guide_stringlegend + > ### Title: String legend + > ### Aliases: guide_stringlegend > > ### ** Examples > - > library(patchwork) - ... - > p4 <- p %>% - + add_clusters(emale_cogs) %>% - + sync() + labs(caption = "shared orthologs") - Joining with `by = join_by(feat_id)` - Flipping: E4-10_086,E4-10_112,RCC970_016B + > p <- ggplot(mpg, aes(displ, hwy)) + + + geom_point(aes(colour = manufacturer)) > - > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") - Error in as.unit(value) : object is not coercible to a unit - Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘flip.Rmd’ - ... - > p4 <- p %>% add_clusters(emale_cogs) %>% sync() + - + labs(caption = "shared orthologs") - Joining with `by = join_by(feat_id)` - Flipping: E4-10_086,E4-10_112,RCC970_016B - - > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") - - When sourcing ‘flip.R’: - Error: object is not coercible to a unit - Execution halted - - ‘emales.Rmd’ using ‘UTF-8’... OK - ‘flip.Rmd’ using ‘UTF-8’... failed - ‘gggenomes.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘emales.Rmd’ using rmarkdown - --- finished re-building ‘emales.Rmd’ - - --- re-building ‘flip.Rmd’ using rmarkdown - - Quitting from lines 17-44 [unnamed-chunk-2] (flip.Rmd) - Error: processing vignette 'flip.Rmd' failed with diagnostics: - object is not coercible to a unit - --- failed re-building ‘flip.Rmd’ - ... - virophages) - emale_tirs Terminal inverted repeats of 6 EMALE genomes - - --- finished re-building ‘gggenomes.Rmd’ - - SUMMARY: processing the following file failed: - ‘flip.Rmd’ - - Error: Vignette re-building failed. + > # String legend can be set in the `guides()` function + > p + guides(colour = guide_stringlegend(ncol = 2)) + Error in get_layer_key(...) : + unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, + NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, N + Calls: ... -> -> process_layers -> Execution halted ``` -# ggh4x - -
- -* Version: 0.2.8 -* GitHub: https://github.com/teunbrand/ggh4x -* Source code: https://github.com/cran/ggh4x -* Date/Publication: 2024-01-23 21:00:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "ggh4x")` for more info - -
- -## Newly broken - * checking tests ... ERROR ``` Running ‘testthat.R’ @@ -10440,55 +8738,52 @@ Run `revdepcheck::cloud_details(, "ggh4x")` for more info > library(testthat) > library(ggh4x) Loading required package: ggplot2 - > - > test_check("ggh4x") - [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-facet_wrap2.R:64:3'): facet_wrap2() can some repeat axes ───── - sum(ctrl) (`actual`) not equal to 4L (`expected`). + Attaching package: 'ggplot2' - `actual`: 3 - `expected`: 4 + The following object is masked from 'package:base': + ... + 11. └─base::Map(...) + 12. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 13. └─ggplot2 (local) ``(guide = dots[[1L]][[1L]], param = dots[[2L]][[1L]]) + 14. └─guide$process_layers(param, layers, data, theme) + 15. └─ggplot2 (local) process_layers(..., self = self) + 16. └─self$get_layer_key(params, layers[include], data[include], theme) - [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] + [ FAIL 1 | WARN 0 | SKIP 15 | PASS 663 ] Error: Test failures Execution halted ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Facets.Rmd’ using rmarkdown - ``` - -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Statistics.Rmd’ + when running code in ‘Miscellaneous.Rmd’ ... - > incorrect$x[15] <- sqrt(2) + + aest .... [TRUNCATED] - > ggplot(incorrect, aes(x, colour = group)) + stat_theodensity(distri = "nbinom") + > ggplot(diamonds, aes(price, carat, colour = clarity)) + + + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", + + guide = "stri ..." ... [TRUNCATED] - When sourcing ‘Statistics.R’: - Error: Problem while computing stat. - ℹ Error occurred in the 1st layer. - Caused by error in `setup_params()`: - ! A discrete 'nbinom' distribution cannot be fitted to continuous data. + When sourcing ‘Miscellaneous.R’: + Error: unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, + NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NUL Execution halted ‘Facets.Rmd’ using ‘UTF-8’... OK - ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK - ‘PositionGuides.Rmd’ using ‘UTF-8’... OK - ‘Statistics.Rmd’ using ‘UTF-8’... failed + ‘Miscellaneous.Rmd’ using ‘UTF-8’... failed + ‘Statistics.Rmd’ using ‘UTF-8’... OK ‘ggh4x.Rmd’ using ‘UTF-8’... OK ``` -# gghighlight +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Facets.Rmd’ using rmarkdown + ``` + +# gghighlight
@@ -10537,10 +8832,10 @@ Run `revdepcheck::cloud_details(, "gghighlight")` for more info > library(testthat) > library(gghighlight) Loading required package: ggplot2 - > - > test_check("gghighlight") - label_key: type - label_key: type + + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': ... 15. └─cli::cli_abort(...) 16. └─rlang::abort(...) @@ -10579,56 +8874,14 @@ Run `revdepcheck::cloud_details(, "gghighlight")` for more info --- re-building ‘gghighlight.Rmd’ using rmarkdown ``` -# ggHoriPlot - -
- -* Version: 1.0.1 -* GitHub: https://github.com/rivasiker/ggHoriPlot -* Source code: https://github.com/cran/ggHoriPlot -* Date/Publication: 2022-10-11 16:22:33 UTC -* Number of recursive dependencies: 117 - -Run `revdepcheck::cloud_details(, "ggHoriPlot")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggHoriPlot.Rmd’ - ... - > mid <- sum(range(dat_tab$y, na.rm = T))/2 - - > b <- plotAllLayers(dat_tab, mid, cutpoints$cuts, cutpoints$color) - - > b/a + plot_layout(guides = "collect", heights = c(6, - + 1)) - - When sourcing ‘ggHoriPlot.R’: - Error: object is not a unit - Execution halted - - ‘examples.Rmd’ using ‘UTF-8’... OK - ‘ggHoriPlot.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘examples.Rmd’ using rmarkdown - ``` - # ggiraph
-* Version: 0.8.10 +* Version: 0.8.12 * GitHub: https://github.com/davidgohel/ggiraph * Source code: https://github.com/cran/ggiraph -* Date/Publication: 2024-05-17 12:10:02 UTC +* Date/Publication: 2025-01-08 11:10:02 UTC * Number of recursive dependencies: 89 Run `revdepcheck::cloud_details(, "ggiraph")` for more info @@ -10642,23 +8895,23 @@ Run `revdepcheck::cloud_details(, "ggiraph")` for more info Running examples in ‘ggiraph-Ex.R’ failed The error most likely occurred in: - > ### Name: annotate_interactive - > ### Title: Create interactive annotations - > ### Aliases: annotate_interactive + > ### Name: geom_path_interactive + > ### Title: Create interactive observations connections + > ### Aliases: geom_path_interactive geom_line_interactive + > ### geom_step_interactive > > ### ** Examples > - > # add interactive annotation to a ggplot ------- ... - > - > gg <- ggplot(mtcars, aes(x = disp, y = qsec )) + - + geom_point(size=2) + - + annotate_interactive( - + "rect", xmin = 100, xmax = 400, fill = "red", - + data_id = "an_id", tooltip = "a tooltip", - + ymin = 18, ymax = 20, alpha = .5) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + 20. │ └─base::lapply(...) + 21. │ └─ggplot2 (local) FUN(X[[i]], ...) + 22. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 23. │ └─self$draw_panel(...) + 24. └─base::.handleSimpleError(...) + 25. └─rlang (local) h(simpleError(msg, call)) + 26. └─handlers[[1L]](cnd) + 27. └─cli::cli_abort(...) + 28. └─rlang::abort(...) Execution halted ``` @@ -10673,17 +8926,17 @@ Run `revdepcheck::cloud_details(, "ggiraph")` for more info test-annotate_interactive.R... 0 tests test-annotate_interactive.R... 0 tests - test-annotate_interactive.R... 0 tests + Attaching package: 'ggplot2' ... - test-geom_density_interactive.R 8 tests OK 8ms - - test-geom_dotplot_interactive.R 0 tests - test-geom_dotplot_interactive.R 0 tests - test-geom_dotplot_interactive.R 0 tests - test-geom_dotplot_interactive.R 0 tests - test-geom_dotplot_interactive.R 0 tests - test-geom_dotplot_interactive.R 8 tests OK Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + 30. │ └─base::lapply(...) + 31. │ └─ggplot2 (local) FUN(X[[i]], ...) + 32. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 33. │ └─self$draw_panel(...) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) Execution halted ``` @@ -10691,95 +8944,55 @@ Run `revdepcheck::cloud_details(, "ggiraph")` for more info * checking installed package size ... NOTE ``` - installed size is 9.9Mb + installed size is 8.1Mb sub-directories of 1Mb or more: R 1.5Mb - libs 7.1Mb + libs 5.2Mb ``` -# ggiraphExtra +# ggmap
-* Version: 0.3.0 -* GitHub: https://github.com/cardiomoon/ggiraphExtra -* Source code: https://github.com/cran/ggiraphExtra -* Date/Publication: 2020-10-06 07:00:02 UTC -* Number of recursive dependencies: 111 +* Version: 4.0.0 +* GitHub: https://github.com/dkahle/ggmap +* Source code: https://github.com/cran/ggmap +* Date/Publication: 2023-11-19 08:10:02 UTC +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info +Run `revdepcheck::cloud_details(, "ggmap")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘ggmap’ can be installed ... WARNING ``` - Running examples in ‘ggiraphExtra-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggAncova - > ### Title: Make an interactive plot for an ANCOVA model - > ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm - > - > ### ** Examples - > - > require(moonBook) - ... - addLabelDf, getMapping - - > require(ggplot2) - Loading required package: ggplot2 - > require(ggiraph) - Loading required package: ggiraph - > ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggAncova ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted + Found the following significant warnings: + Warning: `aes_()` was deprecated in ggplot2 3.0.0. + See ‘/tmp/workdir/ggmap/new/ggmap.Rcheck/00install.out’ for details. ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggPredict.Rmd’ - ... - - - > require(plyr) - Loading required package: plyr - - > ggPredict(fit, se = TRUE, interactive = TRUE) - - ... - - > ggPoints(aes(x = wt, y = mpg, color = am), data = mtcars, - + method = "lm", interactive = TRUE) - - When sourcing ‘introduction.R’: - Error: argument is of length zero - Execution halted - - ‘ggPredict.Rmd’ using ‘UTF-8’... failed - ‘introduction.Rmd’ using ‘UTF-8’... failed - ``` +## In both -* checking re-building of vignette outputs ... NOTE +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘ggPredict.Rmd’ using rmarkdown + installed size is 7.4Mb + sub-directories of 1Mb or more: + data 7.0Mb ``` -# ggmatplot +# ggmcmc
-* Version: 0.1.2 -* GitHub: https://github.com/xuan-liang/ggmatplot -* Source code: https://github.com/cran/ggmatplot -* Date/Publication: 2022-05-17 02:20:02 UTC -* Number of recursive dependencies: 81 +* Version: 1.5.1.1 +* GitHub: https://github.com/xfim/ggmcmc +* Source code: https://github.com/cran/ggmcmc +* Date/Publication: 2021-02-10 10:50:10 UTC +* Number of recursive dependencies: 74 -Run `revdepcheck::cloud_details(, "ggmatplot")` for more info +Run `revdepcheck::cloud_details(, "ggmcmc")` for more info
@@ -10787,84 +9000,54 @@ Run `revdepcheck::cloud_details(, "ggmatplot")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggmatplot-Ex.R’ failed + Running examples in ‘ggmcmc-Ex.R’ failed The error most likely occurred in: - > ### Name: ggmatplot - > ### Title: ggmatplot - > ### Aliases: ggmatplot + > ### Name: ggs_geweke + > ### Title: Dotplot of the Geweke diagnostic, the standard Z-score + > ### Aliases: ggs_geweke > > ### ** Examples > - > - > # Define a data set - > iris_sub <- subset(iris, Species == "setosa") - > ggmatplot(iris_sub[, c(1, 3)], iris_sub[, c(2, 4)]) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggmatplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > data(linear) + > ggs_geweke(ggs(s)) + Error in grid.Call.graphics(C_polygon, x$x, x$y, index) : + invalid line type + Calls: ... drawDetails -> drawDetails.polygon -> grid.Call.graphics Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggmatplot) - Loading required package: ggplot2 - > library(tibble) - > library(stats) - > - > test_check("ggmatplot") - ... - • ggmatplot_parameters/single-color-scatterplot.svg - • ggmatplot_parameters/single-fill-density-plot.svg - • ggmatplot_parameters/single-linetype-line-plot.svg - • ggmatplot_parameters/single-shape-scatterplot.svg - • ggmatplot_parameters/three-color-violin-plot.svg - • ggmatplot_parameters/three-fill-color-violin-plot.svg - • ggmatplot_parameters/three-linetype-line-plot.svg - • ggmatplot_parameters/three-shape-scatterplot.svg - Error: Test failures - Execution halted - ``` +## In both * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘ggmatplot.Rmd’ + when running code in ‘using_ggmcmc.Rmd’ ... - 6 -0.5325916 -0.54457006 - > library(ggmatplot) - Loading required package: ggplot2 + > ggs_crosscorrelation(S) + + > ggs_Rhat(S) + xlab("R_hat") - > ggmatplot(x, z) + > ggs_geweke(S) - When sourcing ‘ggmatplot.R’: + ... + + par(mar = c(4, 4, 0.1, 0.1), cex .... [TRUNCATED] + + > knit_theme$set("print") + + When sourcing 'v70i09.R': Error: argument is of length zero Execution halted - ‘ggmatplot.Rmd’ using ‘UTF-8’... failed + ‘using_ggmcmc.Rmd’ using ‘UTF-8’... failed + ‘v70i09.Rnw’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘ggmatplot.Rmd’ using rmarkdown - - Quitting from lines 47-50 [point-plot] (ggmatplot.Rmd) - Error: processing vignette 'ggmatplot.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggmatplot.Rmd’ - - SUMMARY: processing the following file failed: - ‘ggmatplot.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘using_ggmcmc.Rmd’ using rmarkdown ``` # ggmice @@ -10875,7 +9058,7 @@ Run `revdepcheck::cloud_details(, "ggmatplot")` for more info * GitHub: https://github.com/amices/ggmice * Source code: https://github.com/cran/ggmice * Date/Publication: 2023-08-07 14:20:02 UTC -* Number of recursive dependencies: 120 +* Number of recursive dependencies: 122 Run `revdepcheck::cloud_details(, "ggmice")` for more info @@ -10938,14 +9121,14 @@ Run `revdepcheck::cloud_details(, "ggmulti")` for more info > > if(require("dplyr")) { ... - The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union + Warning: Duplicated aesthetics after name standardisation: PTS Error in use_defaults(..., self = self) : unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, Calls: ... -> -> compute_geom_2 -> Execution halted ``` @@ -10961,7 +9144,7 @@ Run `revdepcheck::cloud_details(, "ggmulti")` for more info > library(ggmulti) Loading required package: ggplot2 - Attaching package: 'ggmulti' + Attaching package: 'ggplot2' ... 16. └─base::Map(...) 17. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) @@ -10988,11 +9171,11 @@ Run `revdepcheck::cloud_details(, "ggmulti")` for more info # Bad: myquosure / rhs ... - > p When sourcing ‘highDim.R’: - Error: argument is of length zero + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list( + NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, Execution halted ‘glyph.Rmd’ using ‘UTF-8’... failed @@ -11006,106 +9189,6 @@ Run `revdepcheck::cloud_details(, "ggmulti")` for more info --- re-building ‘glyph.Rmd’ using rmarkdown ``` -# ggpackets - -
- -* Version: 0.2.1 -* GitHub: https://github.com/dgkf/ggpackets -* Source code: https://github.com/cran/ggpackets -* Date/Publication: 2022-10-10 23:30:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "ggpackets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggpackets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggpacket - > ### Title: A container for lazy ggplot layers - > ### Aliases: ggpacket - > - > ### ** Examples - > - > library(ggplot2) - > - > # create a ggpacket directly, setting some fixed argument settings - > ggpk_simple <- ggpacket() %+% geom_line(color = "red") %+% geom_point() - > ggplot(mtcars, aes(x = wt, y = mpg)) + ggpk_simple() - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > - > library(ggplot2) - > library(ggpackets) - - Attaching package: 'ggpackets' - - ... - 10. └─ggpackets (local) f(init, x[[i]]) - 11. └─ggplot2:::`+.gg`(gg, ggpk_i) - 12. └─ggplot2:::add_ggplot(e1, e2, e2name) - 13. ├─ggplot2::ggplot_add(object, p, objectname) - 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 4 | WARN 1 | SKIP 0 | PASS 27 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘composing-functions.Rmd’ - ... - + geom_point(size = 3) - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - > ggplot(Loblolly) + aes(x = age, y = height, color = Seed) + - + ggpk_my_template() + ggtitle("Growth of Loblolly Pines") - - ... - > diamonds %>% sample_frac(0.01) %>% arrange(cut) %>% - + ggplot() + aes(color = cut) + ggpk_dot_matrix(size = 3, width = 30) - - When sourcing ‘miscellaneous-examples.R’: - Error: argument is of length zero - Execution halted - - ‘composing-functions.Rmd’ using ‘UTF-8’... failed - ‘ggpackets.Rmd’ using ‘UTF-8’... failed - ‘miscellaneous-examples.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘composing-functions.Rmd’ using rmarkdown - - Quitting from lines 58-62 [simple_ggpacket_output] (composing-functions.Rmd) - Error: processing vignette 'composing-functions.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘composing-functions.Rmd’ - - --- re-building ‘ggpackets.Rmd’ using rmarkdown - ``` - # ggparallel
@@ -11114,7 +9197,7 @@ Run `revdepcheck::cloud_details(, "ggpackets")` for more info * GitHub: https://github.com/heike/ggparallel * Source code: https://github.com/cran/ggparallel * Date/Publication: 2024-03-09 22:00:02 UTC -* Number of recursive dependencies: 51 +* Number of recursive dependencies: 50 Run `revdepcheck::cloud_details(, "ggparallel")` for more info @@ -11135,29 +9218,29 @@ Run `revdepcheck::cloud_details(, "ggparallel")` for more info > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html ... - 12. └─self$get_layer_key(params, layers[include], data[include], theme) - 13. └─ggplot2 (local) get_layer_key(...) - 14. └─base::Map(...) - 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) - 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) - 17. └─layer$compute_geom_2(key, single_params, theme) + 12. │ └─ggplot2 (local) map_statistic(..., self = self) + 13. └─base::.handleSimpleError(...) + 14. └─rlang (local) h(simpleError(msg, call)) + 15. └─handlers[[1L]](cnd) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted ``` -# ggparty +# ggplotlyExtra
-* Version: 1.0.0 -* GitHub: https://github.com/martin-borkovec/ggparty -* Source code: https://github.com/cran/ggparty -* Date/Publication: 2019-07-18 10:54:06 UTC -* Number of recursive dependencies: 115 +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/ggplotlyExtra +* Date/Publication: 2019-12-02 16:20:06 UTC +* Number of recursive dependencies: 70 -Run `revdepcheck::cloud_details(, "ggparty")` for more info +Run `revdepcheck::cloud_details(, "ggplotlyExtra")` for more info
@@ -11165,89 +9248,47 @@ Run `revdepcheck::cloud_details(, "ggparty")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggparty-Ex.R’ failed + Running examples in ‘ggplotlyExtra-Ex.R’ failed The error most likely occurred in: - > ### Name: geom_node_label - > ### Title: Draw (multi-line) labels at nodes - > ### Aliases: geom_node_label geom_node_info geom_node_splitvar + > ### Name: ggplotly_histogram + > ### Title: Clean 'ggplot2' Histogram to be Converted to 'Plotly' + > ### Aliases: ggplotly_histogram > > ### ** Examples > - > library(ggparty) + > ... - 30. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 31. │ ├─ggplot2::ggplot_add(object, p, objectname) - 32. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 33. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 34. └─base::.handleSimpleError(...) - 35. └─rlang (local) h(simpleError(msg, call)) - 36. └─handlers[[1L]](cnd) - 37. └─cli::cli_abort(...) - 38. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggparty-graphic-partying.Rmd’ - ... - + 0.55 .... [TRUNCATED] - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - When sourcing ‘ggparty-graphic-partying.R’: - Error: Problem while converting geom to grob. - ℹ Error occurred in the 5th layer. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero + + xlab("len") + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + Warning in geom_bar(data = layerdata, mapping = aes(x = .data$x, y = .data$count, : + Ignoring unknown aesthetics: label1, label2, and label3 + > + > # convert `ggplot` object to `plotly` object + > ggplotly(p, tooltip = c("Range", "count", "density")) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list Execution halted - - ‘ggparty-graphic-partying.Rmd’ using ‘UTF-8’... failed - ‘on-the-edge.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ggparty-graphic-partying.Rmd’ using rmarkdown - - Quitting from lines 42-122 [unnamed-chunk-2] (ggparty-graphic-partying.Rmd) - Error: processing vignette 'ggparty-graphic-partying.Rmd' failed with diagnostics: - Problem while converting geom to grob. - ℹ Error occurred in the 5th layer. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - --- failed re-building ‘ggparty-graphic-partying.Rmd’ - - --- re-building ‘on-the-edge.Rmd’ using rmarkdown ``` ## In both -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘survival’ - All declared Imports should be used. - ``` - * checking LazyData ... NOTE ``` 'LazyData' is specified without a 'data' directory ``` -# ggpicrust2 +# ggpol
-* Version: 1.7.3 -* GitHub: https://github.com/cafferychen777/ggpicrust2 -* Source code: https://github.com/cran/ggpicrust2 -* Date/Publication: 2023-11-08 16:10:02 UTC -* Number of recursive dependencies: 231 +* Version: 0.0.7 +* GitHub: https://github.com/erocoar/ggpol +* Source code: https://github.com/cran/ggpol +* Date/Publication: 2020-11-08 13:40:02 UTC +* Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "ggpicrust2")` for more info +Run `revdepcheck::cloud_details(, "ggpol")` for more info
@@ -11255,103 +9296,95 @@ Run `revdepcheck::cloud_details(, "ggpicrust2")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggpicrust2-Ex.R’ failed + Running examples in ‘ggpol-Ex.R’ failed The error most likely occurred in: - > ### Name: pathway_pca - > ### Title: Perform Principal Component Analysis (PCA) on functional pathway - > ### abundance data and create visualizations of the PCA results. - > ### Aliases: pathway_pca + > ### Name: GeomConfmat + > ### Title: Confusion Matrix + > ### Aliases: GeomConfmat geom_confmat stat_confmat > > ### ** Examples > + > x <- sample(LETTERS[seq(4)], 50, replace = TRUE) ... - > - > # Create example metadata - > # Please ensure the sample IDs in the metadata have the column name "sample_name" - > metadata_example <- data.frame(sample_name = colnames(kegg_abundance_example), - + group = factor(rep(c("Control", "Treatment"), each = 5))) - > - > pca_plot <- pathway_pca(kegg_abundance_example, metadata_example, "group") - Error in identicalUnits(x) : object is not a unit - Calls: pathway_pca ... assemble_guides -> guides_build -> unit.c -> identicalUnits + 21. │ └─ggpol (local) draw_panel(...) + 22. │ └─base::lapply(GeomText$default_aes[missing_aes], rlang::eval_tidy) + 23. │ └─rlang (local) FUN(X[[i]], ...) + 24. ├─ggplot2::from_theme(fontsize) + 25. └─base::.handleSimpleError(...) + 26. └─rlang (local) h(simpleError(msg, call)) + 27. └─handlers[[1L]](cnd) + 28. └─cli::cli_abort(...) + 29. └─rlang::abort(...) Execution halted ``` ## In both -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘ComplexHeatmap’ +* checking dependencies in R code ... NOTE ``` - -* checking installed package size ... NOTE + Namespaces in Imports field not imported from: + ‘dplyr’ ‘grDevices’ + All declared Imports should be used. ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - R 2.1Mb - data 2.0Mb + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory ``` -# ggplotlyExtra +# ggpubr
-* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/ggplotlyExtra -* Date/Publication: 2019-12-02 16:20:06 UTC -* Number of recursive dependencies: 70 +* Version: 0.6.0 +* GitHub: https://github.com/kassambara/ggpubr +* Source code: https://github.com/cran/ggpubr +* Date/Publication: 2023-02-10 16:20:02 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "ggplotlyExtra")` for more info +Run `revdepcheck::cloud_details(, "ggpubr")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘ggplotlyExtra-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggplotly_histogram - > ### Title: Clean 'ggplot2' Histogram to be Converted to 'Plotly' - > ### Aliases: ggplotly_histogram - > - > ### ** Examples - > - > + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggpubr) + Loading required package: ggplot2 + + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': ... - + xlab("len") - `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. - Warning in geom_bar(data = layerdata, mapping = aes(x = .data$x, y = .data$count, : - Ignoring unknown aesthetics: label1, label2, and label3 - > - > # convert `ggplot` object to `plotly` object - > ggplotly(p, tooltip = c("Range", "count", "density")) - Error in pm[[2]] : subscript out of bounds - Calls: ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory + [6] 6 - 10 == -4 + [7] 19 - 9 == 10 + [9] 1 - 7 == -6 + [10] 6 - 7 == -1 + [11] 13 - 6 == 7 + ... + + [ FAIL 2 | WARN 5 | SKIP 0 | PASS 183 ] + Error: Test failures + Execution halted ``` -# ggPMX +# ggraph
-* Version: 1.2.11 -* GitHub: https://github.com/ggPMXdevelopment/ggPMX -* Source code: https://github.com/cran/ggPMX -* Date/Publication: 2023-11-30 16:10:06 UTC -* Number of recursive dependencies: 181 +* Version: 2.2.1 +* GitHub: https://github.com/thomasp85/ggraph +* Source code: https://github.com/cran/ggraph +* Date/Publication: 2024-03-07 12:40:02 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "ggPMX")` for more info +Run `revdepcheck::cloud_details(, "ggraph")` for more info
@@ -11359,93 +9392,82 @@ Run `revdepcheck::cloud_details(, "ggPMX")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggPMX-Ex.R’ failed + Running examples in ‘ggraph-Ex.R’ failed The error most likely occurred in: - > ### Name: pmx_config - > ### Title: This function can be used to define the pmx configuration used - > ### in plots. e.g. Monolix/Nonmem - > ### Aliases: pmx_config + > ### Name: geom_conn_bundle + > ### Title: Create hierarchical edge bundles between node connections + > ### Aliases: geom_conn_bundle geom_conn_bundle2 geom_conn_bundle0 > > ### ** Examples > + > # Create a graph of the flare class system ... - + cats = c("SEX"), - + conts = c("WT0", "AGE0"), - + strats = "STUD" - + ) - NO FINEGRID FILE: - we will use instead predictions.txt for individual plots - Warning: Duplicated aesthetics after name standardisation: colour - Error in if (new_name %in% existing) { : argument is of length zero - Calls: pmx_mlx ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggPMX-guide.Rmd’ - ... - - > work_dir <- file.path(theophylline, "Monolix") - - > input_data <- file.path(theophylline, "data_pk.csv") - - > ctr <- theophylline() - - When sourcing ‘ggPMX-guide.R’: - Error: argument is of length zero + + ) + + + geom_node_point(aes(filter = leaf, colour = class)) + + + scale_edge_colour_distiller('', direction = 1, guide = 'edge_direction') + + + coord_fixed() + + + ggforce::theme_no_axes() + Error in get_layer_key(...) : + unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, + Calls: ... -> -> process_layers -> Execution halted - - ‘ggPMX-guide.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘ggPMX-guide.Rmd’ using rmarkdown - - Quitting from lines 25-37 [load_package] (ggPMX-guide.Rmd) - Error: processing vignette 'ggPMX-guide.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggPMX-guide.Rmd’ - - SUMMARY: processing the following file failed: - ‘ggPMX-guide.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘Edges.Rmd’ using rmarkdown ``` ## In both -* checking package dependencies ... NOTE +* checking running R code from vignettes ... ERROR ``` - Package suggested but not available for checking: ‘lixoftConnectors’ + Errors in running code in vignettes: + when running code in ‘Edges.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + ... + font family 'Arial' not found in PostScript font database + + When sourcing ‘tidygraph.R’: + Error: invalid font type + Execution halted + + ‘Edges.Rmd’ using ‘UTF-8’... failed + ‘Layouts.Rmd’ using ‘UTF-8’... failed + ‘Nodes.Rmd’ using ‘UTF-8’... failed + ‘tidygraph.Rmd’ using ‘UTF-8’... failed ``` * checking installed package size ... NOTE ``` installed size is 8.9Mb sub-directories of 1Mb or more: - doc 1.1Mb - help 2.4Mb - testdata 4.8Mb + R 1.5Mb + doc 3.9Mb + libs 2.8Mb ``` -# ggpol +# ggredist
-* Version: 0.0.7 -* GitHub: https://github.com/erocoar/ggpol -* Source code: https://github.com/cran/ggpol -* Date/Publication: 2020-11-08 13:40:02 UTC -* Number of recursive dependencies: 54 +* Version: 0.0.2 +* GitHub: https://github.com/alarm-redist/ggredist +* Source code: https://github.com/cran/ggredist +* Date/Publication: 2022-11-23 11:20:02 UTC +* Number of recursive dependencies: 67 -Run `revdepcheck::cloud_details(, "ggpol")` for more info +Run `revdepcheck::cloud_details(, "ggredist")` for more info
@@ -11453,151 +9475,127 @@ Run `revdepcheck::cloud_details(, "ggpol")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggpol-Ex.R’ failed + Running examples in ‘ggredist-Ex.R’ failed The error most likely occurred in: - > ### Name: GeomConfmat - > ### Title: Confusion Matrix - > ### Aliases: GeomConfmat geom_confmat stat_confmat + > ### Name: geom_district_text + > ### Title: Label Map Regions + > ### Aliases: geom_district_text geom_district_label + > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText + > ### Keywords: datasets > > ### ** Examples - > - > x <- sample(LETTERS[seq(4)], 50, replace = TRUE) ... - 21. │ └─ggpol (local) draw_panel(...) - 22. │ └─base::lapply(GeomText$default_aes[missing_aes], rlang::eval_tidy) - 23. │ └─rlang (local) FUN(X[[i]], ...) - 24. ├─ggplot2::from_theme(fontsize) - 25. └─base::.handleSimpleError(...) - 26. └─rlang (local) h(simpleError(msg, call)) - 27. └─handlers[[1L]](cnd) - 28. └─cli::cli_abort(...) - 29. └─rlang::abort(...) + 22. │ └─coord$transform(data, panel_params) + 23. │ └─ggplot2 (local) transform(..., self = self) + 24. │ └─ggplot2:::sf_rescale01(...) + 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) + 26. └─base::.handleSimpleError(...) + 27. └─rlang (local) h(simpleError(msg, call)) + 28. └─handlers[[1L]](cnd) + 29. └─cli::cli_abort(...) + 30. └─rlang::abort(...) Execution halted ``` -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘dplyr’ ‘grDevices’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# ggprism +# ggRtsy
-* Version: 1.0.5 -* GitHub: https://github.com/csdaw/ggprism -* Source code: https://github.com/cran/ggprism -* Date/Publication: 2024-03-21 10:50:02 UTC -* Number of recursive dependencies: 97 +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ggRtsy +* Date/Publication: 2023-09-15 19:12:05 UTC +* Number of recursive dependencies: 68 -Run `revdepcheck::cloud_details(, "ggprism")` for more info +Run `revdepcheck::cloud_details(, "ggRtsy")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘ggprism-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_pvalue - > ### Title: Add p-values to a ggplot - > ### Aliases: add_pvalue - > - > ### ** Examples - > - > library(ggplot2) - ... - + "OJ", "VC", 0.0606, 36 - + ) - > - > # boxplot (or another geom...) - > ggplot(tg, aes(x = supp, y = len)) + - + geom_boxplot() + - + add_pvalue(two.means) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - * checking tests ... ERROR ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. Complete output: - > - > if ( requireNamespace("tinytest", quietly=TRUE) ){ - + tinytest::test_package("ggprism") - + } + > library(testthat) + > library(ggplot2) + + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': + + ... + 13. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) + 14. │ └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call) + 15. └─vctrs (local) ``() + 16. └─vctrs:::stop_subscript_oob(...) + 17. └─vctrs:::stop_subscript(...) + 18. └─rlang::abort(...) - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - ... - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests - test-add_pvalue.R............. 0 tests Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘ggprism.Rmd’ + when running code in ‘Vignette.Rmd’ ... - + p.adj = 0.0606, y.position = 36) - - > p1 <- ggplot(ToothGrowth, aes(x = factor(supp), y = len)) + - + geom_boxplot(aes(fill = factor(supp))) + scale_fill_prism(palette = "candy_bright ..." ... [TRUNCATED] - - > p2 <- p1 + add_pvalue(df_p_val) + |Antique White |(238, 223, 204) |#eedfcc | - ... + > RectangleFiller(plotExample, c("#e32636", "#9966cc", + + "#f4c2c2", "#e16827")) - When sourcing ‘pvalues.R’: - Error: argument is of length zero + When sourcing ‘Vignette.R’: + Error: Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. Execution halted - ‘axes.Rmd’ using ‘UTF-8’... OK - ‘colours.Rmd’ using ‘UTF-8’... OK - ‘ggprism.Rmd’ using ‘UTF-8’... failed - ‘pvalues.Rmd’ using ‘UTF-8’... failed - ‘themes.Rmd’ using ‘UTF-8’... OK + ‘Vignette.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘axes.Rmd’ using rmarkdown - ``` - -# ggpubr - -
+ ... + --- re-building ‘Vignette.Rmd’ using rmarkdown + + Quitting from lines 48-49 [unnamed-chunk-2] (Vignette.Rmd) + Error: processing vignette 'Vignette.Rmd' failed with diagnostics: + Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. + --- failed re-building ‘Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` -* Version: 0.6.0 -* GitHub: https://github.com/kassambara/ggpubr -* Source code: https://github.com/cran/ggpubr -* Date/Publication: 2023-02-10 16:20:02 UTC -* Number of recursive dependencies: 88 +## In both -Run `revdepcheck::cloud_details(, "ggpubr")` for more info +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 19 marked UTF-8 strings + ``` + +# ggseqplot + +
+ +* Version: 0.8.5 +* GitHub: https://github.com/maraab23/ggseqplot +* Source code: https://github.com/cran/ggseqplot +* Date/Publication: 2024-10-29 16:30:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ggseqplot")` for more info
@@ -11605,26 +9603,26 @@ Run `revdepcheck::cloud_details(, "ggpubr")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggpubr-Ex.R’ failed + Running examples in ‘ggseqplot-Ex.R’ failed The error most likely occurred in: - > ### Name: add_summary - > ### Title: Add Summary Statistics onto a ggplot. - > ### Aliases: add_summary mean_se_ mean_sd mean_ci mean_range median_iqr - > ### median_hilow_ median_q1q3 median_mad median_range + > ### Name: ggseqtrplot + > ### Title: Sequence Transition Rate Plot + > ### Aliases: ggseqtrplot > > ### ** Examples > + > # Use example data from TraMineR: biofam data set ... - 10. │ └─ggplot2:::`+.gg`(...) - 11. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 12. │ ├─ggplot2::ggplot_add(object, p, objectname) - 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 15. └─base::.handleSimpleError(...) - 16. └─purrr (local) h(simpleError(msg, call)) - 17. └─cli::cli_abort(...) - 18. └─rlang::abort(...) + 8 7 7 Divorced + [>] sum of weights: 330.07 - min/max: 0/6.02881860733032 + [>] 300 sequences in the data set + [>] min/max sequence length: 16/16 + > + > # Basic transition rate plot (with adjusted x-axis labels) + > ggseqtrplot(biofam.seq, x_n.dodge = 2) + Error in ggseqtrplot(biofam.seq, x_n.dodge = 2) : + labsize must be a single number Execution halted ``` @@ -11634,36 +9632,61 @@ Run `revdepcheck::cloud_details(, "ggpubr")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(ggpubr) - Loading required package: ggplot2 - > - > test_check("ggpubr") - [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + > library(ggseqplot) + Loading required package: TraMineR + TraMineR stable version 2.2-11 (Built: 2024-12-09) + Website: http://traminer.unige.ch + Please type 'citation("TraMineR")' for citation information. ... - 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 15. └─base::.handleSimpleError(...) - 16. └─purrr (local) h(simpleError(msg, call)) - 17. └─cli::cli_abort(...) - 18. └─rlang::abort(...) + Backtrace: + ▆ + 1. ├─testthat::expect_s3_class(ggseqtrplot(biofam.seq), "ggplot") at test-ggseqtrplot.R:35:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─ggseqplot::ggseqtrplot(biofam.seq) - [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + [ FAIL 1 | WARN 16 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted ``` -# ggrain +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggseqplot.Rmd’ + ... + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + + > ggseqtrplot(actcal.seq, group = actcal$sex) + + When sourcing ‘ggseqplot.R’: + Error: labsize must be a single number + Execution halted + + ‘ggseqplot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggseqplot.Rmd’ using rmarkdown + ``` + +# ggside
-* Version: 0.0.4 -* GitHub: https://github.com/njudd/ggrain -* Source code: https://github.com/cran/ggrain -* Date/Publication: 2024-01-23 11:50:02 UTC -* Number of recursive dependencies: 63 +* Version: 0.3.1 +* GitHub: https://github.com/jtlandis/ggside +* Source code: https://github.com/cran/ggside +* Date/Publication: 2024-03-01 09:12:37 UTC +* Number of recursive dependencies: 75 -Run `revdepcheck::cloud_details(, "ggrain")` for more info +Run `revdepcheck::cloud_details(, "ggside")` for more info
@@ -11671,153 +9694,187 @@ Run `revdepcheck::cloud_details(, "ggrain")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggrain-Ex.R’ failed + Running examples in ‘ggside-Ex.R’ failed The error most likely occurred in: - > ### Name: geom_rain - > ### Title: Raincloud Plots - > ### Aliases: geom_rain + > ### Name: geom_xsidebar + > ### Title: Side bar Charts + > ### Aliases: geom_xsidebar geom_*sidebar geom_ysidebar geom_xsidecol + > ### geom_ysidecol > > ### ** Examples > - > e1 <- ggplot(iris, aes(Species, Sepal.Width, fill = Species)) - > e1 + geom_rain() - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + ... + + geom_point() + > + > #sidebar - uses StatCount + > p + + + geom_xsidebar() + + + geom_ysidebar() + Error in is.element(panel_type, c("x", "y")) : + unused argument (c("x", "y")) + Calls: ... -> draw_panel -> -> render_fg Execution halted ``` +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggplot2) + + Attaching package: 'ggplot2' + + The following object is masked from 'package:base': + + ... + • ops_meaningful/alpha-0-5-from-function.svg + • side_layers/boxplot2.svg + • vdiff_irisScatter/collapsed-histo.svg + • vdiff_irisScatter/facetgrid-collapsed-density.svg + • vdiff_irisScatter/facetgrid-histo.svg + • vdiff_irisScatter/facetgrid-side-density.svg + • vdiff_irisScatter/stacked-side-density.svg + • vdiff_irisScatter/yside-histo.svg + Error: Test failures + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘ggrain.Rmd’ + when running code in ‘ggside_aes_mapping.Rmd’ ... - > library(ggrain) - Loading required package: ggplot2 + +.gg ggplot2 - > ggplot(iris, aes(1, Sepal.Width)) + geom_rain() + - + theme_classic() + theme(axis.title.x = element_blank(), axis.text.x = element_blank(), - + .... [TRUNCATED] + > p <- ggplot(mpg, aes(displ, hwy, colour = class)) + + + geom_point(size = 2) + theme_bw() - When sourcing ‘ggrain.R’: - Error: argument is of length zero + > p + geom_xsidedensity() + geom_ysidedensity() + + ... + Warning in max(x) : no non-missing arguments to max; returning -Inf + Warning in min(x) : no non-missing arguments to min; returning Inf + Warning in max(x) : no non-missing arguments to max; returning -Inf + + When sourcing ‘ggside_basic_usage.R’: + Error: unused argument (c("x", "y")) Execution halted - ‘ggrain.Rmd’ using ‘UTF-8’... failed + ‘ggside_aes_mapping.Rmd’ using ‘UTF-8’... failed + ‘ggside_basic_usage.Rmd’ using ‘UTF-8’... failed + ``` + +* checking whether package ‘ggside’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(panel_type, ': unused argument (c("x", "y")) + Note: possible error in 'is.element(self$rescale, ': unused argument (suggested_var) + See ‘/tmp/workdir/ggside/new/ggside.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'geom_xsideabline': + geom_xsidehline + Code: function(mapping = NULL, data = NULL, position = "identity", + ..., yintercept, na.rm = FALSE, show.legend = NA) + Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = + FALSE, show.legend = NA) + Argument names in code not in docs: + position + Mismatches in argument names (first 3): + Position: 3 Code: position Docs: ... + ... + Docs: function(mapping = NULL, data = NULL, stat = "identity", + position = "identity", ..., lineend = "butt", linejoin + = "round", linemitre = 10, arrow = NULL, na.rm = + FALSE, show.legend = NA, inherit.aes = TRUE) + Argument names in code not in docs: + arrow.fill + Mismatches in argument names: + Position: 10 Code: arrow.fill Docs: na.rm + Position: 11 Code: na.rm Docs: show.legend + Position: 12 Code: show.legend Docs: inherit.aes + ``` + +* checking R code for possible problems ... NOTE + ``` + ggside_render_fg: possible error in is.element(panel_type, c("x", + "y")): unused argument (c("x", "y")) ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘ggrain.Rmd’ using rmarkdown + --- re-building ‘ggside_aes_mapping.Rmd’ using rmarkdown - Quitting from lines 36-41 [most basic raincloud possible] (ggrain.Rmd) - Error: processing vignette 'ggrain.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘ggrain.Rmd’ + Quitting from lines 43-46 [ggside_updated_aes_usage] (ggside_aes_mapping.Rmd) + Error: processing vignette 'ggside_aes_mapping.Rmd' failed with diagnostics: + unused argument (c("x", "y")) + --- failed re-building ‘ggside_aes_mapping.Rmd’ - SUMMARY: processing the following file failed: - ‘ggrain.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘ggside_basic_usage.Rmd’ using rmarkdown ``` -# ggraph +# ggsmc
-* Version: 2.2.1 -* GitHub: https://github.com/thomasp85/ggraph -* Source code: https://github.com/cran/ggraph -* Date/Publication: 2024-03-07 12:40:02 UTC -* Number of recursive dependencies: 115 +* Version: 0.1.2.0 +* GitHub: https://github.com/richardgeveritt/ggsmc +* Source code: https://github.com/cran/ggsmc +* Date/Publication: 2024-07-27 17:00:02 UTC +* Number of recursive dependencies: 83 -Run `revdepcheck::cloud_details(, "ggraph")` for more info +Run `revdepcheck::cloud_details(, "ggsmc")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘ggraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_conn_bundle - > ### Title: Create hierarchical edge bundles between node connections - > ### Aliases: geom_conn_bundle geom_conn_bundle2 geom_conn_bundle0 - > - > ### ** Examples - > - > # Create a graph of the flare class system - ... - + ) + - + geom_node_point(aes(filter = leaf, colour = class)) + - + scale_edge_colour_distiller('', direction = 1, guide = 'edge_direction') + - + coord_fixed() + - + ggforce::theme_no_axes() - Error in get_layer_key(...) : - unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, - 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, - Calls: ... -> -> process_layers -> - Execution halted - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Edges.Rmd’ using rmarkdown - ``` - -## In both - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Edges.Rmd’ + when running code in ‘Visualising.Rmd’ ... - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database + 20 /tmp/RtmpKyNdR5/b96ef7031e/gganim_plot0020.png - ... - font family 'Arial' not found in PostScript font database + > data(lv_output) - When sourcing ‘tidygraph.R’: - Error: invalid font type + > animate_reveal_time_series(lv_output, parameters = c("X", + + "Y"), alpha = 0.5, ylimits = c(0, 600), duration = 10) + + When sourcing ‘Visualising.R’: + Error: argument "theme" is missing, with no default Execution halted - ‘Edges.Rmd’ using ‘UTF-8’... failed - ‘Layouts.Rmd’ using ‘UTF-8’... failed - ‘Nodes.Rmd’ using ‘UTF-8’... failed - ‘tidygraph.Rmd’ using ‘UTF-8’... failed + ‘Visualising.Rmd’ using ‘UTF-8’... failed ``` -* checking installed package size ... NOTE +## In both + +* checking data for non-ASCII characters ... NOTE ``` - installed size is 8.9Mb - sub-directories of 1Mb or more: - R 1.5Mb - doc 3.9Mb - libs 2.8Mb + Note: found 175 marked UTF-8 strings ``` -# ggredist +# ggspatial
-* Version: 0.0.2 -* GitHub: https://github.com/alarm-redist/ggredist -* Source code: https://github.com/cran/ggredist -* Date/Publication: 2022-11-23 11:20:02 UTC -* Number of recursive dependencies: 67 +* Version: 1.1.9 +* GitHub: https://github.com/paleolimbot/ggspatial +* Source code: https://github.com/cran/ggspatial +* Date/Publication: 2023-08-17 15:32:38 UTC +* Number of recursive dependencies: 107 -Run `revdepcheck::cloud_details(, "ggredist")` for more info +Run `revdepcheck::cloud_details(, "ggspatial")` for more info
@@ -11825,127 +9882,65 @@ Run `revdepcheck::cloud_details(, "ggredist")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggredist-Ex.R’ failed + Running examples in ‘ggspatial-Ex.R’ failed The error most likely occurred in: - > ### Name: geom_district_text - > ### Title: Label Map Regions - > ### Aliases: geom_district_text geom_district_label - > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText + > ### Name: annotation_spatial_hline + > ### Title: Projected horizontal and vertical lines + > ### Aliases: annotation_spatial_hline annotation_spatial_vline + > ### GeomSpatialXline > ### Keywords: datasets > > ### ** Examples ... - 22. │ └─coord$transform(data, panel_params) - 23. │ └─ggplot2 (local) transform(..., self = self) - 24. │ └─ggplot2:::sf_rescale01(...) - 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) - 26. └─base::.handleSimpleError(...) - 27. └─rlang (local) h(simpleError(msg, call)) - 28. └─handlers[[1L]](cnd) - 29. └─cli::cli_abort(...) - 30. └─rlang::abort(...) + 25. │ └─grid:::validGP(list(...)) + 26. │ └─grid (local) numnotnull("fontsize") + 27. │ └─grid (local) check.length(gparname) + 28. │ └─base::stop(...) + 29. └─base::.handleSimpleError(...) + 30. └─rlang (local) h(simpleError(msg, call)) + 31. └─handlers[[1L]](cnd) + 32. └─cli::cli_abort(...) + 33. └─rlang::abort(...) Execution halted ``` -# ggRtsy - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/ggRtsy -* Date/Publication: 2023-09-15 19:12:05 UTC -* Number of recursive dependencies: 69 - -Run `revdepcheck::cloud_details(, "ggRtsy")` for more info - -
- -## Newly broken - * checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(ggplot2) - > library(dplyr) - - Attaching package: 'dplyr' + > library(ggspatial) + > + > test_check("ggspatial") + Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] - The following object is masked from 'package:testthat': ... - 13. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) - 14. │ └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call) - 15. └─vctrs (local) ``() - 16. └─vctrs:::stop_subscript_oob(...) - 17. └─vctrs:::stop_subscript(...) - 18. └─rlang::abort(...) + 33. │ └─base::stop(...) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] Error: Test failures Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Vignette.Rmd’ - ... - |Antique White |(238, 223, 204) |#eedfcc | - - > RectangleFiller(plotExample, c("#e32636", "#9966cc", - + "#f4c2c2", "#e16827")) - - When sourcing ‘Vignette.R’: - Error: Can't extract rows past the end. - ℹ Location 1 doesn't exist. - ℹ There are only 0 rows. - Execution halted - - ‘Vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Vignette.Rmd’ using rmarkdown - - Quitting from lines 48-49 [unnamed-chunk-2] (Vignette.Rmd) - Error: processing vignette 'Vignette.Rmd' failed with diagnostics: - Can't extract rows past the end. - ℹ Location 1 doesn't exist. - ℹ There are only 0 rows. - --- failed re-building ‘Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 19 marked UTF-8 strings - ``` - -# ggseqplot +# ggstatsplot
-* Version: 0.8.4 -* GitHub: https://github.com/maraab23/ggseqplot -* Source code: https://github.com/cran/ggseqplot -* Date/Publication: 2024-05-17 21:40:03 UTC -* Number of recursive dependencies: 128 +* Version: 0.13.0 +* GitHub: https://github.com/IndrajeetPatil/ggstatsplot +* Source code: https://github.com/cran/ggstatsplot +* Date/Publication: 2024-12-04 15:10:02 UTC +* Number of recursive dependencies: 176 -Run `revdepcheck::cloud_details(, "ggseqplot")` for more info +Run `revdepcheck::cloud_details(, "ggstatsplot")` for more info
@@ -11953,5035 +9948,247 @@ Run `revdepcheck::cloud_details(, "ggseqplot")` for more info * checking examples ... ERROR ``` - Running examples in ‘ggseqplot-Ex.R’ failed + Running examples in ‘ggstatsplot-Ex.R’ failed The error most likely occurred in: - > ### Name: ggseqrfplot - > ### Title: Relative Frequency Sequence Plot - > ### Aliases: ggseqrfplot + > ### Name: ggscatterstats + > ### Title: Scatterplot with marginal distributions and statistical results + > ### Aliases: ggscatterstats > > ### ** Examples > - > # Load additional library for fine-tuning the plots + > set.seed(123) ... - [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 + + ggplot2::geom_rug(sides = "b") > - > # ... with ggseqrfplot - > ggseqrfplot(biofam.seq, weighted = FALSE, diss = diss, k = 12, grp.meth="first") - [>] Using k=12 frequency groups with grp.meth='first' - [>] Pseudo/medoid-based-R2: 0.4620155 - [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + > # looking at the plot + > p + `stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`. + `stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`. + Error in is.element(panel_type, c("x", "y")) : + unused argument (c("x", "y")) + Calls: ... -> draw_panel -> -> render_fg Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggseqplot) - Loading required package: TraMineR - - TraMineR stable version 2.2-10 (Built: 2024-05-22) - Website: http://traminer.unige.ch - Please type 'citation("TraMineR")' for citation information. - ... - Backtrace: - ▆ - 1. ├─testthat::expect_s3_class(ggseqtrplot(biofam.seq), "ggplot") at test-ggseqtrplot.R:35:3 - 2. │ └─testthat::quasi_label(enquo(object), arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─ggseqplot::ggseqtrplot(biofam.seq) - - [ FAIL 1 | WARN 1045 | SKIP 0 | PASS 131 ] - Error: Test failures - Execution halted - ``` +## In both * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘ggseqplot.Rmd’ + when running code in ‘ggstatsplot.Rmd’ ... - > p1 + p2 + plot_layout(guides = "collect") & scale_fill_manual(values = canva_palettes$`Fun and tropical`[1:4]) & - + theme_ipsum(base_family = "" .... [TRUNCATED] - Scale for fill is already present. - Adding another scale for fill, which will replace the existing scale. - Scale for fill is already present. - Adding another scale for fill, which will replace the existing scale. - When sourcing ‘ggseqplot.R’: - Error: object is not coercible to a unit + > try({ + + ggbetweenstats(iris, Species, Sepal.Length) + + }) + + > knitr::include_graphics("../man/figures/stats_reporting_format.png") + + When sourcing ‘ggstatsplot.R’: + Error: Cannot find the file(s): "../man/figures/stats_reporting_format.png" Execution halted - ‘ggseqplot.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ggseqplot.Rmd’ using rmarkdown + ‘additional.Rmd’ using ‘UTF-8’... OK + ‘ggstatsplot.Rmd’ using ‘UTF-8’... failed ``` -# ggside +# ggswissmaps
-* Version: 0.3.1 -* GitHub: https://github.com/jtlandis/ggside -* Source code: https://github.com/cran/ggside -* Date/Publication: 2024-03-01 09:12:37 UTC -* Number of recursive dependencies: 76 +* Version: 0.1.1 +* GitHub: https://github.com/gibonet/ggswissmaps +* Source code: https://github.com/cran/ggswissmaps +* Date/Publication: 2016-10-29 10:48:24 +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "ggside")` for more info +Run `revdepcheck::cloud_details(, "ggswissmaps")` for more info
## Newly broken -* checking tests ... ERROR +* checking whether package ‘ggswissmaps’ can be installed ... WARNING ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggplot2) - > library(ggside) - Registered S3 method overwritten by 'ggside': - method from - +.gg ggplot2 - > - ... - • ops_meaningful/alpha-0-5-from-function.svg - • side_layers/boxplot2.svg - • vdiff_irisScatter/collapsed-histo.svg - • vdiff_irisScatter/facetgrid-collapsed-density.svg - • vdiff_irisScatter/facetgrid-histo.svg - • vdiff_irisScatter/facetgrid-side-density.svg - • vdiff_irisScatter/stacked-side-density.svg - • vdiff_irisScatter/yside-histo.svg - Error: Test failures - Execution halted + Found the following significant warnings: + Warning: `aes_string()` was deprecated in ggplot2 3.0.0. + See ‘/tmp/workdir/ggswissmaps/new/ggswissmaps.Rcheck/00install.out’ for details. ``` -* checking for code/documentation mismatches ... WARNING +* checking whether the namespace can be loaded with stated dependencies ... NOTE ``` - Codoc mismatches from documentation object 'geom_xsideabline': - geom_xsidehline - Code: function(mapping = NULL, data = NULL, position = "identity", - ..., yintercept, na.rm = FALSE, show.legend = NA) - Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = - FALSE, show.legend = NA) - Argument names in code not in docs: - position - Mismatches in argument names (first 3): - Position: 3 Code: position Docs: ... - ... - Docs: function(mapping = NULL, data = NULL, stat = "identity", - position = "identity", ..., lineend = "butt", linejoin - = "round", linemitre = 10, arrow = NULL, na.rm = - FALSE, show.legend = NA, inherit.aes = TRUE) - Argument names in code not in docs: - arrow.fill - Mismatches in argument names: - Position: 10 Code: arrow.fill Docs: na.rm - Position: 11 Code: na.rm Docs: show.legend - Position: 12 Code: show.legend Docs: inherit.aes + Warning: `aes_string()` was deprecated in ggplot2 3.0.0. + ℹ Please use tidy evaluation idioms with `aes()`. + ℹ See also `vignette("ggplot2-in-packages")` for more information. + ℹ The deprecated feature was likely used in the ggswissmaps package. + Please report the issue to the authors. + + A namespace must be able to be loaded with just the base namespace + loaded: otherwise if the namespace gets loaded by a saved object, the + session will be unable to start. + + Probably some imports need to be declared in the NAMESPACE file. ``` -# ggsmc +# ggtern
-* Version: 0.1.2.0 -* GitHub: https://github.com/richardgeveritt/ggsmc -* Source code: https://github.com/cran/ggsmc -* Date/Publication: 2024-07-27 17:00:02 UTC -* Number of recursive dependencies: 84 +* Version: 3.5.0 +* GitHub: NA +* Source code: https://github.com/cran/ggtern +* Date/Publication: 2024-03-24 21:50:02 UTC +* Number of recursive dependencies: 42 -Run `revdepcheck::cloud_details(, "ggsmc")` for more info +Run `revdepcheck::cloud_details(, "ggtern")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking whether package ‘ggtern’ can be installed ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘Visualising.Rmd’ - ... - 20 /tmp/RtmpuaCJEi/100d113de41a/gganim_plot0020.png - - > data(lv_output) - - > animate_reveal_time_series(lv_output, parameters = c("X", - + "Y"), alpha = 0.5, ylimits = c(0, 600), duration = 10) - - When sourcing ‘Visualising.R’: - Error: argument "theme" is missing, with no default - Execution halted - - ‘Visualising.Rmd’ using ‘UTF-8’... failed + Installation failed. + See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details. ``` -## In both +## Newly fixed -* checking data for non-ASCII characters ... NOTE +* checking Rd cross-references ... NOTE ``` - Note: found 175 marked UTF-8 strings + Package unavailable to check Rd xrefs: ‘chemometrics’ ``` -# ggspatial - -
- -* Version: 1.1.9 -* GitHub: https://github.com/paleolimbot/ggspatial -* Source code: https://github.com/cran/ggspatial -* Date/Publication: 2023-08-17 15:32:38 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "ggspatial")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggspatial-Ex.R’ failed - The error most likely occurred in: - - > ### Name: annotation_spatial_hline - > ### Title: Projected horizontal and vertical lines - > ### Aliases: annotation_spatial_hline annotation_spatial_vline - > ### GeomSpatialXline - > ### Keywords: datasets - > - > ### ** Examples - ... - 25. │ └─grid:::validGP(list(...)) - 26. │ └─grid (local) numnotnull("fontsize") - 27. │ └─grid (local) check.length(gparname) - 28. │ └─base::stop(...) - 29. └─base::.handleSimpleError(...) - 30. └─rlang (local) h(simpleError(msg, call)) - 31. └─handlers[[1L]](cnd) - 32. └─cli::cli_abort(...) - 33. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggspatial) - > - > test_check("ggspatial") - Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE - [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] - - ... - 33. │ └─base::stop(...) - 34. └─base::.handleSimpleError(...) - 35. └─rlang (local) h(simpleError(msg, call)) - 36. └─handlers[[1L]](cnd) - 37. └─cli::cli_abort(...) - 38. └─rlang::abort(...) - - [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] - Error: Test failures - Execution halted - ``` - -# ggstatsplot - -
- -* Version: 0.12.4 -* GitHub: https://github.com/IndrajeetPatil/ggstatsplot -* Source code: https://github.com/cran/ggstatsplot -* Date/Publication: 2024-07-06 16:22:07 UTC -* Number of recursive dependencies: 174 - -Run `revdepcheck::cloud_details(, "ggstatsplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggstatsplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggscatterstats - > ### Title: Scatterplot with marginal distributions and statistical results - > ### Aliases: ggscatterstats - > - > ### ** Examples - > - > set.seed(123) - ... - + iris, - + x = Sepal.Width, - + y = Petal.Length, - + label.var = Species, - + label.expression = Sepal.Length > 7.6 - + ) + - + ggplot2::geom_rug(sides = "b") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggscatterstats ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggstatsplot.Rmd’ - ... - author = {Indrajeet Patil}, - title = {{Visualizations with statistical details: The {'ggstatsplot'} approach}}, - journal = {{Journal of Open Source Software}}, - } - - > ggbetweenstats(iris, Species, Sepal.Length) - - When sourcing ‘ggstatsplot.R’: - Error: argument is of length zero - Execution halted - - ‘additional.Rmd’ using ‘UTF-8’... OK - ‘ggstatsplot.Rmd’ using ‘UTF-8’... failed - ``` - -# ggtern - -
- -* Version: 3.5.0 -* GitHub: NA -* Source code: https://github.com/cran/ggtern -* Date/Publication: 2024-03-24 21:50:02 UTC -* Number of recursive dependencies: 42 - -Run `revdepcheck::cloud_details(, "ggtern")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggtern-Ex.R’ failed - The error most likely occurred in: - - > ### Name: annotate - > ### Title: Create an annotation layer (ggtern version). - > ### Aliases: annotate - > - > ### ** Examples - > - > ggtern() + - ... - 3. ├─ggtern::ggplot_build(x) - 4. └─ggtern:::ggplot_build.ggplot(x) - 5. └─ggtern:::layers_add_or_remove_mask(plot) - 6. └─ggint$plot_theme(plot) - 7. └─ggplot2:::validate_theme(theme) - 8. └─base::mapply(...) - 9. └─ggplot2 (local) ``(...) - 10. └─cli::cli_abort(...) - 11. └─rlang::abort(...) - Execution halted - ``` - -## In both +## In both * checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘sp’ ``` -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘chemometrics’ - ``` - -# ggupset - -
- -* Version: 0.4.0 -* GitHub: https://github.com/const-ae/ggupset -* Source code: https://github.com/cran/ggupset -* Date/Publication: 2024-06-24 10:10:04 UTC -* Number of recursive dependencies: 46 - -Run `revdepcheck::cloud_details(, "ggupset")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggupset-Ex.R’ failed - The error most likely occurred in: - - > ### Name: axis_combmatrix - > ### Title: Convert delimited text labels into a combination matrix axis - > ### Aliases: axis_combmatrix - > - > ### ** Examples - > - > library(ggplot2) - ... - Datsun 710 Cyl: 4_Gears: 4 - Hornet 4 Drive Cyl: 6_Gears: 3 - Hornet Sportabout Cyl: 8_Gears: 3 - Valiant Cyl: 6_Gears: 3 - > ggplot(mtcars, aes(x=combined)) + - + geom_bar() + - + axis_combmatrix(sep = "_") - Error in as.unit(e2) : object is not coercible to a unit - Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit - Execution halted - ``` - -# ggVennDiagram +## Installation -
+### Devel -* Version: 1.5.2 -* GitHub: https://github.com/gaospecial/ggVennDiagram -* Source code: https://github.com/cran/ggVennDiagram -* Date/Publication: 2024-02-20 08:10:02 UTC -* Number of recursive dependencies: 98 +``` +* installing *source* package ‘ggtern’ ... +** package ‘ggtern’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** demo +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'update_guides' not found +Error: unable to load R code in package ‘ggtern’ +Execution halted +ERROR: lazy loading failed for package ‘ggtern’ +* removing ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/ggtern’ -Run `revdepcheck::cloud_details(, "ggVennDiagram")` for more info -
+``` +### CRAN -## Newly broken +``` +* installing *source* package ‘ggtern’ ... +** package ‘ggtern’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** demo +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (ggtern) -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘fully-customed.Rmd’ - ... - [1] "b" "c" "e" "h" "k" "q" "s" "y" - - - > ggVennDiagram(y, show_intersect = TRUE, set_color = "black") - Warning in geom_text(aes(label = .data$count, text = .data$item), data = region_label) : - Ignoring unknown aesthetics: text - - ... - Ignoring unknown aesthetics: text - - When sourcing ‘using-ggVennDiagram.R’: - Error: subscript out of bounds - Execution halted - - ‘VennCalculator.Rmd’ using ‘UTF-8’... OK - ‘fully-customed.Rmd’ using ‘UTF-8’... failed - ‘using-ggVennDiagram.Rmd’ using ‘UTF-8’... failed - ‘using-new-shapes.Rmd’ using ‘UTF-8’... OK - ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘VennCalculator.Rmd’ using rmarkdown - --- finished re-building ‘VennCalculator.Rmd’ - - --- re-building ‘fully-customed.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.1Mb - sub-directories of 1Mb or more: - doc 9.5Mb - help 1.1Mb - ``` - -# GimmeMyPlot - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/GimmeMyPlot -* Date/Publication: 2023-10-18 16:10:02 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GimmeMyPlot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_violin - > ### Title: Violin plot - > ### Aliases: plot_violin - > - > ### ** Examples - > - > library(RColorBrewer) - ... - + width_text = 5, - + pch_colour = "gray30", - + pch_alpha = 0.5, - + width_title = 30, - + lwd = 1.25, - + digits = 2 - + ) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot_violin ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - 4. └─GimmeMyPlot::plot_violin(df) - 5. └─ggplot2:::`+.gg`(...) - 6. └─ggplot2:::add_ggplot(e1, e2, e2name) - 7. ├─ggplot2::ggplot_add(object, p, objectname) - 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Tutorial.Rmd’ - ... - > df[, 3] <- runif(10, 1, 2) - - > colnames(df) <- paste0("X", seq(3)) - - > plot_violin(df, title = "Some random variables", colour = brewer.pal(9, - + "Set1")[seq(3)]) - - When sourcing ‘Tutorial.R’: - Error: argument is of length zero - Execution halted - - ‘Tutorial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Tutorial.Rmd’ using rmarkdown - - Quitting from lines 24-57 [violin] (Tutorial.Rmd) - Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘Tutorial.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# giniVarCI - -
- -* Version: 0.0.1-3 -* GitHub: NA -* Source code: https://github.com/cran/giniVarCI -* Date/Publication: 2024-01-08 10:30:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "giniVarCI")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘giniVarCI-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fcompareCI - > ### Title: Comparisons of variance estimates and confidence intervals for - > ### the Gini index in finite populations - > ### Aliases: fcompareCI - > - > ### ** Examples - > - ... - > data(eusilc, package="laeken") - > y <- eusilc$eqIncome[eusilc$db040 == "Burgenland"] - > w <- eusilc$rb050[eusilc$db040 == "Burgenland"] - > - > # Estimation of the Gini index and confidence intervals using different methods. - > fcompareCI(y, w) - Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: fcompareCI - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.5Mb - sub-directories of 1Mb or more: - libs 12.0Mb - ``` - -# gMCPLite - -
- -* Version: 0.1.5 -* GitHub: https://github.com/Merck/gMCPLite -* Source code: https://github.com/cran/gMCPLite -* Date/Publication: 2024-01-11 19:30:02 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "gMCPLite")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘GraphicalMultiplicity.Rmd’ - ... - 0.8600 - 0.1400 - - - - > plot(os, plottype = "HR", xlab = "Events") - - When sourcing ‘GraphicalMultiplicity.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘GraphicalMultiplicity.Rmd’ using ‘UTF-8’... failed - ‘hGraph.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘GraphicalMultiplicity.Rmd’ using rmarkdown - ``` - -# gMOIP - -
- -* Version: 1.5.2 -* GitHub: https://github.com/relund/gMOIP -* Source code: https://github.com/cran/gMOIP -* Date/Publication: 2024-02-21 21:30:05 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "gMOIP")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gMOIP-Ex.R’ failed - The error most likely occurred in: - - > ### Name: convexHull - > ### Title: Find the convex hull of a set of points. - > ### Aliases: convexHull - > - > ### ** Examples - > - > ## 1D - ... - - $pts - p1 p2 pt vtx - 1 1 1 1 TRUE - 2 2 2 1 TRUE - - > plotHull2D(pts, drawPoints = TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plotHull2D ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘bi-objective_2x.Rmd’ - ... - - > b <- c(3, 27, 90) - - > obj <- matrix(c(7, -10, -10, -10), nrow = 2) - - > plotBiObj2D(A, b, obj, addTriangles = FALSE) - - ... - When sourcing ‘polytope_2d.R’: - Error: argument is of length zero - Execution halted - - ‘bi-objective_2x.Rmd’ using ‘UTF-8’... failed - ‘bi-objective_3x_ex1.Rmd’ using ‘UTF-8’... OK - ‘intro.Rmd’ using ‘UTF-8’... failed - ‘polytope_2d.Rmd’ using ‘UTF-8’... failed - ‘polytope_3d_ex1.Rmd’ using ‘UTF-8’... OK - ‘tri-objective.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘bi-objective_2x.Rmd’ using rmarkdown - - Quitting from lines 73-78 [2DLP] (bi-objective_2x.Rmd) - Error: processing vignette 'bi-objective_2x.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘bi-objective_2x.Rmd’ - - --- re-building ‘bi-objective_3x_ex1.Rmd’ using rmarkdown - ``` - -# GofCens - -
- -* Version: 1.1 -* GitHub: NA -* Source code: https://github.com/cran/GofCens -* Date/Publication: 2024-07-29 08:40:02 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "GofCens")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GofCens-Ex.R’ failed - The error most likely occurred in: - - > ### Name: kmPlot - > ### Title: Plot of the Kaplen-Meier and parametric estimations - > ### Aliases: kmPlot kmPlot.default kmPlot.formula kmPlot.probPlot - > ### kmPlot.probPlot - > - > ### ** Examples - > - ... - Scale: 10.039 - - > - > # Plots for censored data using ggplot2 - > data(colon) - Warning in data(colon) : data set ‘colon’ not found - > kmPlot(Surv(time, status) ~ 1, colon, distr= "lognormal", ggp = TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: kmPlot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# greatR - -
- -* Version: 2.0.0 -* GitHub: https://github.com/ruthkr/greatR -* Source code: https://github.com/cran/greatR -* Date/Publication: 2024-04-09 22:40:07 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "greatR")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘process-results.Rmd’ - ... - - > reg_summary$non_registered_genes - [1] "BRAA02G018970.3C" - - > plot(reg_summary, type = "registered", scatterplot_size = c(4, - + 3.5)) - - When sourcing ‘process-results.R’: - Error: object is not a unit - Execution halted - - ‘data-requirement.Rmd’ using ‘UTF-8’... OK - ‘process-results.Rmd’ using ‘UTF-8’... failed - ‘register-data-manually.Rmd’ using ‘UTF-8’... OK - ‘register-data.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘data-requirement.Rmd’ using rmarkdown - --- finished re-building ‘data-requirement.Rmd’ - - --- re-building ‘process-results.Rmd’ using rmarkdown - - Quitting from lines 76-81 [plot-summary-results] (process-results.Rmd) - Error: processing vignette 'process-results.Rmd' failed with diagnostics: - object is not a unit - ... - --- finished re-building ‘register-data-manually.Rmd’ - - --- re-building ‘register-data.Rmd’ using rmarkdown - --- finished re-building ‘register-data.Rmd’ - - SUMMARY: processing the following file failed: - ‘process-results.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# Greymodels - -
- -* Version: 2.0.1 -* GitHub: https://github.com/havishaJ/Greymodels -* Source code: https://github.com/cran/Greymodels -* Date/Publication: 2022-12-05 12:42:35 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "Greymodels")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Greymodels-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Plots - > ### Title: plots - > ### Aliases: plots plotrm plotsmv1 plotsmv2 plotsigndgm plots_mdbgm12 - > - > ### ** Examples - > - > # Plots - EPGM (1, 1) model - ... - + geom_point(data = set4, aes(x = CI, y = y), shape = 23, color = "black") + - + geom_line(data = xy1, aes(x = x, y = y,color = "Raw Data")) + - + geom_line(data = xy2, aes(x = x, y = y,color = "Fitted&Forecasts")) + - + geom_line(data = set3, aes(x = CI, y = y,color = "LowerBound"), linetype=2) + - + geom_line(data = set4, aes(x = CI, y = y,color = "UpperBound"), linetype=2) + - + scale_color_manual(name = "Label",values = colors) - > r <- ggplotly(p) - Error in pm[[2]] : subscript out of bounds - Calls: ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# gsDesign - -
- -* Version: 3.6.4 -* GitHub: https://github.com/keaven/gsDesign -* Source code: https://github.com/cran/gsDesign -* Date/Publication: 2024-07-26 23:20:10 UTC -* Number of recursive dependencies: 102 - -Run `revdepcheck::cloud_details(, "gsDesign")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gsDesign-Ex.R’ failed - The error most likely occurred in: - - > ### Name: summary.gsDesign - > ### Title: Bound Summary and Z-transformations - > ### Aliases: summary.gsDesign print.gsDesign gsBoundSummary xprint - > ### print.gsBoundSummary gsBValue gsDelta gsRR gsHR gsCPz - > ### Keywords: design - > - > ### ** Examples - ... - ~RR at bound 0.6605 0.6605 - P(Cross) if RR=1 0.0239 0.9761 - P(Cross) if RR=0.5 0.9000 0.1000 - > gsRR(z = xp$lower$bound, i = 1:3, xrr) - [1] 1.0732500 0.8211496 NA - > plot(xrr, plottype = "RR") - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(gsDesign) - > - > test_check("gsDesign") - Linear spending function with none = [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] - - ══ Skipped tests (98) ══════════════════════════════════════════════════════════ - ... - 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) - 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) - 22. └─grid:::drawGrob(x) - 23. ├─grid::drawDetails(x, recording = FALSE) - 24. └─grid:::drawDetails.polyline(x, recording = FALSE) - 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) - - [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ConditionalPowerPlot.Rmd’ - ... - - > cp <- gsCP(x = update, i = 1, zi = -qnorm(p), theta = theta) - - > plot(cp, xval = hr, xlab = "Future HR", ylab = "Conditional Power/Error", - + main = "Conditional probability of crossing future bound", - + o .... [TRUNCATED] - - ... - ‘PoissonMixtureModel.Rmd’ using ‘UTF-8’... OK - ‘SpendingFunctionOverview.Rmd’ using ‘UTF-8’... OK - ‘SurvivalOverview.Rmd’ using ‘UTF-8’... OK - ‘VaccineEfficacy.Rmd’ using ‘UTF-8’... OK - ‘binomialSPRTExample.Rmd’ using ‘UTF-8’... OK - ‘gsDesignPackageOverview.Rmd’ using ‘UTF-8’... failed - ‘gsSurvBasicExamples.Rmd’ using ‘UTF-8’... failed - ‘hGraph.Rmd’ using ‘UTF-8’... OK - ‘nNormal.Rmd’ using ‘UTF-8’... OK - ‘toInteger.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ConditionalErrorSpending.Rmd’ using rmarkdown - ``` - -# gtExtras - -
- -* Version: 0.5.0 -* GitHub: https://github.com/jthomasmock/gtExtras -* Source code: https://github.com/cran/gtExtras -* Date/Publication: 2023-09-15 22:32:06 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "gtExtras")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(gtExtras) - Loading required package: gt - - Attaching package: 'gt' - - The following object is masked from 'package:testthat': - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── - `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). - - `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" - `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" - - [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] - Error: Test failures - Execution halted - ``` - -# HaploCatcher - -
- -* Version: 1.0.4 -* GitHub: NA -* Source code: https://github.com/cran/HaploCatcher -* Date/Publication: 2023-04-21 23:32:39 UTC -* Number of recursive dependencies: 112 - -Run `revdepcheck::cloud_details(, "HaploCatcher")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘An_Intro_to_HaploCatcher.Rmd’ - ... - > set.seed(NULL) - - > results1 <- auto_locus(geno_mat = geno_mat, gene_file = gene_comp, - + gene_name = "sst1_solid_stem", marker_info = marker_info, - + chromosom .... [TRUNCATED] - Loading required package: lattice - - When sourcing ‘An_Intro_to_HaploCatcher.R’: - Error: object is not a unit - Execution halted - - ‘An_Intro_to_HaploCatcher.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘An_Intro_to_HaploCatcher.Rmd’ using rmarkdown - - Quitting from lines 242-253 [example_models_1] (An_Intro_to_HaploCatcher.Rmd) - Error: processing vignette 'An_Intro_to_HaploCatcher.Rmd' failed with diagnostics: - object is not a unit - --- failed re-building ‘An_Intro_to_HaploCatcher.Rmd’ - - SUMMARY: processing the following file failed: - ‘An_Intro_to_HaploCatcher.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# healthyR - -
- -* Version: 0.2.2 -* GitHub: https://github.com/spsanderson/healthyR -* Source code: https://github.com/cran/healthyR -* Date/Publication: 2024-07-01 13:20:02 UTC -* Number of recursive dependencies: 146 - -Run `revdepcheck::cloud_details(, "healthyR")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘getting-started.Rmd’ - ... - + .by = "month", .interactive = FALSE) - Warning: Ignoring unknown labels: - • `colour = "Legend"` - - > ts_alos_plt(.data = df_tbl, .date_col = Date, .value_col = Values, - + .by = "month", .interactive = TRUE) - - When sourcing ‘getting-started.R’: - Error: subscript out of bounds - Execution halted - - ‘getting-started.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘getting-started.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.6Mb - sub-directories of 1Mb or more: - data 2.5Mb - doc 3.7Mb - ``` - -# healthyR.ts - -
- -* Version: 0.3.0 -* GitHub: https://github.com/spsanderson/healthyR.ts -* Source code: https://github.com/cran/healthyR.ts -* Date/Publication: 2023-11-15 06:00:05 UTC -* Number of recursive dependencies: 200 - -Run `revdepcheck::cloud_details(, "healthyR.ts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘healthyR.ts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tidy_fft - > ### Title: Tidy Style FFT - > ### Aliases: tidy_fft - > - > ### ** Examples - > - > suppressPackageStartupMessages(library(dplyr)) - ... - > a <- tidy_fft( - + .data = data_tbl, - + .value_col = value, - + .date_col = date_col, - + .harmonics = 3, - + .frequency = 12 - + ) - Error in pm[[2]] : subscript out of bounds - Calls: tidy_fft -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘using-tidy-fft.Rmd’ - ... - $ value 112, 118, 132, 129, 121, 135, 148, 148, 136, 119, 104, 118, 1… - - > suppressPackageStartupMessages(library(timetk)) - - > data_tbl %>% plot_time_series(.date_var = date_col, - + .value = value) - - When sourcing ‘using-tidy-fft.R’: - Error: subscript out of bounds - Execution halted - - ‘getting-started.Rmd’ using ‘UTF-8’... OK - ‘using-tidy-fft.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘getting-started.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - doc 5.2Mb - ``` - -# heatmaply - -
- -* Version: 1.5.0 -* GitHub: https://github.com/talgalili/heatmaply -* Source code: https://github.com/cran/heatmaply -* Date/Publication: 2023-10-06 20:50:02 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "heatmaply")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(heatmaply) - Loading required package: plotly - Loading required package: ggplot2 - - Attaching package: 'plotly' - - ... - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. ├─heatmaply:::predict_colors(ggplotly(g), plot_method = "ggplot") - 7. ├─plotly::ggplotly(g) - 8. └─plotly:::ggplotly.ggplot(g) - 9. └─plotly::gg2list(...) - - [ FAIL 58 | WARN 0 | SKIP 0 | PASS 193 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘heatmaply.Rmd’ - ... - - > library("heatmaply") - - > library("heatmaply") - - > heatmaply(mtcars) - - When sourcing ‘heatmaply.R’: - Error: subscript out of bounds - Execution halted - - ‘heatmaply.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘heatmaply.Rmd’ using rmarkdown - - Quitting from lines 109-111 [unnamed-chunk-5] (heatmaply.Rmd) - Error: processing vignette 'heatmaply.Rmd' failed with diagnostics: - subscript out of bounds - --- failed re-building ‘heatmaply.Rmd’ - - SUMMARY: processing the following file failed: - ‘heatmaply.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - doc 5.1Mb - ``` - -# hermiter - -
- -* Version: 2.3.1 -* GitHub: https://github.com/MikeJaredS/hermiter -* Source code: https://github.com/cran/hermiter -* Date/Publication: 2024-03-06 23:50:02 UTC -* Number of recursive dependencies: 79 - -Run `revdepcheck::cloud_details(, "hermiter")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘hermiter.Rmd’ - ... - > p2 <- ggplot(df_pdf_cdf) + geom_tile(aes(X, Y, fill = pdf_est)) + - + scale_fill_continuous_sequential(palette = "Oslo", breaks = seq(0, - + .... [TRUNCATED] - - > p1 + ggtitle("Actual PDF") + theme(legend.title = element_blank()) + - + p2 + ggtitle("Estimated PDF") + theme(legend.title = element_blank()) + .... [TRUNCATED] - - When sourcing ‘hermiter.R’: - Error: object is not a unit - Execution halted - - ‘hermiter.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘hermiter.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - R 2.6Mb - doc 1.9Mb - libs 2.0Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# heumilkr - -
- -* Version: 0.2.0 -* GitHub: https://github.com/lschneiderbauer/heumilkr -* Source code: https://github.com/cran/heumilkr -* Date/Publication: 2024-04-01 13:50:06 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "heumilkr")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘clarke_wright_performance.Rmd’ - ... - + "F", "tai"), group_desc = c("Augerat A, 1995", "Augerat B, 1995", - + "Christofides and ..." ... [TRUNCATED] - - > ggMarginal(ggplot(merge(result, description, by = "group"), - + aes(x = n_site, y = clarke_wright_perf_xi, color = group_desc)) + - + geom_poi .... [TRUNCATED] - - When sourcing ‘clarke_wright_performance.R’: - Error: argument is of length zero - Execution halted - - ‘clarke_wright_performance.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘clarke_wright_performance.Rmd’ using rmarkdown - - Quitting from lines 69-97 [perf_scale_based_graph] (clarke_wright_performance.Rmd) - Error: processing vignette 'clarke_wright_performance.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘clarke_wright_performance.Rmd’ - - SUMMARY: processing the following file failed: - ‘clarke_wright_performance.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# hilldiv - -
- -* Version: 1.5.1 -* GitHub: https://github.com/anttonalberdi/hilldiv -* Source code: https://github.com/cran/hilldiv -* Date/Publication: 2019-10-01 14:40:02 UTC -* Number of recursive dependencies: 144 - -Run `revdepcheck::cloud_details(, "hilldiv")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘hilldiv-Ex.R’ failed - The error most likely occurred in: - - > ### Name: div_test_plot - > ### Title: Diversity test plotting - > ### Aliases: div_test_plot - > ### Keywords: chart comparison hill numbers - > - > ### ** Examples - > - ... - 11. │ └─ggplot2:::`+.gg`(...) - 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 13. │ ├─ggplot2::ggplot_add(object, p, objectname) - 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 16. └─base::.handleSimpleError(...) - 17. └─purrr (local) h(simpleError(msg, call)) - 18. └─cli::cli_abort(...) - 19. └─rlang::abort(...) - Execution halted - ``` - -# hmclearn - -
- -* Version: 0.0.5 -* GitHub: NA -* Source code: https://github.com/cran/hmclearn -* Date/Publication: 2020-10-05 06:40:02 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "hmclearn")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘hmclearn-Ex.R’ failed - The error most likely occurred in: - - > ### Name: hmclearn-plots - > ### Title: Plotting for MCMC visualization and diagnostics provided by - > ### 'bayesplot' package - > ### Aliases: hmclearn-plots mcmc_intervals mcmc_intervals.hmclearn - > ### mcmc_areas mcmc_areas.hmclearn mcmc_hist mcmc_hist.hmclearn - > ### mcmc_hist_by_chain mcmc_hist_by_chain.hmclearn mcmc_dens - > ### mcmc_dens.hmclearn mcmc_scatter mcmc_scatter.hmclearn mcmc_hex - ... - + param = list(y=y, X=X), - + parallel=FALSE, chains=2) - > - > mcmc_trace(f, burnin=100) - > mcmc_hist(f, burnin=100) - `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. - > mcmc_intervals(f, burnin=100) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# HTLR - -
- -* Version: 0.4-4 -* GitHub: https://github.com/longhaiSK/HTLR -* Source code: https://github.com/cran/HTLR -* Date/Publication: 2022-10-22 12:47:53 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "HTLR")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘simu.Rmd’ - ... - [1] "median" - - > post.t <- as.matrix(fit.t2, k = 2) - - > mcmc_intervals(post.t, pars = c("Intercept", "V1", - + "V2", "V3", "V1000")) - - When sourcing ‘simu.R’: - Error: argument is of length zero - Execution halted - - ‘simu.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘simu.Rmd’ using rmarkdown - ``` - -## In both - -* checking C++ specification ... NOTE - ``` - Specified C++11: please drop specification unless essential - ``` - -* checking installed package size ... NOTE - ``` - installed size is 8.8Mb - sub-directories of 1Mb or more: - data 2.0Mb - doc 1.1Mb - libs 5.4Mb - ``` - -# HVT - -
- -* Version: 24.5.2 -* GitHub: https://github.com/Mu-Sigma/HVT -* Source code: https://github.com/cran/HVT -* Date/Publication: 2024-05-15 08:50:21 UTC -* Number of recursive dependencies: 200 - -Run `revdepcheck::cloud_details(, "HVT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HVT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getTransitionProbability - > ### Title: Creating Transition Probabilities list - > ### Aliases: getTransitionProbability - > ### Keywords: Transition_or_Prediction - > - > ### ** Examples - > - ... - Ignoring unknown parameters: `check_overlap` - Scale for x is already present. - Adding another scale for x, which will replace the existing scale. - Scale for y is already present. - Adding another scale for y, which will replace the existing scale. - Warning in geom_polygon(data = boundaryCoords2, aes(x = bp.x, y = bp.y, : - Ignoring unknown aesthetics: text - Error in pm[[2]] : subscript out of bounds - Calls: scoreHVT -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# hypsoLoop - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/hypsoLoop -* Date/Publication: 2022-02-08 09:00:02 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "hypsoLoop")` for more info - -
- -## Newly broken - -* checking whether package ‘hypsoLoop’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘ggplot2::set_theme’ by ‘sjPlot::set_theme’ when loading ‘hypsoLoop’ - See ‘/tmp/workdir/hypsoLoop/new/hypsoLoop.Rcheck/00install.out’ for details. - ``` - -# ibdsim2 - -
- -* Version: 2.1.1 -* GitHub: https://github.com/magnusdv/ibdsim2 -* Source code: https://github.com/cran/ibdsim2 -* Date/Publication: 2024-09-08 07:40:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "ibdsim2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ibdsim2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotSegmentDistribution - > ### Title: Scatter plots of IBD segment distributions - > ### Aliases: plotSegmentDistribution - > - > ### ** Examples - > - > - ... - Skip recomb : - - Total time used: 0.00288 secs - > - > # By default, the IBD segments of the "leaves" are computed and plotted - > plotSegmentDistribution(simPat, simMat, type = "ibd1", ids = 4:5, - + labels = c("HSpat", "HSmat")) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -# ICtest - -
- -* Version: 0.3-5 -* GitHub: NA -* Source code: https://github.com/cran/ICtest -* Date/Publication: 2022-05-18 07:30:29 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "ICtest")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ICtest-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggplot.ictest - > ### Title: Scatterplot Matrix for a ictest Object using ggplot2 - > ### Aliases: ggplot.ictest - > ### Keywords: hplot - > - > ### ** Examples - > - ... - > # The aesthetics variables - > mapvar <- data.frame(iris[, 5]) - > colnames(mapvar) <- "species" - > - > TestCov <- PCAasymp(X, k = 2) - > ggplot(TestCov) - > ggplot(TestCov, aes(color = species), mapvar = mapvar, which = "k") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.7Mb - sub-directories of 1Mb or more: - doc 2.5Mb - libs 2.9Mb - ``` - -# idiogramFISH - -
- -* Version: 2.0.13 -* GitHub: NA -* Source code: https://github.com/cran/idiogramFISH -* Date/Publication: 2023-08-22 16:50:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "idiogramFISH")` for more info - -
- -## Newly broken - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - R 1.5Mb - doc 2.0Mb - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘index.Rmd’ - ... - > if (requireNamespace("RCurl", quietly = TRUE)) { - + v <- sub("Version: ", "", readLines("../DESCRIPTION")[3]) - + pkg <- "idiogramFISH" - + l .... [TRUNCATED] - Warning in file(con, "r") : - cannot open file '../DESCRIPTION': No such file or directory - - When sourcing ‘index.R’: - Error: cannot open the connection - Execution halted - - ‘AVignette.Rmd’ using ‘UTF-8’... OK - ‘index.Rmd’ using ‘UTF-8’... failed - ``` - -# IDMIR - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/IDMIR -* Date/Publication: 2023-11-09 15:30:02 UTC -* Number of recursive dependencies: 112 - -Run `revdepcheck::cloud_details(, "IDMIR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IDMIR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: PlotSurvival - > ### Title: PlotSurvival - > ### Aliases: PlotSurvival - > - > ### ** Examples - > - > # Obtain the example data - ... - > GEP<-GetData_Mirna("GEP") - > survival<-GetData_Mirna("survival") - > MiRNAs<-c("hsa-miR-21-5p","hsa-miR-26a-5p","hsa-miR-369-5p","hsa-miR-1238-3p","hsa-miR-10b-5p") - > # Run the function - > SingleMiRNA_CRData<-SingleMiRNA_CRModel(GEP, - + "hsa-miR-21-5p",survival,cutoff.point=NULL) - > PlotSurvival(SingleMiRNA_CRData) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: PlotSurvival ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘IDMIR.Rmd’ - ... - > survival <- GetData_Mirna("survival") - - > SingleMiRNA_CRData <- SingleMiRNA_CRModel(GEP, "hsa-miR-21-5p", - + cutoff.point = NULL, survival) - - > PlotSurvival(SingleMiRNA_CRData) - - When sourcing ‘IDMIR.R’: - Error: argument is of length zero - Execution halted - - ‘IDMIR.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘IDMIR.Rmd’ using rmarkdown - - Quitting from lines 120-130 [unnamed-chunk-7] (IDMIR.Rmd) - Error: processing vignette 'IDMIR.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘IDMIR.Rmd’ - - SUMMARY: processing the following file failed: - ‘IDMIR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# idopNetwork - -
- -* Version: 0.1.2 -* GitHub: https://github.com/cxzdsa2332/idopNetwork -* Source code: https://github.com/cran/idopNetwork -* Date/Publication: 2023-04-18 06:50:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "idopNetwork")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘idopNetwork_vignette.Rmd’ - ... - - > qdODE_plot_base(ode.test) - - > ode.module = test_result$d1_module - - > qdODE_plot_all(ode.module) - - When sourcing ‘idopNetwork_vignette.R’: - Error: object is not a unit - Execution halted - - ‘idopNetwork_vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘idopNetwork_vignette.Rmd’ using rmarkdown - ``` - -# ihclust - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/ihclust -* Date/Publication: 2022-04-27 07:20:02 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "ihclust")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ihclust-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ihclust - > ### Title: Iterative Hierarchical Clustering (IHC) - > ### Aliases: ihclust - > - > ### ** Examples - > - > # This is an example not using the permutation approach - ... - 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - Execution halted - ``` - -# immunarch - -
- -* Version: 0.9.1 -* GitHub: https://github.com/immunomind/immunarch -* Source code: https://github.com/cran/immunarch -* Date/Publication: 2024-03-18 19:10:06 UTC -* Number of recursive dependencies: 198 - -Run `revdepcheck::cloud_details(, "immunarch")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘immunarch-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geneUsageAnalysis - > ### Title: Post-analysis of V-gene and J-gene statistics: PCA, clustering, - > ### etc. - > ### Aliases: geneUsageAnalysis - > - > ### ** Examples - > - ... - 17. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) - 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 19. │ ├─ggplot2::ggplot_add(object, p, objectname) - 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 22. └─base::.handleSimpleError(...) - 23. └─purrr (local) h(simpleError(msg, call)) - 24. └─cli::cli_abort(...) - 25. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.6Mb - sub-directories of 1Mb or more: - R 1.5Mb - data 5.5Mb - doc 1.6Mb - ``` - -# incidental - -
- -* Version: 0.1 -* GitHub: NA -* Source code: https://github.com/cran/incidental -* Date/Publication: 2020-09-16 09:50:03 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "incidental")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘incidental-tutorial.Rmd’ - ... - - > data_subset = do.call("rbind", model_df_list) - - > ggplot(data_subset, aes(x = Time, y = Reported)) + - + geom_point(color = "coral2", shape = 3) + geom_line(aes(x = Time, - + y = Ihat), color .... [TRUNCATED] - - When sourcing ‘incidental-tutorial.R’: - Error: `x` must be a vector, not a object. - Execution halted - - ‘incidental-tutorial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘incidental-tutorial.Rmd’ using rmarkdown - ``` - -# infer - -
- -* Version: 1.0.7 -* GitHub: https://github.com/tidymodels/infer -* Source code: https://github.com/cran/infer -* Date/Publication: 2024-03-25 21:50:02 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "infer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘infer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: shade_confidence_interval - > ### Title: Add information about confidence interval - > ### Aliases: shade_confidence_interval shade_ci - > - > ### ** Examples - > - > # find the point estimate---mean number of hours worked per week - ... - + type = "se") - > - > - > # and plot it! - > boot_dist %>% - + visualize() + - + shade_confidence_interval(ci) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files - ... - 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 19. │ ├─ggplot2::ggplot_add(object, p, objectname) - 20. │ └─ggplot2:::ggplot_add.list(object, p, objectname) - 21. │ ├─ggplot2::ggplot_add(o, plot, object_name) - 22. │ └─ggplot2:::ggplot_add.Layer(o, plot, object_name) - 23. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 24. └─base::.handleSimpleError(...) - 25. └─testthat (local) h(simpleError(msg, call)) - 26. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘anova.Rmd’ - ... - + generate(reps = 1000, type = "permute") %>% calculate( .... [TRUNCATED] - Dropping unused factor levels DK from the supplied explanatory variable - 'partyid'. - - > null_dist %>% visualize() + shade_p_value(observed_f_statistic, - + direction = "greater") - - ... - When sourcing ‘t_test.R’: - Error: argument is of length zero - Execution halted - - ‘anova.Rmd’ using ‘UTF-8’... failed - ‘chi_squared.Rmd’ using ‘UTF-8’... failed - ‘infer.Rmd’ using ‘UTF-8’... failed - ‘observed_stat_examples.Rmd’ using ‘UTF-8’... failed - ‘paired.Rmd’ using ‘UTF-8’... failed - ‘t_test.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘anova.Rmd’ using rmarkdown - ``` - -# injurytools - -
- -* Version: 1.0.3 -* GitHub: https://github.com/lzumeta/injurytools -* Source code: https://github.com/cran/injurytools -* Date/Publication: 2023-11-14 17:20:05 UTC -* Number of recursive dependencies: 155 - -Run `revdepcheck::cloud_details(, "injurytools")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘model-injury-data-ii.Rmd’ - ... - n events median 0.95LCL 0.95UCL - seasonb=2017/2018 23 16 265 152 NA - seasonb=2018/2019 19 17 106 84 165 - - > ggsurvplot(fit, data = injd_sub, palette = c("#E7B800", - + "#2E9FDF")) + xlab("Time [calendar days]") + ylab(expression("Survival probability ( ..." ... [TRUNCATED] - - When sourcing ‘model-injury-data-ii.R’: - Error: argument is of length zero - Execution halted - - ‘estimate-epi-measures.Rmd’ using ‘UTF-8’... OK - ‘model-injury-data-i.Rmd’ using ‘UTF-8’... OK - ‘model-injury-data-ii.Rmd’ using ‘UTF-8’... failed - ‘prepare-injury-data.Rmd’ using ‘UTF-8’... OK - ‘visualize-injury-data.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘estimate-epi-measures.Rmd’ using rmarkdown - --- finished re-building ‘estimate-epi-measures.Rmd’ - - --- re-building ‘model-injury-data-i.Rmd’ using rmarkdown - ``` - -# inlabru - -
- -* Version: 2.11.1 -* GitHub: https://github.com/inlabru-org/inlabru -* Source code: https://github.com/cran/inlabru -* Date/Publication: 2024-07-01 23:30:02 UTC -* Number of recursive dependencies: 141 - -Run `revdepcheck::cloud_details(, "inlabru")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘inlabru-Ex.R’ failed - The error most likely occurred in: - - > ### Name: seals - > ### Title: Seal pups - > ### Aliases: seals seals_sp - > ### Keywords: datasets - > - > ### ** Examples - > - > if (require(ggplot2, quietly = TRUE)) { - + ggplot() + - + geom_fm(data = seals_sp$mesh) + - + gg(seals_sp$points) - + } - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > if (require(testthat, quietly = TRUE)) { - + test_check("inlabru") - + } - Loading required package: inlabru - Loading required package: fmesher - Starting 2 test processes - [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] - ... - 9. │ └─INLA:::expand.inla.stack.responses(responses) - 10. │ └─base::lapply(...) - 11. │ └─INLA (local) FUN(X[[i]], ...) - 12. │ └─dplyr::bind_rows(...) - 13. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env()) - 14. └─rlang::abort(message = message) - - [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] - Error: Test failures - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘stars’ - ``` - -# insurancerating - -
- -* Version: 0.7.4 -* GitHub: https://github.com/mharinga/insurancerating -* Source code: https://github.com/cran/insurancerating -* Date/Publication: 2024-05-20 11:30:03 UTC -* Number of recursive dependencies: 133 - -Run `revdepcheck::cloud_details(, "insurancerating")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘insurancerating-Ex.R’ failed - The error most likely occurred in: - - > ### Name: autoplot.univariate - > ### Title: Automatically create a ggplot for objects obtained from - > ### univariate() - > ### Aliases: autoplot.univariate - > - > ### ** Examples - > - ... - > xzip <- univariate(MTPL, x = bm, severity = amount, nclaims = nclaims, - + exposure = exposure, by = zip) - > autoplot(xzip, show_plots = 1:2) - Warning: Removed 16 rows containing missing values or values outside the scale range - (`geom_point()`). - Warning: Removed 5 rows containing missing values or values outside the scale range - (`geom_line()`). - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits - Execution halted - ``` - -# inTextSummaryTable - -
- -* Version: 3.3.3 -* GitHub: https://github.com/openanalytics/inTextSummaryTable -* Source code: https://github.com/cran/inTextSummaryTable -* Date/Publication: 2024-06-12 18:30:02 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(inTextSummaryTable) - > - > test_check("inTextSummaryTable") - [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - 6. └─inTextSummaryTable::subjectProfileSummaryPlot(...) - 7. └─ggplot2:::`+.gg`(gg, do.call(geom_line, argsGeomLine)) - 8. └─ggplot2:::add_ggplot(e1, e2, e2name) - 9. ├─ggplot2::ggplot_add(object, p, objectname) - 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘inTextSummaryTable-aesthetics.Rmd’ - ... - - > summaryTable <- data.frame(visit = c(1, 2, 1, 2), - + TRT = c("A", "A", "B", "B"), statMean = rnorm(4)) - - > subjectProfileSummaryPlot(data = summaryTable, xVar = "visit", - + colorVar = "TRT") - - ... - Error: argument is of length zero - Execution halted - - ‘inTextSummaryTable-advanced.Rmd’ using ‘UTF-8’... OK - ‘inTextSummaryTable-aesthetics.Rmd’ using ‘UTF-8’... failed - ‘inTextSummaryTable-createTables.Rmd’ using ‘UTF-8’... OK - ‘inTextSummaryTable-exportTables.Rmd’ using ‘UTF-8’... OK - ‘inTextSummaryTable-introduction.Rmd’ using ‘UTF-8’... OK - ‘inTextSummaryTable-standardTables.Rmd’ using ‘UTF-8’... OK - ‘inTextSummaryTable-visualization.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown - --- finished re-building ‘inTextSummaryTable-advanced.Rmd’ - - --- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown - - Quitting from lines 211-224 [aesthetics-defaultsVisualization] (inTextSummaryTable-aesthetics.Rmd) - Error: processing vignette 'inTextSummaryTable-aesthetics.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘inTextSummaryTable-aesthetics.Rmd’ - ... - Error: processing vignette 'inTextSummaryTable-visualization.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘inTextSummaryTable-visualization.Rmd’ - - SUMMARY: processing the following files failed: - ‘inTextSummaryTable-aesthetics.Rmd’ - ‘inTextSummaryTable-visualization.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.3Mb - sub-directories of 1Mb or more: - doc 9.7Mb - ``` - -# inventorize - -
- -* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/inventorize -* Date/Publication: 2022-05-31 22:20:09 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "inventorize")` for more info - -
- -## Newly broken - -* checking whether package ‘inventorize’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘inventorize’ ... -** package ‘inventorize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in pm[[2]] : subscript out of bounds -Error: unable to load R code in package ‘inventorize’ -Execution halted -ERROR: lazy loading failed for package ‘inventorize’ -* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ - - -``` -### CRAN - -``` -* installing *source* package ‘inventorize’ ... -** package ‘inventorize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Warning in qgamma(service_level, alpha, beta) : NaNs produced -** help -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (inventorize) - - -``` -# IPV - -
- -* Version: 1.0.0 -* GitHub: https://github.com/NilsPetras/IPV -* Source code: https://github.com/cran/IPV -* Date/Publication: 2022-09-30 15:00:02 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "IPV")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IPV-Ex.R’ failed - The error most likely occurred in: - - > ### Name: nested_chart - > ### Title: Nested Chart - > ### Aliases: nested_chart - > - > ### ** Examples - > - > # as simple as that - ... - 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) - 8. └─vctrs::vec_as_names(names, repair = "check_unique") - 9. └─vctrs (local) ``() - 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) - 11. └─vctrs:::stop_names_cannot_be_empty(names, call = call) - 12. └─vctrs:::stop_names(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ipv-vignette.Rmd’ - ... - Facet circle radius set to 0.211 based on the data. - cor_spacing set to 0.193 based on the data. - Relative scaling set to 3.78 based on the data. - Axis tick set to 0.1 based on the data. - dist_construct_label set to 0.5 based on the data. - - When sourcing ‘ipv-vignette.R’: - Error: Names can't be empty. - ✖ Empty name found at location 4. - Execution halted - - ‘ipv-vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ipv-vignette.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.0Mb - sub-directories of 1Mb or more: - data 7.0Mb - ``` - -# IRon - -
- -* Version: 0.1.4 -* GitHub: https://github.com/nunompmoniz/IRon -* Source code: https://github.com/cran/IRon -* Date/Publication: 2023-01-20 07:20:06 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "IRon")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IRon-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sera - > ### Title: Squared Error-Relevance Area (SERA) - > ### Aliases: sera - > - > ### ** Examples - > - > library(IRon) - ... - 16. │ └─self$stat$setup_params(data, self$stat_params) - 17. │ └─ggplot2 (local) setup_params(...) - 18. │ └─base::match.fun(method) - 19. │ └─base::get(as.character(FUN), mode = "function", envir = envir) - 20. └─base::.handleSimpleError(...) - 21. └─rlang (local) h(simpleError(msg, call)) - 22. └─handlers[[1L]](cnd) - 23. └─cli::cli_abort(...) - 24. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.7Mb - sub-directories of 1Mb or more: - data 6.5Mb - ``` - -# irt - -
- -* Version: 0.2.9 -* GitHub: https://github.com/egonulates/irt -* Source code: https://github.com/cran/irt -* Date/Publication: 2024-02-20 20:40:02 UTC -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "irt")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘irt-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_distractor_icc - > ### Title: Plot Empirical Item or Test characteristic curve - > ### Aliases: plot_distractor_icc - > - > ### ** Examples - > - > n_item <- 10 # sample(8:12, 1) - ... - > raw_resp <- matrix(sample(LETTERS[1:4], n_item * n_theta, replace = TRUE), - + nrow = n_theta, ncol = n_item, - + dimnames = list(paste0("Examinee-", 1:n_theta), - + paste0("Item_", 1:n_item))) - > key <- sample(LETTERS[1:4], n_item, replace = TRUE) - > plot_distractor_icc(raw_resp, 3, key) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: plot_distractor_icc ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 20.3Mb - sub-directories of 1Mb or more: - R 1.5Mb - libs 18.0Mb - ``` - -# isoorbi - -
- -* Version: 1.3.1 -* GitHub: https://github.com/isoverse/isoorbi -* Source code: https://github.com/cran/isoorbi -* Date/Publication: 2024-08-27 05:10:03 UTC -* Number of recursive dependencies: 123 - -Run `revdepcheck::cloud_details(, "isoorbi")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘dual_inlet.Rmd’ - ... - |20230518_05_USGS32_vs_USGS34 | 16| 7|reference |changeover | NA| 10695| 11020| 65.019| 66.994| - |20230518_05_USGS32_vs_USGS34 | 17| 7|reference |data | NA| 11025| 12335| 67.025| 74.985| - - > orbi_plot_raw_data(df_w_blocks, isotopocules = "15N", - + y = ions.incremental) - - When sourcing ‘dual_inlet.R’: - ... - - When sourcing ‘shot_noise.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘dual_inlet.Rmd’ using ‘UTF-8’... failed - ‘flow_injection.Rmd’ using ‘UTF-8’... OK - ‘isoxl_demo.Rmd’ using ‘UTF-8’... OK - ‘quick_start.Rmd’ using ‘UTF-8’... OK - ‘shot_noise.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘dual_inlet.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.2Mb - sub-directories of 1Mb or more: - doc 2.0Mb - extdata 3.3Mb - ``` - -# ivDiag - -
- -* Version: 1.0.6 -* GitHub: NA -* Source code: https://github.com/cran/ivDiag -* Date/Publication: 2023-09-17 06:00:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "ivDiag")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ivDiag-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ltz - > ### Title: Local-to-Zero Test - > ### Aliases: ltz - > - > ### ** Examples - > - > data(ivDiag) - > controls <- c('altitudine', 'escursione', 'costal', 'nearsea', 'population', - + 'pop2', 'gini_land', 'gini_income') - > ltz_out <- ltz(data = gsz, Y = "totassoc_p", D = "libero_comune_allnord", - + Z = "bishopcity", controls = controls, weights = "population", - + prior = c(0.178, 0.137)) - > plot_ltz(ltz_out) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot_ltz ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# ivreg - -
- -* Version: 0.6-3 -* GitHub: https://github.com/zeileis/ivreg -* Source code: https://github.com/cran/ivreg -* Date/Publication: 2024-04-20 15:22:35 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "ivreg")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ivreg.Rmd’ - ... - | F | 204.932 | | - +----------------------+-----------+---------+ - | RMSE | 0.37 | 0.40 | - +----------------------+-----------+---------+ - - > modelplot(m_list, coef_omit = "Intercept|experience") - - When sourcing ‘ivreg.R’: - Error: argument is of length zero - Execution halted - - ‘Diagnostics-for-2SLS-Regression.Rmd’ using ‘UTF-8’... OK - ‘ivreg.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Diagnostics-for-2SLS-Regression.Rmd’ using rmarkdown - ``` - -# jarbes - -
- -* Version: 2.2.1 -* GitHub: NA -* Source code: https://github.com/cran/jarbes -* Date/Publication: 2024-06-07 09:20:02 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "jarbes")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘hmr.Rmd’ - ... - Warning: Contour data has duplicated x, y coordinates. - ℹ 15940 duplicated rows have been dropped. - Warning: Removed 161 rows containing non-finite outside the scale range - (`stat_contour()`). - Warning: Removed 92 rows containing missing values or values outside the scale range - (`geom_point()`). - - When sourcing ‘hmr.R’: - Error: argument is of length zero - Execution halted - - ‘bmeta.Rmd’ using ‘UTF-8’... OK - ‘hmr.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘bmeta.Rmd’ using rmarkdown - ``` - -# karel - -
- -* Version: 0.1.1 -* GitHub: https://github.com/mpru/karel -* Source code: https://github.com/cran/karel -* Date/Publication: 2022-03-26 21:50:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "karel")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘karel-Ex.R’ failed - The error most likely occurred in: - - > ### Name: acciones - > ### Title: Acciones que Karel puede realizar - > ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso - > ### girar_derecha darse_vuelta - > - > ### ** Examples - > - ... - 1. └─karel::ejecutar_acciones() - 2. ├─base::suppressWarnings(...) - 3. │ └─base::withCallingHandlers(...) - 4. ├─gganimate::animate(...) - 5. └─gganimate:::animate.gganim(...) - 6. └─args$renderer(frames_vars$frame_source, args$fps) - 7. └─gganimate:::png_dim(frames[1]) - 8. └─cli::cli_abort("Provided file ({file}) does not exist") - 9. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(karel) - > - > test_check("karel") - [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - 5. ├─gganimate::animate(...) - 6. └─gganimate:::animate.gganim(...) - 7. └─args$renderer(frames_vars$frame_source, args$fps) - 8. └─gganimate:::png_dim(frames[1]) - 9. └─cli::cli_abort("Provided file ({file}) does not exist") - 10. └─rlang::abort(...) - - [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘gifski’ - All declared Imports should be used. - ``` - -# kDGLM - -
- -* Version: 1.2.0 -* GitHub: https://github.com/silvaneojunior/kDGLM -* Source code: https://github.com/cran/kDGLM -* Date/Publication: 2024-05-25 09:50:03 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "kDGLM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘kDGLM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: forecast.fitted_dlm - > ### Title: Auxiliary function for forecasting - > ### Aliases: forecast.fitted_dlm - > - > ### ** Examples - > - > - ... - > forecast(fitted.data, 24, - + chickenPox = list(Total = rep(175, 24)), # Optional - + Vaccine.1.Covariate = rep(TRUE, 24), - + Vaccine.2.Covariate = rep(TRUE, 24) - + ) - Scale for y is already present. - Adding another scale for y, which will replace the existing scale. - Error in pm[[2]] : subscript out of bounds - Calls: forecast ... lapply -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘fitting.Rmd’ - ... - > outcome <- Multinom(p = c("p.1", "p.2"), data = chickenPox[, - + c(2, 3, 5)]) - - > fitted.model <- fit_model(structure * 2, chickenPox = outcome) - - > forecast(fitted.model, t = 24, plot = "base") - - When sourcing ‘fitting.R’: - Error: Error: Missing extra argument: Vaccine.1.Covariate - Execution halted - - ‘example1.Rmd’ using ‘UTF-8’... OK - ‘fitting.Rmd’ using ‘UTF-8’... failed - ‘intro.Rmd’ using ‘UTF-8’... OK - ‘outcomes.Rmd’ using ‘UTF-8’... OK - ‘structures.Rmd’ using ‘UTF-8’... OK - ``` - -# KMEANS.KNN - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/KMEANS.KNN -* Date/Publication: 2024-05-17 09:20:12 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "KMEANS.KNN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘KMEANS.KNN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: KMEANS_FUNCTION - > ### Title: KMEANS_FUNCTION - > ### Aliases: KMEANS_FUNCTION - > - > ### ** Examples - > - > data(iris) - ... - 12. │ └─ggplot2:::`+.gg`(...) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -# latentcor - -
- -* Version: 2.0.1 -* GitHub: NA -* Source code: https://github.com/cran/latentcor -* Date/Publication: 2022-09-05 20:50:02 UTC -* Number of recursive dependencies: 143 - -Run `revdepcheck::cloud_details(, "latentcor")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘latentcor-Ex.R’ failed - The error most likely occurred in: - - > ### Name: latentcor - > ### Title: Estimate latent correlation for mixed types. - > ### Aliases: latentcor - > - > ### ** Examples - > - > # Example 1 - truncated data type, same type for all variables - ... - > R_approx = latentcor(X = X, types = "tru", method = "approx")$R - > proc.time() - start_time - user system elapsed - 0.027 0.000 0.027 - > # Heatmap for latent correlation matrix. - > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx", - + showplot = TRUE)$plotR - Error in pm[[2]] : subscript out of bounds - Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# lcars - -
- -* Version: 0.3.8 -* GitHub: https://github.com/leonawicz/lcars -* Source code: https://github.com/cran/lcars -* Date/Publication: 2023-09-10 04:10:02 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "lcars")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lcars-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lcars_border - > ### Title: LCARS border plot - > ### Aliases: lcars_border - > - > ### ** Examples - > - > lcars_border() - ... - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - invalid font type - Calls: lcars_border ... drawDetails -> drawDetails.text -> grid.Call.graphics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘lcars.Rmd’ - ... - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family '0.5' not found in PostScript font database - - When sourcing ‘lcars.R’: - Error: invalid font type - Execution halted - - ‘lcars.Rmd’ using ‘UTF-8’... failed - ``` - -# lemon - -
- -* Version: 0.4.9 -* GitHub: https://github.com/stefanedwards/lemon -* Source code: https://github.com/cran/lemon -* Date/Publication: 2024-02-08 08:00:08 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "lemon")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lemon-Ex.R’ failed - The error most likely occurred in: - - > ### Name: annotate_y_axis - > ### Title: Annotations on the axis - > ### Aliases: annotate_y_axis annotate_x_axis - > - > ### ** Examples - > - > library(ggplot2) - > - > p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point() - > - > l <- p + annotate_y_axis('mark at', y=200, tick=TRUE) - > l - Error in identicalUnits(x) : object is not a unit - Calls: ... polylineGrob -> is.unit -> unit.c -> identicalUnits - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(lemon) - > - > - > if (TRUE) { - + test_check("lemon") - + } #else { - ... - 17. ├─grid::unit.c(unit(1, "npc"), unit(1, "npc") - tick.length) - 18. └─grid:::Ops.unit(unit(1, "npc"), tick.length) - 19. └─grid:::as.unit(e2) - - [ FAIL 1 | WARN 0 | SKIP 3 | PASS 138 ] - Deleting unused snapshots: - • facet/facet-rep-wrap-spacing.svg - • facet_aux/facet-rep-wrap.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘capped-axes.Rmd’ - ... - > p + coord_capped_cart(bottom = "right") - - > p + coord_capped_cart(bottom = "right", left = "none") - - > ggplot(dat1, aes(gp, y)) + geom_point(position = position_jitter(width = 0.2, - + height = 0)) + coord_capped_cart(left = "none", bottom = bracke .... [TRUNCATED] - - ... - When sourcing ‘legends.R’: - Error: Could not find panel named `panel-1-5`. - Execution halted - - ‘capped-axes.Rmd’ using ‘UTF-8’... failed - ‘facet-rep-labels.Rmd’ using ‘UTF-8’... failed - ‘geoms.Rmd’ using ‘UTF-8’... OK - ‘gtable_show_lemonade.Rmd’ using ‘UTF-8’... OK - ‘legends.Rmd’ using ‘UTF-8’... failed - ‘lemon_print.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘capped-axes.Rmd’ using rmarkdown - ``` - -# lfproQC - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/lfproQC -* Date/Publication: 2024-09-06 13:00:02 UTC -* Number of recursive dependencies: 143 - -Run `revdepcheck::cloud_details(, "lfproQC")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lfproQC-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Boxplot_data - > ### Title: Creating Boxplot for a dataset - > ### Aliases: Boxplot_data - > - > ### ** Examples - > - > Boxplot_data(yeast_data) - Using Majority protein IDs as id variables - Warning: Removed 269 rows containing non-finite outside the scale range - (`stat_boxplot()`). - Error in pm[[2]] : subscript out of bounds - Calls: Boxplot_data -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘user_guide.Rmd’ - ... - > yeast$`Best combinations` - PCV_best_combination PEV_best_combination PMAD_best_combination - 1 knn_rlr lls_vsn lls_rlr - - > Boxplot_data(yeast$knn_rlr_data) - Using Majority protein IDs as id variables - - When sourcing ‘user_guide.R’: - Error: subscript out of bounds - Execution halted - - ‘user_guide.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘user_guide.Rmd’ using rmarkdown - - Quitting from lines 53-54 [unnamed-chunk-8] (user_guide.Rmd) - Error: processing vignette 'user_guide.Rmd' failed with diagnostics: - subscript out of bounds - --- failed re-building ‘user_guide.Rmd’ - - SUMMARY: processing the following file failed: - ‘user_guide.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.1Mb - sub-directories of 1Mb or more: - doc 5.8Mb - ``` - -# lgpr - -
- -* Version: 1.2.4 -* GitHub: https://github.com/jtimonen/lgpr -* Source code: https://github.com/cran/lgpr -* Date/Publication: 2023-09-24 06:50:02 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "lgpr")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # Short tests - > # - focus on testing that everything runs - > # - should take less than minute - > library(testthat) - > library(lgpr) - Attached lgpr 1.2.4, using rstan 2.32.6. Type ?lgpr to get started. - > - ... - 3. └─bayesplot::mcmc_areas(sf, regex_pars = regex_pars, ...) - 4. └─ggplot2:::`+.gg`(...) - 5. └─ggplot2:::add_ggplot(e1, e2, e2name) - 6. ├─ggplot2::ggplot_add(object, p, objectname) - 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 3 | WARN 1 | SKIP 0 | PASS 434 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 156.9Mb - sub-directories of 1Mb or more: - R 1.5Mb - libs 155.0Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# LightLogR - -
- -* Version: 0.3.8 -* GitHub: https://github.com/tscnlab/LightLogR -* Source code: https://github.com/cran/LightLogR -* Date/Publication: 2024-07-04 17:00:02 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "LightLogR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘LightLogR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: aggregate_Date - > ### Title: Aggregate dates to a single day - > ### Aliases: aggregate_Date - > - > ### ** Examples - > - > library(ggplot2) - > #gg_days without aggregation - > sample.data.environment %>% - + gg_days() - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# LMoFit - -
- -* Version: 0.1.7 -* GitHub: NA -* Source code: https://github.com/cran/LMoFit -* Date/Publication: 2024-05-14 07:33:23 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "LMoFit")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘LMoFit.Rmd’ - ... - - > lspace_BrIII - - When sourcing ‘LMoFit.R’: - Error: Problem while setting up geom aesthetics. - ℹ Error occurred in the 1st layer. - Caused by error in `compute_geom_2()`: - ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, - c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, - Execution halted - - ‘LMoFit.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘LMoFit.Rmd’ using rmarkdown - - Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd) - Error: processing vignette 'LMoFit.Rmd' failed with diagnostics: - Problem while setting up geom aesthetics. - ℹ Error occurred in the 1st layer. - Caused by error in `compute_geom_2()`: - ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, - ... - NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 11, list("white", NA, NULL, NULL, TRUE), list(), 5.5, NULL, NULL, list("grey92", NULL, NULL, NULL, FALSE, TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, - 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, c(5.5, 5.5, 5.5, 5.5), list("white", "black", 2, NULL, TRUE), NULL, NULL, "inherit", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, - NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75, list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5))) - --- failed re-building ‘LMoFit.Rmd’ - - SUMMARY: processing the following file failed: - ‘LMoFit.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.0Mb - sub-directories of 1Mb or more: - data 6.5Mb - ``` - -# lnmixsurv - -
- -* Version: 3.1.6 -* GitHub: NA -* Source code: https://github.com/cran/lnmixsurv -* Date/Publication: 2024-09-03 15:20:08 UTC -* Number of recursive dependencies: 196 - -Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files - ... - - Error in `pm[[2]]`: subscript out of bounds - Backtrace: - ▆ - 1. └─testthat::expect_snapshot(plot(mod1)) at test-survival_ln_mixture_em-methods.R:25:3 - 2. └─rlang::cnd_signal(state$error) - - [ FAIL 1 | WARN 0 | SKIP 7 | PASS 50 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘expectation_maximization.Rmd’ - ... - + x, data = data, iter = 200, starting_seed = 20, number_em_search = 0) - - > gg <- plot_fit_on_data(model_em, data)$ggplot - - > plot(model_em) - Loading required namespace: plotly - - When sourcing ‘expectation_maximization.R’: - Error: subscript out of bounds - Execution halted - - ‘compare.Rmd’ using ‘UTF-8’... OK - ‘expectation_maximization.Rmd’ using ‘UTF-8’... failed - ‘intercept_only.Rmd’ using ‘UTF-8’... OK - ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK - ‘parallel_computation.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘compare.Rmd’ using rmarkdown - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - ... - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - - warning: solve(): system is singular; attempting approx solution - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.0Mb - sub-directories of 1Mb or more: - doc 4.0Mb - libs 5.7Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘purrr’ ‘readr’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘rstanarm’ - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# LocalControl - -
- -* Version: 1.1.4 -* GitHub: https://github.com/OHDSI/LocalControl -* Source code: https://github.com/cran/LocalControl -* Date/Publication: 2024-09-04 22:30:18 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "LocalControl")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘LocalControl-jss-2020.Rnw’ - ... - Warning: A numeric `legend.position` argument in `theme()` was deprecated in - ggplot2 3.5.0. - ℹ Please use the `legend.position.inside` argument of `theme()` - instead. - - > grid.arrange(plotz$rad_1, plotz$rad_11, ncol = 1) - - When sourcing 'LocalControl-jss-2020.R': - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘LocalControl-jss-2020.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - doc 2.0Mb - libs 2.7Mb - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘LocalControl-jss-2020.Rnw’ using Sweave - Loading required package: data.table - Loading required package: colorspace - Loading required package: RColorBrewer - Loading required package: gridExtra - Loading required package: ggplot2 - Loading required package: rpart - Loading required package: rpart.plot - Loading required package: LocalControl - ... - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - - --- failed re-building 'LocalControl-jss-2020.Rnw' - - SUMMARY: processing the following file failed: - 'LocalControl-jss-2020.Rnw' - - Error: Vignette re-building failed. - Execution halted - ``` - -# LocalCop - -
- -* Version: 0.0.1 -* GitHub: https://github.com/mlysy/LocalCop -* Source code: https://github.com/cran/LocalCop -* Date/Publication: 2024-03-21 14:50:06 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "LocalCop")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘LocalCop-vignette.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘LocalCop-vignette.Rmd’ - ... - > tibble(x = x0, True = BiCopEta2Tau(family, eta = eta_fun(x0)), - + Fitted = BiCopEta2Tau(fitseq$eta, family = family)) %>% pivot_longer(True:Fitt .... [TRUNCATED] - Warning: Removed 51 rows containing missing values or values outside the scale range - (`geom_line()`). - Warning: Removed 51 rows containing missing values or values outside the scale range - (`geom_point()`). - - When sourcing ‘LocalCop-vignette.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘LocalCop-vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking installed package size ... NOTE - ``` - installed size is 55.7Mb - sub-directories of 1Mb or more: - libs 55.3Mb - ``` - -# LongDat - -
- -* Version: 1.1.2 -* GitHub: https://github.com/CCY-dev/LongDat -* Source code: https://github.com/cran/LongDat -* Date/Publication: 2023-07-17 05:40:02 UTC -* Number of recursive dependencies: 135 - -Run `revdepcheck::cloud_details(, "LongDat")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘LongDat_cont_tutorial.Rmd’ - ... - - > test_plot <- cuneiform_plot(result_table = test_cont[[1]], - + title_size = 15) - [1] "Finished plotting successfully!" - - > test_plot - - ... - [1] "Finished plotting successfully!" - - > test_plot - - When sourcing ‘LongDat_disc_tutorial.R’: - Error: object is not coercible to a unit - Execution halted - - ‘LongDat_cont_tutorial.Rmd’ using ‘UTF-8’... failed - ‘LongDat_disc_tutorial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘LongDat_cont_tutorial.Rmd’ using rmarkdown - Warning in eng_r(options) : - Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: - Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. - - Warning in eng_r(options) : - Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: - Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. - - ... - Quitting from lines 181-182 [unnamed-chunk-11] (LongDat_disc_tutorial.Rmd) - Error: processing vignette 'LongDat_disc_tutorial.Rmd' failed with diagnostics: - object is not coercible to a unit - --- failed re-building ‘LongDat_disc_tutorial.Rmd’ - - SUMMARY: processing the following files failed: - ‘LongDat_cont_tutorial.Rmd’ ‘LongDat_disc_tutorial.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# longreadvqs - -
- -* Version: 0.1.3 -* GitHub: https://github.com/NakarinP/longreadvqs -* Source code: https://github.com/cran/longreadvqs -* Date/Publication: 2024-08-26 19:30:05 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "longreadvqs")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘longreadvqs-Ex.R’ failed - The error most likely occurred in: - - > ### Name: vqscompare - > ### Title: Comparing viral quasispecies profile and operational taxonomic - > ### unit (OTU) classified by k-means clustering between samples - > ### Aliases: vqscompare - > - > ### ** Examples - > - ... - 13. │ └─ggplot2:::`+.gg`(...) - 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. │ ├─ggplot2::ggplot_add(object, p, objectname) - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘longreadvqs-vignette.Rmd’ - ... - - > comp <- vqscompare(samplelist = list(s1, s2, s3, s4_fix), - + lab_name = "Sample", kmeans.n = 10) - - When sourcing ‘longreadvqs-vignette.R’: - Error: ℹ In index: 1. - ℹ With name: Dim.2. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - Execution halted - - ‘longreadvqs-vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘longreadvqs-vignette.Rmd’ using rmarkdown - ``` - -# lpdensity - -
- -* Version: 2.4 -* GitHub: NA -* Source code: https://github.com/cran/lpdensity -* Date/Publication: 2023-01-21 23:50:02 UTC -* Number of recursive dependencies: 28 - -Run `revdepcheck::cloud_details(, "lpdensity")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lpdensity-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lpdensity - > ### Title: Local Polynomial Density Estimation and Inference - > ### Aliases: lpdensity - > - > ### ** Examples - > - > # Generate a random sample - ... - 18 1.2878 0.6298 457 0.1749 0.0097 0.1222 , 0.2179 - 19 1.5768 0.6298 299 0.1221 0.0086 0.0863 , 0.1719 - ============================================================================= - > - > # Plot the estimates and confidence intervals - > plot(est1, legendTitle="My Plot", legendGroups=c("X")) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -# lspartition - -
- -* Version: 0.4 -* GitHub: NA -* Source code: https://github.com/cran/lspartition -* Date/Publication: 2019-08-08 22:40:06 UTC -* Number of recursive dependencies: 34 - -Run `revdepcheck::cloud_details(, "lspartition")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lspartition-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lsprobust.plot - > ### Title: Graphic Presentation of Results for 'lspartition' Package - > ### Aliases: lsprobust.plot - > - > ### ** Examples - > - > x <- runif(500) - > y <- sin(4*x)+rnorm(500) - > est <- lsprobust(y, x) - > lsprobust.plot(est) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# LSTbook - -
- -* Version: 0.5.0 -* GitHub: https://github.com/dtkaplan/LSTbook -* Source code: https://github.com/cran/LSTbook -* Date/Publication: 2024-02-23 19:20:15 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "LSTbook")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files - ... - - [ FAIL 1 | WARN 1 | SKIP 4 | PASS 73 ] - Deleting unused snapshots: - • model_plot/four-facets.png - • pointplot/1-var-plot.png - • pointplot/bird-logistic-plot.png - • pointplot/color-and-facet-na.png - • pointplot/logistic-fun-plot.png - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘DAGs.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘DAGs.Rmd’ - ... - 3 -1.35 -11.9 - 4 0.429 0.171 - 5 0.622 5.85 - 6 2.35 16.5 - - > Wrong_way <- datasim_make(x = rnorm(n, mean = 0, sd = 2)) - - ... - - > model_plot(height_model) - - When sourcing ‘modeling.R’: - Error: argument is of length zero - Execution halted - - ‘DAGs.Rmd’ using ‘UTF-8’... failed - ‘LSTbook.Rmd’ using ‘UTF-8’... OK - ‘modeling.Rmd’ using ‘UTF-8’... failed - ``` - -* checking loading without being on the library search path ... WARNING - ``` - Error: package or namespace load failed for ‘LSTbook’: - .onLoad failed in loadNamespace() for 'LSTbook', details: - call: loadNamespace(name) - error: there is no package called ‘mosaicData’ - Execution halted - - It looks like this package has a loading problem when not on .libPaths: - see the messages for details. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 20 marked UTF-8 strings - ``` - -# manydata - -
- -* Version: 0.9.3 -* GitHub: https://github.com/globalgov/manydata -* Source code: https://github.com/cran/manydata -* Date/Publication: 2024-05-06 19:00:02 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "manydata")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(manydata) - manydata 0.9.3 - Please see manydata.ch for more information. - Type 'citation("manydata")' for citing this R package in publications. - > - > test_check("manydata") - ... - ── Failure ('test_compare.R:8:3'): plot for compare_categories returns the correct output format ── - Names of `db` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' - ── Failure ('test_compare.R:74:3'): compare_missing() and plot_missing() returns the correct output format ── - `pl` has length 11, not length 10. - ── Failure ('test_compare.R:76:3'): compare_missing() and plot_missing() returns the correct output format ── - Names of `pl` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' - - [ FAIL 4 | WARN 0 | SKIP 3 | PASS 121 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 3 marked UTF-8 strings - ``` - -# manymome - -
- -* Version: 0.2.2 -* GitHub: https://github.com/sfcheung/manymome -* Source code: https://github.com/cran/manymome -* Date/Publication: 2024-06-05 23:30:03 UTC -* Number of recursive dependencies: 158 - -Run `revdepcheck::cloud_details(, "manymome")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘manymome-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_effect_vs_w - > ### Title: Plot an Effect Against a Moderator - > ### Aliases: plot_effect_vs_w - > - > ### ** Examples - > - > - ... - + y = "y", - + m = "m", - + fit = fit_lm, - + sd_from_mean = seq(-2, 2, length.out = 10), - + boot_ci = TRUE, - + boot_out = boot_out_lm) - > p <- plot_effect_vs_w(out_lm) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plot_effect_vs_w ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# mapbayr - -
- -* Version: 0.10.0 -* GitHub: https://github.com/FelicienLL/mapbayr -* Source code: https://github.com/cran/mapbayr -* Date/Publication: 2023-07-17 08:20:02 UTC -* Number of recursive dependencies: 68 - -Run `revdepcheck::cloud_details(, "mapbayr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mapbayr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mapbayr_plot - > ### Title: Make mapbayr plot - > ### Aliases: mapbayr_plot - > - > ### ** Examples - > - > aug <- data.frame( - ... - > obs <- data.frame( - + ID = 1, time = c(6, 20), evid = 0, - + mdv = c(0,1), DV = c(0.5, 5), cmt = 2 - + ) - > - > mapbayr_plot(aug, obs) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -# MBNMAdose - -
- -* Version: 0.4.3 -* GitHub: NA -* Source code: https://github.com/cran/MBNMAdose -* Date/Publication: 2024-04-18 12:42:47 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "MBNMAdose")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘outputs-4.Rmd’ - ... - - > plot(trip.emax) - - When sourcing ‘outputs-4.R’: - Error: Problem while setting up geom aesthetics. - ℹ Error occurred in the 1st layer. - Caused by error in `use_defaults()`: - ... - Execution halted - - ‘consistencychecking-3.Rmd’ using ‘UTF-8’... OK - ‘dataexploration-1.Rmd’ using ‘UTF-8’... OK - ‘mbnmadose-overview.Rmd’ using ‘UTF-8’... OK - ‘metaregression-6.Rmd’ using ‘UTF-8’... OK - ‘nma_in_mbnmadose.Rmd’ using ‘UTF-8’... OK - ‘outputs-4.Rmd’ using ‘UTF-8’... failed - ‘predictions-5.Rmd’ using ‘UTF-8’... OK - ‘runmbnmadose-2.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6 marked Latin-1 strings - ``` - -# MBNMAtime - -
- -* Version: 0.2.4 -* GitHub: NA -* Source code: https://github.com/cran/MBNMAtime -* Date/Publication: 2023-10-14 15:20:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "MBNMAtime")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown - - Quitting from lines 141-146 [unnamed-chunk-8] (consistencychecking-3.Rmd) - Error: processing vignette 'consistencychecking-3.Rmd' failed with diagnostics: - unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, - NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.2, 0, 2.2), NULL, TRUE), list("grey20", NULL, NULL, NULL, FALSE, "grey20", TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, - NULL, NULL, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), NULL, 2, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list(), list(NULL, "grey20", NULL, NULL, TRUE), NULL, NULL, - NULL, list("grey92", NULL, NULL, NULL, FALSE, "grey92", TRUE), list("grey95", NULL, NULL, NULL, FALSE, "grey95", FALSE), list("grey95", 0.5, NULL, NULL, FALSE, "grey95", FALSE), NULL, NULL, NULL, NULL, FALSE, list("white", NA, NULL, NULL, FALSE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list( - NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list("lightsteelblue1", "black", NULL, NULL, FALSE), NULL, NULL, "on", "inside", list(NULL, NULL, "black", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, FALSE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) - --- failed re-building ‘consistencychecking-3.Rmd’ - - --- re-building ‘dataexploration-1.Rmd’ using rmarkdown - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘consistencychecking-3.Rmd’ - ... - |-> direct | | 0.228| -0.213| 0.684| - |-> indirect | | -0.515| -0.891| -0.137| - | | | | | | - - > plot(nodesplit, plot.type = "forest") - - When sourcing ‘consistencychecking-3.R’: - ... - ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, - Execution halted - - ‘consistencychecking-3.Rmd’ using ‘UTF-8’... failed - ‘dataexploration-1.Rmd’ using ‘UTF-8’... failed - ‘mbnmatime-overview.Rmd’ using ‘UTF-8’... OK - ‘outputs-4.Rmd’ using ‘UTF-8’... failed - ‘predictions-5.Rmd’ using ‘UTF-8’... OK - ‘runmbnmatime-2.Rmd’ using ‘UTF-8’... OK - ``` - -# mecoturn - -
- -* Version: 0.3.0 -* GitHub: https://github.com/ChiLiubio/mecoturn -* Source code: https://github.com/cran/mecoturn -* Date/Publication: 2023-09-10 13:40:02 UTC -* Number of recursive dependencies: 109 - -Run `revdepcheck::cloud_details(, "mecoturn")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mecoturn-Ex.R’ failed - The error most likely occurred in: - - > ### Name: betaturn - > ### Title: Analyze the 'turnover' of microbial communities. - > ### Aliases: betaturn - > - > ### ** Examples - > - > - ... - 13. │ └─ggplot2:::`+.gg`(...) - 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. │ ├─ggplot2::ggplot_add(object, p, objectname) - 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 18. └─base::.handleSimpleError(...) - 19. └─purrr (local) h(simpleError(msg, call)) - 20. └─cli::cli_abort(...) - 21. └─rlang::abort(...) - Execution halted - ``` - -# MetaNet - -
- -* Version: 0.1.2 -* GitHub: https://github.com/Asa12138/MetaNet -* Source code: https://github.com/cran/MetaNet -* Date/Publication: 2024-03-25 20:40:07 UTC -* Number of recursive dependencies: 151 - -Run `revdepcheck::cloud_details(, "MetaNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MetaNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as.ggig - > ### Title: Transfer an igraph object to a ggig - > ### Aliases: as.ggig - > - > ### ** Examples - > - > as.ggig(co_net, coors = c_net_layout(co_net)) -> ggig - > plot(ggig) - Warning: Removed 446 rows containing missing values or values outside the scale range - (`geom_text()`). - Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics - Execution halted - ``` - -# metR - -
- -* Version: 0.15.0 -* GitHub: https://github.com/eliocamp/metR -* Source code: https://github.com/cran/metR -* Date/Publication: 2024-02-09 00:40:02 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "metR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘metR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_contour_tanaka - > ### Title: Illuminated contours - > ### Aliases: geom_contour_tanaka GeomContourTanaka - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) - 20. │ └─self$draw_panel(...) - 21. │ └─metR (local) draw_panel(...) - 22. │ └─metR:::stopf(...) - 23. │ └─base::stop(e) - 24. └─rlang (local) ``(``) - 25. └─handlers[[1L]](cnd) - 26. └─cli::cli_abort(...) - 27. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(metR) - > # library(vdiffr) - > - > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false"))) - > if (on_cran) data.table::setDTthreads(2) - > - ... - • vis-streamline/streamline-ywrapped.svg - • vis-text-contour/labels-text.svg - • vis-text-contour/minsize.svg - • vis-text-contour/placement-fraction.svg - • vis-text-contour/placement-minmax-horizontal.svg - • vis-text-contour/placement-minmax-vertical.svg - • vis-text-contour/placement-n.svg - • vis-text-contour/text-contour-norotate.svg - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Visualization-tools.Rmd’ - ... - - > ggplot(temperature[lev == 300], aes(lon, lat, z = air.z)) + - + geom_contour_fill() + geom_contour_tanaka() + scale_fill_divergent() - - When sourcing ‘Visualization-tools.R’: - Error: Problem while converting geom to grob. - ℹ Error occurred in the 2nd layer. - Caused by error: - ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. - Execution halted - - ‘Visualization-tools.Rmd’ using ‘UTF-8’... failed - ‘Working-with-data.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Visualization-tools.Rmd’ using knitr - - Quitting from lines 241-245 [unnamed-chunk-16] (Visualization-tools.Rmd) - Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics: - Problem while converting geom to grob. - ℹ Error occurred in the 2nd layer. - Caused by error: - ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. - ... - --- failed re-building ‘Visualization-tools.Rmd’ - - --- re-building ‘Working-with-data.Rmd’ using knitr - --- finished re-building ‘Working-with-data.Rmd’ - - SUMMARY: processing the following file failed: - ‘Visualization-tools.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.6Mb - sub-directories of 1Mb or more: - R 1.5Mb - data 2.0Mb - doc 1.8Mb - ``` - -# metrica - -
- -* Version: 2.1.0 -* GitHub: https://github.com/adriancorrendo/metrica -* Source code: https://github.com/cran/metrica -* Date/Publication: 2024-06-30 14:20:02 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "metrica")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘regression_case.Rmd’ - ... - + mutate(Year = seq(2001, 2020, by = 1)) - - > wheat_time %>% ggplot2::ggplot(aes(x = Year)) + geom_point(aes(y = pred, - + fill = "Predicted", shape = "Predicted")) + geom_point(aes(y = obs, .... [TRUNCATED] - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - ... - Execution halted - - ‘Cheatsheet.Rmd’ using ‘UTF-8’... OK - ‘JOSS_publication.Rmd’ using ‘UTF-8’... OK - ‘Shinyapp.Rmd’ using ‘UTF-8’... OK - ‘apsim_open.Rmd’ using ‘UTF-8’... OK - ‘available_metrics_classification.Rmd’ using ‘UTF-8’... OK - ‘available_metrics_regression.Rmd’ using ‘UTF-8’... OK - ‘classification_case.Rmd’ using ‘UTF-8’... OK - ‘regression_case.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Cheatsheet.Rmd’ using rmarkdown - --- finished re-building ‘Cheatsheet.Rmd’ - - --- re-building ‘JOSS_publication.Rmd’ using rmarkdown - --- finished re-building ‘JOSS_publication.Rmd’ - - --- re-building ‘Shinyapp.Rmd’ using rmarkdown - --- finished re-building ‘Shinyapp.Rmd’ - - ... - --- re-building ‘apsim_open.Rmd’ using rmarkdown - --- finished re-building ‘apsim_open.Rmd’ - - --- re-building ‘available_metrics_classification.Rmd’ using rmarkdown - --- finished re-building ‘available_metrics_classification.Rmd’ - - --- re-building ‘available_metrics_regression.Rmd’ using rmarkdown - --- finished re-building ‘available_metrics_regression.Rmd’ - - --- re-building ‘classification_case.Rmd’ using rmarkdown - ``` - -# miceRanger - -
- -* Version: 1.5.0 -* GitHub: https://github.com/FarrellDay/miceRanger -* Source code: https://github.com/cran/miceRanger -* Date/Publication: 2021-09-06 15:20:02 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "miceRanger")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘usingMiceRanger.Rmd’ - ... - > plotList <- lapply(plotVars, function(x) { - + missIndx <- is.na(ampIris[, get(x)]) - + impVsAmp <- data.table(originalData = iris[missIndx, x], .... [TRUNCATED] - - When sourcing ‘usingMiceRanger.R’: - Error: ℹ In index: 1. - ℹ With name: imputedData. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - Execution halted - - ‘diagnosticPlotting.Rmd’ using ‘UTF-8’... OK - ‘miceAlgorithm.Rmd’ using ‘UTF-8’... OK - ‘usingMiceRanger.Rmd’ using ‘UTF-8’... failed - ``` - -# microbial - -
- -* Version: 0.0.21 -* GitHub: NA -* Source code: https://github.com/cran/microbial -* Date/Publication: 2024-05-15 18:20:02 UTC -* Number of recursive dependencies: 179 - -Run `revdepcheck::cloud_details(, "microbial")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘microbial-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotalpha - > ### Title: plot alpha diversity - > ### Aliases: plotalpha - > - > ### ** Examples - > - > { - ... - 12. │ └─ggplot2:::`+.gg`(...) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘microbial.Rmd’ - ... - > plotbar(phy, level = "Phylum") - - > plotalpha(physeq, group = "group") - - When sourcing ‘microbial.R’: - Error: ℹ In index: 1. - ℹ With name: val. - Caused by error in `if (new_name %in% existing) ...`: - ! argument is of length zero - Execution halted - - ‘microbial.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘microbial.Rmd’ using knitr - ``` - -# MicrobiomeSurv - -
- -* Version: 0.1.0 -* GitHub: https://github.com/N-T-Huyen/MicrobiomeSurv -* Source code: https://github.com/cran/MicrobiomeSurv -* Date/Publication: 2023-10-12 06:20:02 UTC -* Number of recursive dependencies: 158 - -Run `revdepcheck::cloud_details(, "MicrobiomeSurv")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MicrobiomeSurv-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EstimateHR - > ### Title: Classification, Survival Estimation and Visualization - > ### Aliases: EstimateHR - > - > ### ** Examples - > - > # Prepare data - ... - + Mean = TRUE) - > - > # Using the function - > est_HR_fam_shan_w3 = EstimateHR(Risk.Scores = lasso_fam_shan_w3$Risk.Scores, - + Data.Survival = lasso_fam_shan_w3$Data.Survival, - + Prognostic = prog_fam_shan_w3, Plots = TRUE, - + Mean = TRUE) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: EstimateHR ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -# migraph - -
- -* Version: 1.4.2 -* GitHub: https://github.com/stocnet/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2024-09-04 12:00:02 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "migraph")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(manynet) - > library(migraph) - > - > test_check("migraph") - Starting 2 test processes - [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] - ... - `expected` is a character vector ('Statistic') - ── Failure ('test-model_tests.R:73:3'): qap plot works ───────────────────────── - qapplot$labels$x (`actual`) not identical to "Statistic" (`expected`). - - `actual` is NULL - `expected` is a character vector ('Statistic') - - [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] - Error: Test failures - Execution halted - ``` - -# mikropml - -
- -* Version: 1.6.1 -* GitHub: https://github.com/SchlossLab/mikropml -* Source code: https://github.com/cran/mikropml -* Date/Publication: 2023-08-21 15:10:05 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "mikropml")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(mikropml) - > test_check("mikropml") - Fraction of data in the training set: 0.778 - Groups in the training set: A C D - Groups in the testing set: B - Fraction of data in the training set: 0.778 - ... - `names(expected)` is absent - ── Failure ('test-plot.R:140:3'): plot_mean_prc uses geom ribbon, line, and hline ── - ... %>% unlist() (`actual`) not equal to c(...) (`expected`). - - `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...) - `names(expected)` is absent - - [ FAIL 2 | WARN 19 | SKIP 12 | PASS 314 ] - Error: Test failures - Execution halted - ``` - -# MiMIR - -
- -* Version: 1.5 -* GitHub: NA -* Source code: https://github.com/cran/MiMIR -* Date/Publication: 2024-02-01 08:50:02 UTC -* Number of recursive dependencies: 191 - -Run `revdepcheck::cloud_details(, "MiMIR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MiMIR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: LOBOV_accuracies - > ### Title: LOBOV_accuracies - > ### Aliases: LOBOV_accuracies - > - > ### ** Examples - > - > require(pROC) - ... - 56 metabolites x 500 samples - | Pruning samples on5SD: - 56 metabolites x 500 samples - | Performing scaling ... DONE! - | Imputation ... DONE! - > p_avail<-colnames(b_p)[c(1:5)] - > LOBOV_accuracies(sur$surrogates, b_p, p_avail, MiMIR::acc_LOBOV) - Error in pm[[2]] : subscript out of bounds - Calls: LOBOV_accuracies -> -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# miRetrieve - -
- -* Version: 1.3.4 -* GitHub: NA -* Source code: https://github.com/cran/miRetrieve -* Date/Publication: 2021-09-18 17:30:02 UTC -* Number of recursive dependencies: 126 - -Run `revdepcheck::cloud_details(, "miRetrieve")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(miRetrieve) - > - > test_check("miRetrieve") - [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - Backtrace: - ▆ - 1. └─miRetrieve::compare_mir_terms_scatter(df_merged, "miR-21", title = "Test_title") at test-comparemirterms.R:56:1 - 2. ├─plotly::ggplotly(plot) - 3. └─plotly:::ggplotly.ggplot(plot) - 4. └─plotly::gg2list(...) - - [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] - Error: Test failures - Execution halted - ``` - -# MiscMetabar - -
- -* Version: 0.9.3 -* GitHub: https://github.com/adrientaudiere/MiscMetabar -* Source code: https://github.com/cran/MiscMetabar -* Date/Publication: 2024-09-09 09:20:01 UTC -* Number of recursive dependencies: 420 - -Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MiscMetabar-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggscatt_pq - > ### Title: Scatterplot with marginal distributions and statistical results - > ### against Hill diversity of phyloseq object - > ### Aliases: ggscatt_pq - > - > ### ** Examples - > - ... - + ) - + } - Loading required namespace: ggstatsplot - Taxa are now in columns. - Cleaning suppress 0 taxa and 0 samples. - Taxa are now in rows. - Joining with `by = join_by(Sample)` - Error in if (new_name %in% existing) { : argument is of length zero - Calls: ggscatt_pq ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(MiscMetabar) - Loading required package: phyloseq - Loading required package: ggplot2 - Loading required package: dada2 - Loading required package: Rcpp - Loading required package: dplyr - ... - 14. └─ggplot2:::add_ggplot(e1, e2, e2name) - 15. ├─ggplot2::ggplot_add(object, p, objectname) - 16. └─ggplot2:::ggplot_add.list(object, p, objectname) - 17. ├─ggplot2::ggplot_add(o, plot, object_name) - 18. └─ggplot2:::ggplot_add.Layer(o, plot, object_name) - 19. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 2 | WARN 0 | SKIP 76 | PASS 82 ] - Error: Test failures - Execution halted - ``` - -# misspi - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/misspi -* Date/Publication: 2023-10-17 09:50:02 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "misspi")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘misspi-Ex.R’ failed - The error most likely occurred in: - - > ### Name: evaliq - > ### Title: Evaluate the Imputation Quality - > ### Aliases: evaliq - > - > ### ** Examples - > - > # A very quick example - ... - > # Default plot - > er.eval <- evaliq(x.true[na.idx], x.est[na.idx]) - `geom_smooth()` using formula = 'y ~ x' - > - > # Interactive plot - > er.eval <- evaliq(x.true[na.idx], x.est[na.idx], interactive = TRUE) - `geom_smooth()` using formula = 'y ~ x' - Error in pm[[2]] : subscript out of bounds - Calls: evaliq -> print -> ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# mixpoissonreg - -
- -* Version: 1.0.0 -* GitHub: https://github.com/vpnsctl/mixpoissonreg -* Source code: https://github.com/cran/mixpoissonreg -* Date/Publication: 2021-03-10 19:50:06 UTC -* Number of recursive dependencies: 139 - -Run `revdepcheck::cloud_details(, "mixpoissonreg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mixpoissonreg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: autoplot.mixpoissonreg - > ### Title: Autoplot Method for 'mixpoissonreg' Objects - > ### Aliases: autoplot.mixpoissonreg autoplot - > - > ### ** Examples - > - > daysabs_prog <- mixpoissonregML(daysabs ~ prog, data = Attendance) - > autoplot(daysabs_prog) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(mixpoissonreg) - > - > test_check("mixpoissonreg") - - Negative Binomial Regression - Expectation-Maximization Algorithm - - ... - 2. └─mixpoissonreg:::autoplot.mixpoissonreg(fit_ml1, nrow = 2) - 3. └─ggplot2:::`+.gg`(...) - 4. └─ggplot2:::add_ggplot(e1, e2, e2name) - 5. ├─ggplot2::ggplot_add(object, p, objectname) - 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) - - [ FAIL 1 | WARN 28 | SKIP 0 | PASS 35 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘influence-mixpoissonreg.Rmd’ - ... - 5 2.747544 -0.2460342 -0.006644830 -0.4252217 -1.269154 - 6 2.746786 -0.2443429 -0.006641383 -0.4268347 -1.269387 - - > plot(fit, which = c(3, 4, 5)) - - > autoplot(fit, which = c(3, 4, 5)) - - ... - - When sourcing ‘tutorial-mixpoissonreg.R’: - Error: argument is of length zero - Execution halted - - ‘influence-mixpoissonreg.Rmd’ using ‘UTF-8’... failed - ‘intervals-mixpoissonreg.Rmd’ using ‘UTF-8’... OK - ‘ml-mixpoissonreg.Rmd’ using ‘UTF-8’... failed - ‘tidyverse-mixpoissonreg.Rmd’ using ‘UTF-8’... failed - ‘tutorial-mixpoissonreg.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘influence-mixpoissonreg.Rmd’ using rmarkdown - ``` - -# mizer +``` +# ggThemeAssist
-* Version: 2.5.1 -* GitHub: https://github.com/sizespectrum/mizer -* Source code: https://github.com/cran/mizer -* Date/Publication: 2024-03-08 23:10:02 UTC -* Number of recursive dependencies: 110 +* Version: 0.1.5 +* GitHub: https://github.com/calligross/ggthemeassist +* Source code: https://github.com/cran/ggThemeAssist +* Date/Publication: 2016-08-13 16:50:55 +* Number of recursive dependencies: 57 -Run `revdepcheck::cloud_details(, "mizer")` for more info +Run `revdepcheck::cloud_details(, "ggThemeAssist")` for more info
## Newly broken -* checking tests ... ERROR +* checking whether package ‘ggThemeAssist’ can be installed ... ERROR ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(mizer) - > - > test_check("mizer") - [ FAIL 10 | WARN 0 | SKIP 5 | PASS 1251 ] - - ... - • plots/plot-spectra.svg - • plots/plot-yield-by-gear.svg - • plots/plot-yield.svg - • plots/plotfishing-mortality.svg - • plots/plotfmort-truncated.svg - • plots/plotpredation-mortality.svg - • plots/plotpredmort-truncated.new.svg - • plots/plotpredmort-truncated.svg - Error: Test failures - Execution halted + Installation failed. + See ‘/tmp/workdir/ggThemeAssist/new/ggThemeAssist.Rcheck/00install.out’ for details. ``` -## In both +## Newly fixed -* checking installed package size ... NOTE +* checking LazyData ... NOTE ``` - installed size is 6.1Mb - sub-directories of 1Mb or more: - doc 1.5Mb - help 1.8Mb + 'LazyData' is specified without a 'data' directory ``` -# mlr3spatiotempcv +## Installation + +### Devel + +``` +* installing *source* package ‘ggThemeAssist’ ... +** package ‘ggThemeAssist’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in is.element("extrafont", installed.packages()[, 1]) : + unused argument (installed.packages()[, 1]) +Error: unable to load R code in package ‘ggThemeAssist’ +Execution halted +ERROR: lazy loading failed for package ‘ggThemeAssist’ +* removing ‘/tmp/workdir/ggThemeAssist/new/ggThemeAssist.Rcheck/ggThemeAssist’ + + +``` +### CRAN + +``` +* installing *source* package ‘ggThemeAssist’ ... +** package ‘ggThemeAssist’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (ggThemeAssist) + + +``` +# ggupset
-* Version: 2.3.1 -* GitHub: https://github.com/mlr-org/mlr3spatiotempcv -* Source code: https://github.com/cran/mlr3spatiotempcv -* Date/Publication: 2024-04-17 12:10:05 UTC -* Number of recursive dependencies: 167 +* Version: 0.4.0 +* GitHub: https://github.com/const-ae/ggupset +* Source code: https://github.com/cran/ggupset +* Date/Publication: 2024-06-24 10:10:04 UTC +* Number of recursive dependencies: 45 -Run `revdepcheck::cloud_details(, "mlr3spatiotempcv")` for more info +Run `revdepcheck::cloud_details(, "ggupset")` for more info
@@ -16989,67 +10196,100 @@ Run `revdepcheck::cloud_details(, "mlr3spatiotempcv")` for more info * checking examples ... ERROR ``` - Running examples in ‘mlr3spatiotempcv-Ex.R’ failed + Running examples in ‘ggupset-Ex.R’ failed The error most likely occurred in: - > ### Name: autoplot.ResamplingCustomCV - > ### Title: Visualization Functions for Non-Spatial CV Methods. - > ### Aliases: autoplot.ResamplingCustomCV plot.ResamplingCustomCV + > ### Name: axis_combmatrix + > ### Title: Convert delimited text labels into a combination matrix axis + > ### Aliases: axis_combmatrix > > ### ** Examples > - > if (mlr3misc::require_namespaces(c("sf", "patchwork"), quietly = TRUE)) { + > library(ggplot2) ... - + - + autoplot(resampling, task) + - + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) - + autoplot(resampling, task, fold_id = 1) - + autoplot(resampling, task, fold_id = c(1, 2)) * - + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) - + } - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Datsun 710 Cyl: 4_Gears: 4 + Hornet 4 Drive Cyl: 6_Gears: 3 + Hornet Sportabout Cyl: 8_Gears: 3 + Valiant Cyl: 6_Gears: 3 + > ggplot(mtcars, aes(x=combined)) + + + geom_bar() + + + axis_combmatrix(sep = "_") + Error in as.unit(e2) : object is not coercible to a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit Execution halted ``` -## In both +# ggVennDiagram + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/gaospecial/ggVennDiagram +* Source code: https://github.com/cran/ggVennDiagram +* Date/Publication: 2024-02-20 08:10:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "ggVennDiagram")` for more info + +
+ +## Newly broken * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘spatiotemp-viz.Rmd’ + when running code in ‘fully-customed.Rmd’ ... + [1] "b" "c" "e" "h" "k" "q" "s" "y" - > knitr::opts_chunk$set(collapse = TRUE, comment = "#>") - > knitr::include_graphics("../man/figures/sptcv_cstf_multiplot.png") + > ggVennDiagram(y, show_intersect = TRUE, set_color = "black") + Warning in geom_text(aes(label = .data$count, text = .data$item), data = region_label) : + Ignoring unknown aesthetics: text + + ... + Ignoring unknown aesthetics: text - When sourcing ‘spatiotemp-viz.R’: - Error: Cannot find the file(s): "../man/figures/sptcv_cstf_multiplot.png" + When sourcing ‘using-ggVennDiagram.R’: + Error: subscript out of bounds Execution halted - ‘mlr3spatiotempcv.Rmd’ using ‘UTF-8’... OK - ‘spatiotemp-viz.Rmd’ using ‘UTF-8’... failed + ‘VennCalculator.Rmd’ using ‘UTF-8’... OK + ‘fully-customed.Rmd’ using ‘UTF-8’... failed + ‘using-ggVennDiagram.Rmd’ using ‘UTF-8’... failed + ‘using-new-shapes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘VennCalculator.Rmd’ using rmarkdown + --- finished re-building ‘VennCalculator.Rmd’ + + --- re-building ‘fully-customed.Rmd’ using rmarkdown ``` +## In both + * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 11.1Mb sub-directories of 1Mb or more: - data 3.5Mb + doc 9.5Mb + help 1.1Mb ``` -# mlr3viz +# Greymodels
-* Version: 0.9.0 -* GitHub: https://github.com/mlr-org/mlr3viz -* Source code: https://github.com/cran/mlr3viz -* Date/Publication: 2024-07-01 12:30:02 UTC -* Number of recursive dependencies: 142 +* Version: 2.0.1 +* GitHub: https://github.com/havishaJ/Greymodels +* Source code: https://github.com/cran/Greymodels +* Date/Publication: 2022-12-05 12:42:35 UTC +* Number of recursive dependencies: 89 -Run `revdepcheck::cloud_details(, "mlr3viz")` for more info +Run `revdepcheck::cloud_details(, "Greymodels")` for more info
@@ -17057,156 +10297,168 @@ Run `revdepcheck::cloud_details(, "mlr3viz")` for more info * checking examples ... ERROR ``` - Running examples in ‘mlr3viz-Ex.R’ failed + Running examples in ‘Greymodels-Ex.R’ failed The error most likely occurred in: - > ### Name: autoplot.OptimInstanceBatchSingleCrit - > ### Title: Plots for Optimization Instances - > ### Aliases: autoplot.OptimInstanceBatchSingleCrit + > ### Name: Plots + > ### Title: plots + > ### Aliases: plots plotrm plotsmv1 plotsmv2 plotsigndgm plots_mdbgm12 > > ### ** Examples > - > if (requireNamespace("mlr3") && requireNamespace("bbotk") && requireNamespace("patchwork")) { + > # Plots - EPGM (1, 1) model ... - INFO [09:22:56.650] [bbotk] 5.884797 2.2371095 -32.51896 - INFO [09:22:56.650] [bbotk] -7.841127 -0.8872557 -91.31148 - INFO [09:22:56.668] [bbotk] Finished optimizing after 20 evaluation(s) - INFO [09:22:56.669] [bbotk] Result: - INFO [09:22:56.670] [bbotk] x1 x2 x_domain y - INFO [09:22:56.670] [bbotk] - INFO [09:22:56.670] [bbotk] 2.582281 -2.940254 9.657379 - Error in identicalUnits(x) : object is not a unit - Calls: print ... assemble_guides -> guides_build -> unit.c -> identicalUnits + + geom_point(data = set4, aes(x = CI, y = y), shape = 23, color = "black") + + + geom_line(data = xy1, aes(x = x, y = y,color = "Raw Data")) + + + geom_line(data = xy2, aes(x = x, y = y,color = "Fitted&Forecasts")) + + + geom_line(data = set3, aes(x = CI, y = y,color = "LowerBound"), linetype=2) + + + geom_line(data = set4, aes(x = CI, y = y,color = "UpperBound"), linetype=2) + + + scale_color_manual(name = "Label",values = colors) + > r <- ggplotly(p) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > if (requireNamespace("testthat", quietly = TRUE)) { - + library("testthat") - + library("mlr3viz") - + test_check("mlr3viz") - + } - Starting 2 test processes - [ FAIL 4 | WARN 1 | SKIP 24 | PASS 84 ] - ... - • TuningInstanceSingleCrit/tisc-surface-grid-50.svg - • TuningInstanceSingleCrit/tisc-surface-regr-lm.svg - • TuningInstanceSingleCrit/tisc-surface.svg - • plot_learner_prediction/learner-prediction-1d-se.svg - • plot_learner_prediction/learner-prediction-binary-prob.svg - • plot_learner_prediction/learner-prediction-binary-response.svg - • plot_learner_prediction/learner-prediction-categorical.svg - • plot_learner_prediction/learner-prediction-prob.svg - Error: Test failures - Execution halted - ``` - -# modeltime.resample +# GWASinspector
-* Version: 0.2.3 -* GitHub: https://github.com/business-science/modeltime.resample -* Source code: https://github.com/cran/modeltime.resample -* Date/Publication: 2023-04-12 15:50:02 UTC -* Number of recursive dependencies: 227 +* Version: 1.7.1 +* GitHub: NA +* Source code: https://github.com/cran/GWASinspector +* Date/Publication: 2024-05-06 18:20:10 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "modeltime.resample")` for more info +Run `revdepcheck::cloud_details(, "GWASinspector")` for more info
## Newly broken -* checking tests ... ERROR +* checking whether package ‘GWASinspector’ can be installed ... WARNING ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > - > # Machine Learning - > library(tidymodels) - ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ── - ✔ broom 1.0.6 ✔ recipes 1.1.0 - ✔ dials 1.3.0 ✔ rsample 1.2.1 - ... - ▆ - 1. ├─m750_models_resample %>% ... at test-modeltime_fit_resamples.R:116:5 - 2. └─modeltime.resample::plot_modeltime_resamples(., .interactive = TRUE) - 3. ├─plotly::ggplotly(g) - 4. └─plotly:::ggplotly.ggplot(g) - 5. └─plotly::gg2list(...) - - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 16 ] - Error: Test failures - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element("hID", names(input.data))': unused argument (names(input.data)) + Note: possible error in 'is.element(toupper(config$supplementaryFiles$allele_ref_std_population), ': unused argument (c("COMMON", "EAS", "AMR", "AFR", "EUR", "SAS")) + Note: possible error in 'is.element("EFFECT", ': unused argument (original.File.Columns.upper) + Note: possible error in 'is.element("EFFECT", ': unused argument (renamed.File.Columns) + Note: possible error in 'is.element("ggplot2", ': unused argument (existing.packages) + Note: possible error in 'is.element("kableExtra", ': unused argument (existing.packages) + Note: possible error in 'is.element("rJava", existing.packages)': unused argument (existing.packages) + Note: possible error in 'is.element("RSQLite", ': unused argument (existing.packages) + Note: possible error in 'is.element("openxlsx", ': unused argument (existing.packages) + ... + Note: possible error in 'is.element("highDiffEAF", ': unused argument (names(dataset)) + Note: possible error in 'is.element("AF", names(dataset))': unused argument (names(dataset)) + Note: possible error in 'is.element("REF_RSID", ': unused argument (names(dataset)) + Note: possible error in 'is.element("EFFECT", ': unused argument (crucial.columns) + Note: possible error in 'is.element(EFFECT_ALL, ': unused argument (c("A", "G", "C", "T")) + Note: possible error in 'is.element(OTHER_ALL, ': unused argument (c("A", "G", "C", "T")) + See ‘/tmp/workdir/GWASinspector/new/GWASinspector.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + add_hIDcolumn: possible error in is.element("hID", names(input.data)): + unused argument (names(input.data)) + checkConfigFile: possible error in + is.element(toupper(config$supplementaryFiles$allele_ref_std_population), + c("COMMON", "EAS", "AMR", "AFR", "EUR", "SAS")): unused argument + (c("COMMON", "EAS", "AMR", "AFR", "EUR", "SAS")) + checkRequiredColumnNames: possible error in is.element("EFFECT", + original.File.Columns.upper): unused argument + (original.File.Columns.upper) + checkRequiredColumnNames: possible error in is.element("EFFECT", + ... + RSQLite::dbListFields(.QC$reference.data, "variants")): unused + argument (RSQLite::dbListFields(.QC$reference.data, "variants")) + validate_Inspector: possible error in is.element(population.Column, + tblFields): unused argument (tblFields) + variable_statistics_post_matching: possible error in is.element("CHR", + names(input.data)): unused argument (names(input.data)) + variantDiscrimination: possible error in is.element(EFFECT_ALL, c("A", + "G", "C", "T")): unused argument (c("A", "G", "C", "T")) + variantDiscrimination: possible error in is.element(OTHER_ALL, c("A", + "G", "C", "T")): unused argument (c("A", "G", "C", "T")) ``` ## In both -* checking dependencies in R code ... NOTE +* checking running R code from vignettes ... ERROR ``` - Namespaces in Imports field not imported from: - ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’ - All declared Imports should be used. + Errors in running code in vignettes: + when running code in ‘GWASinspector.Rmd’ + ... + > knitr::opts_chunk$set(eval = FALSE, results = "hide", + + collapse = TRUE, comment = "#>", results = "asis") + + > install.packages("GWASinspector") + Installing package into ‘/tmp/RtmpR7P8mN/RLIBS_9831403b73’ + (as ‘lib’ is unspecified) + + When sourcing ‘GWASinspector.R’: + Error: trying to use CRAN without setting a mirror + Execution halted + + ‘GWASinspector.Rmd’ using ‘UTF-8’... failed ``` -# moreparty +# GWlasso
-* Version: 0.4 -* GitHub: NA -* Source code: https://github.com/cran/moreparty -* Date/Publication: 2023-11-22 14:30:02 UTC -* Number of recursive dependencies: 165 +* Version: 1.0.1 +* GitHub: https://github.com/nibortolum/GWlasso +* Source code: https://github.com/cran/GWlasso +* Date/Publication: 2024-11-22 09:30:07 UTC +* Number of recursive dependencies: 102 -Run `revdepcheck::cloud_details(, "moreparty")` for more info +Run `revdepcheck::cloud_details(, "GWlasso")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking examples ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘Titanic_example.Rmd’ - ... - 24 Age 57 0.3187270 - 25 Embarked Cherbourg 0.4603041 - [ reached 'max' / getOption("max.print") -- omitted 2 rows ] - - > ggForestEffects(pdep, vline = mean(pred_foret), xlab = "Probability of survival") + - + xlim(c(0, 1)) + Running examples in ‘GWlasso-Ex.R’ failed + The error most likely occurred in: - When sourcing ‘Titanic_example.R’: - Error: `x` must be a vector, not a object. + > ### Name: plot.gwlfit + > ### Title: Plot method for gwlfit object + > ### Aliases: plot.gwlfit + > + > ### ** Examples + > + > + ... + Warning in min(x) : no non-missing arguments to min; returning Inf + Warning in max(x) : no non-missing arguments to max; returning -Inf + Warning in min(d[d > tolerance]) : + no non-missing arguments to min; returning Inf + Warning in min(x) : no non-missing arguments to min; returning Inf + Warning in max(x) : no non-missing arguments to max; returning -Inf + Error in is.element(panel_type, c("x", "y")) : + unused argument (c("x", "y")) + Calls: ... -> draw_panel -> -> render_fg Execution halted - - ‘Titanic_example.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Titanic_example.Rmd’ using rmarkdown ``` -# mosaicCalc +# harbinger
-* Version: 0.6.4 -* GitHub: https://github.com/ProjectMOSAIC/mosaicCalc -* Source code: https://github.com/cran/mosaicCalc -* Date/Publication: 2024-07-26 15:50:02 UTC -* Number of recursive dependencies: 128 +* Version: 1.1.707 +* GitHub: https://github.com/cefet-rj-dal/harbinger +* Source code: https://github.com/cran/harbinger +* Date/Publication: 2024-12-03 20:00:03 UTC +* Number of recursive dependencies: 175 -Run `revdepcheck::cloud_details(, "mosaicCalc")` for more info +Run `revdepcheck::cloud_details(, "harbinger")` for more info
@@ -17214,78 +10466,58 @@ Run `revdepcheck::cloud_details(, "mosaicCalc")` for more info * checking examples ... ERROR ``` - Running examples in ‘mosaicCalc-Ex.R’ failed + Running examples in ‘harbinger-Ex.R’ failed The error most likely occurred in: - > ### Name: box_set - > ### Title: Evenly spaced samples across a one- or two-dim domain - > ### Aliases: box_set + > ### Name: hanr_arima + > ### Title: Anomaly detector using ARIMA. + > ### Aliases: hanr_arima > > ### ** Examples > - > box_set(x*y ~ x & y, domain(x=0:1, y=0:1), n = 4) - ... - [1] 0 - > # a polygon - > poly <- tibble(x = c(1:9, 8:1), y = c(1, 2*(5:3), 2, -1, 17, 9, 8, 2:9)) - > boxes <- box_set(1 ~ x & y, poly, dx = 1) - > gf_polygon(y ~ x, data = poly, color="blue", fill="blue", alpha=0.2) %>% - + gf_rect((y - dy/3) + (y + dy/3) ~ (x - dx/3) + (x + dx/3), - + data = boxes) - Error in if (new_name %in% existing) { : argument is of length zero - Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Calculus_with_R.Rmd’ - ... - - > soln <- integrateODE(SIR, bounds(t = 0:20)) - Solution containing functions S(t), I(t). - - > traj_plot(S(t) ~ I(t), soln, color = "blue") %>% vectorfield_plot(SIR, - + bounds(I = 0:75, S = 60:400), transform = I, npts = 20, alpha = 0.6) - + > library(daltoolbox) ... - - > gf_point(flipper_length_mm ~ body_mass_g, data = palmerpenguins::penguins) - - When sourcing ‘quick-reference.R’: - Error: argument is of length zero + > + > # setting up time series regression model + > model <- hanr_arima() + > + > # fitting the model + > model <- fit(model, dataset$serie) + Error in is.element("drift", names(obj$model$coef)) : + unused argument (names(obj$model$coef)) + Calls: fit -> fit.hanr_arima Execution halted - - ‘Calculus_with_R.Rmd’ using ‘UTF-8’... failed - ‘Instructors.Rmd’ using ‘UTF-8’... failed - ‘quick-reference.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘harbinger’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘Calculus_with_R.Rmd’ using rmarkdown + Found the following significant warnings: + Note: possible error in 'is.element("drift", names(obj$model$coef))': unused argument (names(obj$model$coef)) + See ‘/tmp/workdir/harbinger/new/harbinger.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -## In both - -* checking data for non-ASCII characters ... NOTE +* checking R code for possible problems ... NOTE ``` - Note: found 56 marked UTF-8 strings + fit.hanr_arima: possible error in is.element("drift", + names(obj$model$coef)): unused argument (names(obj$model$coef)) + fit.hcp_cf_arima: possible error in is.element("drift", + names(obj$model$coef)): unused argument (names(obj$model$coef)) ``` -# mosaicData +# HCmodelSets
-* Version: 0.20.4 -* GitHub: https://github.com/ProjectMOSAIC/mosaicData -* Source code: https://github.com/cran/mosaicData -* Date/Publication: 2023-11-05 05:50:02 UTC -* Number of recursive dependencies: 56 +* Version: 1.1.3 +* GitHub: https://github.com/hhhelfer/HCmodelSets +* Source code: https://github.com/cran/HCmodelSets +* Date/Publication: 2023-03-15 18:00:09 UTC +* Number of recursive dependencies: 36 -Run `revdepcheck::cloud_details(, "mosaicData")` for more info +Run `revdepcheck::cloud_details(, "HCmodelSets")` for more info
@@ -17293,47 +10525,53 @@ Run `revdepcheck::cloud_details(, "mosaicData")` for more info * checking examples ... ERROR ``` - Running examples in ‘mosaicData-Ex.R’ failed + Running examples in ‘HCmodelSets-Ex.R’ failed The error most likely occurred in: - > ### Name: Birthdays - > ### Title: US Births in 1969 - 1988 - > ### Aliases: Birthdays + > ### Name: DGP + > ### Title: Data generating process used by Battey, H. S. & Cox, D. R. + > ### (2018). + > ### Aliases: DGP > > ### ** Examples > - > data(Birthdays) - ... - IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test, - quantile, sd, t.test, var - - The following objects are masked from ‘package:base’: - - max, mean, min, prod, range, sample, sum - - Error in if (new_name %in% existing) { : argument is of length zero - Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > ## Generates DGP + > ## Don't show: + > dgp = DGP(s=5, a=3, sigStrength=1, rho=0.9, n=20, intercept=5, noise=1, + + var=1, d=50, DGP.seed = 2019) + Error in is.element(type.response, c("S", "N")) : + unused argument (c("S", "N")) + Calls: DGP Execution halted ``` -## In both +* checking whether package ‘HCmodelSets’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(type.response, ': unused argument (c("S", "N")) + See ‘/tmp/workdir/HCmodelSets/new/HCmodelSets.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` -* checking data for non-ASCII characters ... NOTE +* checking R code for possible problems ... NOTE ``` - Note: found 7 marked UTF-8 strings + DGP: possible error in is.element(type.response, c("S", "N")): unused + argument (c("S", "N")) ``` -# mosaicModel +# healthyR
-* Version: 0.3.0 -* GitHub: NA -* Source code: https://github.com/cran/mosaicModel -* Date/Publication: 2017-09-22 16:21:41 UTC -* Number of recursive dependencies: 157 +* Version: 0.2.2 +* GitHub: https://github.com/spsanderson/healthyR +* Source code: https://github.com/cran/healthyR +* Date/Publication: 2024-07-01 13:20:02 UTC +* Number of recursive dependencies: 146 -Run `revdepcheck::cloud_details(, "mosaicModel")` for more info +Run `revdepcheck::cloud_details(, "healthyR")` for more info
@@ -17342,233 +10580,253 @@ Run `revdepcheck::cloud_details(, "mosaicModel")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘Basics.Rmd’ + when running code in ‘getting-started.Rmd’ ... - + out.width = "45%") - - > mtcars <- mtcars %>% mutate(transmission = ifelse(am, - + "manual", "automatic")) + + .by = "month", .interactive = FALSE) + Warning: Ignoring unknown labels: + • `colour = "Legend"` - > gf_point(mpg ~ hp, color = ~transmission, data = mtcars) + > ts_alos_plt(.data = df_tbl, .date_col = Date, .value_col = Values, + + .by = "month", .interactive = TRUE) - When sourcing ‘Basics.R’: - Error: argument is of length zero + When sourcing ‘getting-started.R’: + Error: subscript out of bounds Execution halted - ‘Basics.Rmd’ using ‘UTF-8’... failed + ‘getting-started.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘Basics.Rmd’ using rmarkdown - - Quitting from lines 66-68 [fuel_intro] (Basics.Rmd) - Error: processing vignette 'Basics.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Basics.Rmd’ - - SUMMARY: processing the following file failed: - ‘Basics.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘getting-started.Rmd’ using rmarkdown ``` ## In both -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Namespaces in Imports field not imported from: - ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’ - All declared Imports should be used. + installed size is 6.6Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 3.7Mb ``` -# mppR +# healthyR.ts
-* Version: 1.5.0 -* GitHub: https://github.com/vincentgarin/mppR -* Source code: https://github.com/cran/mppR -* Date/Publication: 2024-02-22 17:20:02 UTC -* Number of recursive dependencies: 69 +* Version: 0.3.1 +* GitHub: https://github.com/spsanderson/healthyR.ts +* Source code: https://github.com/cran/healthyR.ts +* Date/Publication: 2024-10-11 23:00:03 UTC +* Number of recursive dependencies: 209 -Run `revdepcheck::cloud_details(, "mppR")` for more info +Run `revdepcheck::cloud_details(, "healthyR.ts")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘healthyR.ts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tidy_fft + > ### Title: Tidy Style FFT + > ### Aliases: tidy_fft + > + > ### ** Examples + > + > suppressPackageStartupMessages(library(dplyr)) + ... + > a <- tidy_fft( + + .data = data_tbl, + + .value_col = value, + + .date_col = date_col, + + .harmonics = 3, + + .frequency = 12 + + ) + Error in pm[[2]] : subscript out of bounds + Calls: tidy_fft -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘MPP_ME_QTL_detect.Rmd’ + when running code in ‘using-tidy-fft.Rmd’ ... - F2 -2.9970560 0.18508863 -0.00806081 0.1266095 - F283 10.2417600 1.78749082 -0.04223259 2.0862106 - DK105 0.1792433 0.03829626 NA NA + $ value 112, 118, 132, 129, 121, 135, 148, 148, 136, 119, 104, 118, 1… - > plot_QxEC(Qeff, EC = EC, env_id = c("CIAM", "TUM", - + "INRA", "KWS"), QTL = 2, EC_id = "cum rain", trait_id = "DMY") + > suppressPackageStartupMessages(library(timetk)) - When sourcing ‘MPP_ME_QTL_detect.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + > data_tbl %>% plot_time_series(.date_var = date_col, + + .value = value) + + When sourcing ‘using-tidy-fft.R’: + Error: subscript out of bounds Execution halted - ‘MPP_ME_QTL_detect.Rmd’ using ‘UTF-8’... failed - ‘mppR_gen_vignette.Rmd’ using ‘UTF-8’... OK + ‘getting-started.Rmd’ using ‘UTF-8’... OK + ‘using-tidy-fft.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown + --- re-building ‘getting-started.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + doc 5.3Mb ``` -# MSCMT +# heatmaply
-* Version: 1.4.0 -* GitHub: NA -* Source code: https://github.com/cran/MSCMT -* Date/Publication: 2024-03-19 10:20:02 UTC -* Number of recursive dependencies: 82 +* Version: 1.5.0 +* GitHub: https://github.com/talgalili/heatmaply +* Source code: https://github.com/cran/heatmaply +* Date/Publication: 2023-10-06 20:50:02 UTC +* Number of recursive dependencies: 110 -Run `revdepcheck::cloud_details(, "MSCMT")` for more info +Run `revdepcheck::cloud_details(, "heatmaply")` for more info
## Newly broken +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(heatmaply) + Loading required package: plotly + Loading required package: ggplot2 + + Attaching package: 'ggplot2' + + ... + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─heatmaply:::predict_colors(ggplotly(g), plot_method = "ggplot") + 7. ├─plotly::ggplotly(g) + 8. └─plotly:::ggplotly.ggplot(g) + 9. └─plotly::gg2list(...) + + [ FAIL 58 | WARN 0 | SKIP 0 | PASS 193 ] + Error: Test failures + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘WorkingWithMSCMT.Rmd’ + when running code in ‘heatmaply.Rmd’ ... - (Predictor weights V are standardized by sum(V)=1) - - > library(ggplot2) + > library("heatmaply") + + > library("heatmaply") - > ggplot(res, type = "comparison") + > heatmaply(mtcars) - When sourcing ‘WorkingWithMSCMT.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + When sourcing ‘heatmaply.R’: + Error: subscript out of bounds Execution halted - ‘CheckingSynth.Rmd’ using ‘UTF-8’... OK - ‘UsingTimeSeries.Rmd’ using ‘UTF-8’... OK - ‘WorkingWithMSCMT.Rmd’ using ‘UTF-8’... failed + ‘heatmaply.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... - --- re-building ‘CheckingSynth.Rmd’ using rmarkdown - --- finished re-building ‘CheckingSynth.Rmd’ - - --- re-building ‘UsingTimeSeries.Rmd’ using rmarkdown - --- finished re-building ‘UsingTimeSeries.Rmd’ - - --- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown + --- re-building ‘heatmaply.Rmd’ using rmarkdown - ... - Quitting from lines 156-158 [unnamed-chunk-8] (WorkingWithMSCMT.Rmd) - Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘WorkingWithMSCMT.Rmd’ + Quitting from lines 109-111 [unnamed-chunk-5] (heatmaply.Rmd) + Error: processing vignette 'heatmaply.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘heatmaply.Rmd’ SUMMARY: processing the following file failed: - ‘WorkingWithMSCMT.Rmd’ + ‘heatmaply.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# mstate +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 5.1Mb + ``` + +# heemod
-* Version: 0.3.3 -* GitHub: https://github.com/hputter/mstate -* Source code: https://github.com/cran/mstate -* Date/Publication: 2024-07-11 21:30:06 UTC -* Number of recursive dependencies: 114 +* Version: 1.0.2 +* GitHub: https://github.com/aphp/heemod +* Source code: https://github.com/cran/heemod +* Date/Publication: 2024-09-11 16:00:02 UTC +* Number of recursive dependencies: 139 -Run `revdepcheck::cloud_details(, "mstate")` for more info +Run `revdepcheck::cloud_details(, "heemod")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘mstate-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.Cuminc - > ### Title: Plot method for Cuminc objects - > ### Aliases: plot.Cuminc - > - > ### ** Examples - > - > library(ggplot2) - ... - 4. └─ggplot2:::ggplot_build.ggplot(x) - 5. └─layout$setup(data, plot$data, plot$plot_env) - 6. └─ggplot2 (local) setup(..., self = self) - 7. └─self$coord$setup_params(data) - 8. └─ggplot2 (local) setup_params(..., self = self) - 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) - 10. └─ggplot2:::check_logical(expand) - 11. └─ggplot2:::stop_input_type(...) - 12. └─rlang::abort(message, ..., call = call, arg = arg) - Execution halted - ``` - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘visuals_demo.Rmd’ + when running code in ‘e_probabilistic.Rmd’ ... + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. - > msf.WW <- msfit(object = c1, newdata = WW, trans = tmat) - - > plot(msf.WW) - - > plot(msf.WW, use.ggplot = TRUE) - - When sourcing ‘visuals_demo.R’: - Error: `expand` must be a logical vector, not the number 0. - Execution halted + > bcea <- run_bcea(pm, plot = TRUE, Kmax = 10000) + Loading required namespace: BCEA + No reference selected. Defaulting to first intervention. - ‘visuals_demo.Rmd’ using ‘UTF-8’... failed - ‘Tutorial.Rnw’ using ‘UTF-8’... OK - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘visuals_demo.Rmd’ using rmarkdown + ... + ‘c_homogeneous.Rmd’ using ‘UTF-8’... OK + ‘d_non_homogeneous.Rmd’ using ‘UTF-8’... OK + ‘e_probabilistic.Rmd’ using ‘UTF-8’... failed + ‘f_sensitivity.Rmd’ using ‘UTF-8’... OK + ‘g_heterogeneity.Rmd’ using ‘UTF-8’... OK + ‘h_tabular.Rmd’ using ‘UTF-8’... OK + ‘i_reproduction.Rmd’ using ‘UTF-8’... OK + ‘j_survival.Rmd’ using ‘UTF-8’... OK + ‘j_survival_2_psa.Rmd’ using ‘UTF-8’... OK + ‘k_calibration.Rmd’ using ‘UTF-8’... OK ``` -# mtb +# hesim
-* Version: 0.1.8 -* GitHub: https://github.com/yh202109/mtb -* Source code: https://github.com/cran/mtb -* Date/Publication: 2022-10-20 17:22:35 UTC -* Number of recursive dependencies: 64 +* Version: 0.5.5 +* GitHub: https://github.com/hesim-dev/hesim +* Source code: https://github.com/cran/hesim +* Date/Publication: 2024-09-18 23:10:02 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "mtb")` for more info +Run `revdepcheck::cloud_details(, "hesim")` for more info
@@ -17580,63 +10838,87 @@ Run `revdepcheck::cloud_details(, "mtb")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(mtb) + > library(hesim) > - > test_check("mtb") - [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ + > test_check("hesim") + sample = 1 + sample = 2 + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1121 ] ... - - "yend" [6] - - "xmin" [7] - - "xmax" [8] - - "ymin" [9] - - "ymax" [10] - ... ... ... and 3 more ... + ── Failure ('test-plot.R:95:3'): autoplot.stateprobs() allows confidence intervals ── + p$labels$fill not equal to "strategy_id". + target is NULL, current is character + ── Failure ('test-plot.R:99:3'): autoplot.stateprobs() allows confidence intervals ── + p$labels$fill not equal to "strategy_id". + target is NULL, current is character - [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1121 ] Error: Test failures Execution halted ``` -# mulgar +## In both -
+* checking installed package size ... NOTE + ``` + installed size is 36.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 1.5Mb + doc 2.2Mb + libs 30.8Mb + ``` -* Version: 1.0.2 -* GitHub: https://github.com/dicook/mulgar -* Source code: https://github.com/cran/mulgar -* Date/Publication: 2023-08-25 22:00:02 UTC -* Number of recursive dependencies: 43 +# hmsidwR + +
-Run `revdepcheck::cloud_details(, "mulgar")` for more info +* Version: 1.1.2 +* GitHub: https://github.com/Fgazzelloni/hmsidwR +* Source code: https://github.com/cran/hmsidwR +* Date/Publication: 2024-11-13 15:00:02 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "hmsidwR")` for more info
## Newly broken -* checking examples ... ERROR +* checking running R code from vignettes ... ERROR ``` - Running examples in ‘mulgar-Ex.R’ failed - The error most likely occurred in: + Errors in running code in vignettes: + when running code in ‘hmsidwR.Rmd’ + ... + The following object is masked from ‘package:graphics’: - > ### Name: ggmcbic - > ### Title: Produces an mclust summary plot with ggplot - > ### Aliases: ggmcbic - > - > ### ** Examples - > - > require(mclust) - ... - Type 'citation("mclust")' for citing this R package in publications. - > data(clusters) - > clusters_BIC <- mclustBIC(clusters[,1:5], G=2:6) - > ggmcbic(clusters_BIC) - Warning: Removed 5 rows containing missing values or values outside the scale range - (`geom_line()`). - Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + layout + + + > plotly::ggplotly(id) + + When sourcing ‘hmsidwR.R’: + Error: subscript out of bounds + Execution halted + + ‘hmsidwR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘hmsidwR.Rmd’ using rmarkdown + + Quitting from lines 52-84 [unnamed-chunk-6] (hmsidwR.Rmd) + Error: processing vignette 'hmsidwR.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘hmsidwR.Rmd’ + + SUMMARY: processing the following file failed: + ‘hmsidwR.Rmd’ + + Error: Vignette re-building failed. Execution halted ``` @@ -17644,22 +10926,28 @@ Run `revdepcheck::cloud_details(, "mulgar")` for more info * checking installed package size ... NOTE ``` - installed size is 8.8Mb + installed size is 7.2Mb sub-directories of 1Mb or more: - data 8.5Mb + data 3.0Mb + doc 4.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1686 marked UTF-8 strings ``` -# MultivariateAnalysis +# HVT
-* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/MultivariateAnalysis -* Date/Publication: 2024-04-08 18:40:03 UTC -* Number of recursive dependencies: 128 +* Version: 24.9.1 +* GitHub: https://github.com/Mu-Sigma/HVT +* Source code: https://github.com/cran/HVT +* Date/Publication: 2024-09-11 09:50:02 UTC +* Number of recursive dependencies: 209 -Run `revdepcheck::cloud_details(, "MultivariateAnalysis")` for more info +Run `revdepcheck::cloud_details(, "HVT")` for more info
@@ -17667,152 +10955,154 @@ Run `revdepcheck::cloud_details(, "MultivariateAnalysis")` for more info * checking examples ... ERROR ``` - Running examples in ‘MultivariateAnalysis-Ex.R’ failed + Running examples in ‘HVT-Ex.R’ failed The error most likely occurred in: - > ### Name: ContribuicaoRelativa - > ### Title: Contribuicao das variaveis independentes para o agrupamento - > ### Aliases: ContribuicaoRelativa + > ### Name: clustHVT + > ### Title: Performing Hierarchical Clustering Analysis + > ### Aliases: clustHVT + > ### Keywords: Clustering_Analysis > > ### ** Examples > - > ... - 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) + Ignoring unknown parameters: `check_overlap` + Scale for x is already present. + Adding another scale for x, which will replace the existing scale. + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Warning in geom_polygon(data = boundaryCoords2, aes(x = bp.x, y = bp.y, : + Ignoring unknown aesthetics: text + Error in pm[[2]] : subscript out of bounds + Calls: scoreHVT -> -> ggplotly.ggplot -> gg2list Execution halted ``` -# mxfda +* checking whether package ‘HVT’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(T, unlist(ijresplt))': unused argument (unlist(ijresplt)) + See ‘/tmp/workdir/HVT/new/HVT.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + hvq: possible error in is.element(T, unlist(ijresplt)): unused argument + (unlist(ijresplt)) + ``` + +# hypsoLoop
-* Version: 0.2.1 -* GitHub: https://github.com/julia-wrobel/mxfda -* Source code: https://github.com/cran/mxfda -* Date/Publication: 2024-05-08 11:00:02 UTC -* Number of recursive dependencies: 221 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/hypsoLoop +* Date/Publication: 2022-02-08 09:00:02 UTC +* Number of recursive dependencies: 96 -Run `revdepcheck::cloud_details(, "mxfda")` for more info +Run `revdepcheck::cloud_details(, "hypsoLoop")` for more info
## Newly broken -* checking installed package size ... NOTE +* checking whether package ‘hypsoLoop’ can be installed ... WARNING ``` - installed size is 5.6Mb - sub-directories of 1Mb or more: - data 4.0Mb + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::set_theme’ by ‘sjPlot::set_theme’ when loading ‘hypsoLoop’ + See ‘/tmp/workdir/hypsoLoop/new/hypsoLoop.Rcheck/00install.out’ for details. ``` -# neatmaps +# iCARH
-* Version: 2.1.0 -* GitHub: https://github.com/PhilBoileau/neatmaps -* Source code: https://github.com/cran/neatmaps -* Date/Publication: 2019-05-12 19:10:03 UTC -* Number of recursive dependencies: 99 +* Version: 2.0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/iCARH +* Date/Publication: 2020-08-27 07:50:07 UTC +* Number of recursive dependencies: 121 -Run `revdepcheck::cloud_details(, "neatmaps")` for more info +Run `revdepcheck::cloud_details(, "iCARH")` for more info
## Newly broken -* checking examples ... ERROR +* checking whether package ‘iCARH’ can be installed ... WARNING ``` - Running examples in ‘neatmaps-Ex.R’ failed - The error most likely occurred in: - - > ### Name: consClustResTable - > ### Title: Consensus Cluster Results in a Table - > ### Aliases: consClustResTable - > - > ### ** Examples - > - > # create the data frame using the network, node and edge attributes - ... - > df <- netsDataFrame(network_attr_df, - + node_attr_df, - + edge_df) - > - > # run the neatmap code on df - > neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, - + xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1) - Error in pm[[2]] : subscript out of bounds - Calls: neatmap ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list - Execution halted + Found the following significant warnings: + Note: possible error in 'is.element(unique(paste0("cpd:", ': unused argument (igraph::get.vertex.attribute(x, "name")) + See ‘/tmp/workdir/iCARH/new/iCARH.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -## In both - -* checking installed package size ... NOTE +* checking R code for possible problems ... NOTE ``` - installed size is 6.3Mb + GetDistanceMat : : possible error in + is.element(unique(paste0("cpd:", unlist(metset))), + igraph::get.vertex.attribute(x, "name")): unused argument + (igraph::get.vertex.attribute(x, "name")) ``` -# neatStats +# ICSsmoothing
-* Version: 1.13.3 -* GitHub: https://github.com/gasparl/neatstats -* Source code: https://github.com/cran/neatStats -* Date/Publication: 2022-12-07 20:50:02 UTC -* Number of recursive dependencies: 129 +* Version: 1.2.8 +* GitHub: NA +* Source code: https://github.com/cran/ICSsmoothing +* Date/Publication: 2024-01-10 10:33:21 UTC +* Number of recursive dependencies: 63 -Run `revdepcheck::cloud_details(, "neatStats")` for more info +Run `revdepcheck::cloud_details(, "ICSsmoothing")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘neatStats-Ex.R’ failed - The error most likely occurred in: - - > ### Name: peek_neat - > ### Title: Cursory Summaries and Plots per Group - > ### Aliases: peek_neat - > - > ### ** Examples - > - > + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ICSsmoothing) + Loading required package: polynom + Loading required package: ggplot2 + + Attaching package: 'ggplot2' + ... - 11. │ └─ggplot2:::`+.gg`(...) - 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 13. │ ├─ggplot2::ggplot_add(object, p, objectname) - 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 16. └─base::.handleSimpleError(...) - 17. └─purrr (local) h(simpleError(msg, call)) - 18. └─cli::cli_abort(...) - 19. └─rlang::abort(...) - Execution halted + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_expl_spline.R:95:3'): cics_explicit works correctly. ───────── + `is_spline` not equal to TRUE. + 1 element mismatch + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] + Error: Test failures + Execution halted ``` -# netcom +# incidental
-* Version: 2.1.7 -* GitHub: https://github.com/langendorfr/netcom -* Source code: https://github.com/cran/netcom -* Date/Publication: 2024-06-04 17:50:05 UTC -* Number of recursive dependencies: 103 +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/incidental +* Date/Publication: 2020-09-16 09:50:03 UTC +* Number of recursive dependencies: 66 -Run `revdepcheck::cloud_details(, "netcom")` for more info +Run `revdepcheck::cloud_details(, "incidental")` for more info
@@ -17821,48 +11111,87 @@ Run `revdepcheck::cloud_details(, "netcom")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘tutorial.Rmd’ + when running code in ‘incidental-tutorial.Rmd’ ... - > networks <- c(networks_undisturbed, networks_disturbed) - > comparisons <- netcom::compare(networks, method = "align") + > data_subset = do.call("rbind", model_df_list) - > stats::prcomp(comparisons) %>% ggplot2::autoplot(data = tibble(Kind = c(rep("Undisturbed", - + num_networks), rep("Disturbed", num_networks))), c .... [TRUNCATED] + > ggplot(data_subset, aes(x = Time, y = Reported)) + + + geom_point(color = "coral2", shape = 3) + geom_line(aes(x = Time, + + y = Ihat), color .... [TRUNCATED] - When sourcing ‘tutorial.R’: - Error: argument is of length zero + When sourcing ‘incidental-tutorial.R’: + Error: `x` must be a vector, not a object. Execution halted - ‘tutorial.Rmd’ using ‘UTF-8’... failed + ‘incidental-tutorial.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘tutorial.Rmd’ using rmarkdown + --- re-building ‘incidental-tutorial.Rmd’ using rmarkdown + ``` + +# industRial + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/J-Ramalho/industRial +* Source code: https://github.com/cran/industRial +* Date/Publication: 2021-06-11 09:40:02 UTC +* Number of recursive dependencies: 192 + +Run `revdepcheck::cloud_details(, "industRial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘industRial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: theme_qcc + > ### Title: Custom theme "qcc" for the book industRial Data Science plots + > ### Aliases: theme_qcc + > + > ### ** Examples + > + > library(dplyr) + ... + Backtrace: + ▆ + 1. └─industRial::theme_qcc() + 2. ├─... %+replace% ... + 3. │ └─ggplot2::is.theme(e2) + 4. └─ggplot2::theme(...) + 5. └─lifecycle::deprecate_stop("2.2.0", "theme(panel.margin)", "theme(panel.spacing)") + 6. └─lifecycle:::deprecate_stop0(msg) + 7. └─rlang::cnd_signal(...) + Execution halted ``` ## In both -* checking dependencies in R code ... NOTE +* checking data for non-ASCII characters ... NOTE ``` - Namespaces in Imports field not imported from: - ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’ - All declared Imports should be used. + Note: found 2 marked UTF-8 strings ``` -# NetFACS +# infer
-* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/NetFACS -* Date/Publication: 2022-12-06 17:32:35 UTC -* Number of recursive dependencies: 101 +* Version: 1.0.7 +* GitHub: https://github.com/tidymodels/infer +* Source code: https://github.com/cran/infer +* Date/Publication: 2024-03-25 21:50:02 UTC +* Number of recursive dependencies: 126 -Run `revdepcheck::cloud_details(, "NetFACS")` for more info +Run `revdepcheck::cloud_details(, "infer")` for more info
@@ -17870,59 +11199,71 @@ Run `revdepcheck::cloud_details(, "NetFACS")` for more info * checking examples ... ERROR ``` - Running examples in ‘NetFACS-Ex.R’ failed + Running examples in ‘infer-Ex.R’ failed The error most likely occurred in: - > ### Name: network_conditional - > ### Title: Create a network based on conditional probabilities of dyads of - > ### elements - > ### Aliases: network_conditional + > ### Name: shade_confidence_interval + > ### Title: Add information about confidence interval + > ### Aliases: shade_confidence_interval shade_ci > > ### ** Examples > + > # find the point estimate---mean number of hours worked per week ... - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - invalid font type - Calls: ... drawDetails -> drawDetails.text -> grid.Call.graphics + 10. │ └─ggplot2:::ggplot_add.list(object, p, objectname) + 11. │ ├─ggplot2::ggplot_add(o, plot, object_name) + 12. │ └─ggplot2:::ggplot_add.Layer(o, plot, object_name) + 13. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 14. │ └─vctrs::vec_as_names(names, repair = "check_unique") + 15. │ └─vctrs (local) ``() + 16. │ └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 17. │ └─vctrs:::validate_minimal_names(names, n) + 18. └─rlang::abort(message = message, call = call) Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘netfacs_tutorial.Rmd’ + when running code in ‘infer.Rmd’ ... - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database - Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : - font family 'Arial Narrow' not found in PostScript font database + # A tibble: 1 × 2 + lower_ci upper_ci + + 1 40.1 42.7 - When sourcing ‘netfacs_tutorial.R’: - Error: invalid font type + > visualize(t_dist) + shade_confidence_interval(theor_ci) + + ... + When sourcing ‘observed_stat_examples.R’: + Error: Names repair functions can't return `NA` values. Execution halted - ‘netfacs_tutorial.Rmd’ using ‘UTF-8’... failed + ‘anova.Rmd’ using ‘UTF-8’... OK + ‘chi_squared.Rmd’ using ‘UTF-8’... OK + ‘infer.Rmd’ using ‘UTF-8’... failed + ‘observed_stat_examples.Rmd’ using ‘UTF-8’... failed + ‘paired.Rmd’ using ‘UTF-8’... OK + ‘t_test.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘anova.Rmd’ using rmarkdown ``` -# neuroUp +# inferCSN
-* Version: 0.3.1 -* GitHub: https://github.com/eduardklap/neuroUp -* Source code: https://github.com/cran/neuroUp -* Date/Publication: 2024-08-28 08:20:05 UTC -* Number of recursive dependencies: 82 +* Version: 1.0.8 +* GitHub: https://github.com/mengxu98/inferCSN +* Source code: https://github.com/cran/inferCSN +* Date/Publication: 2024-08-24 05:30:02 UTC +* Number of recursive dependencies: 199 -Run `revdepcheck::cloud_details(, "neuroUp")` for more info +Run `revdepcheck::cloud_details(, "inferCSN")` for more info
@@ -17930,102 +11271,98 @@ Run `revdepcheck::cloud_details(, "neuroUp")` for more info * checking examples ... ERROR ``` - Running examples in ‘neuroUp-Ex.R’ failed + Running examples in ‘inferCSN-Ex.R’ failed The error most likely occurred in: - > ### Name: estim_corr - > ### Title: Estimate correlations - > ### Aliases: estim_corr + > ### Name: plot_dynamic_networks + > ### Title: Plot dynamic networks + > ### Aliases: plot_dynamic_networks > > ### ** Examples > - > data_gambling <- gambling + > data("example_matrix") ... - 8 100 -0.0787 -0.271 0.120 2 NA - 9 140 -0.0555 -0.219 0.111 2 NA - 10 221 -0.0405 -0.172 0.0920 2 NA - # ℹ 45 more rows - - $fig_corr - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + + ) + > + > plot_dynamic_networks( + + network, + + celltypes_order = celltypes_order, + + plot_type = "ggplotly" + + ) + Error in pm[[2]] : subscript out of bounds + Calls: plot_dynamic_networks -> -> ggplotly.ggplot -> gg2list Execution halted ``` -* checking tests ... ERROR +## In both + +* checking installed package size ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files - ... - 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ] - Deleting unused snapshots: - • estim_corr/create-fig-corr-nozero.svg - • estim_diff/create-fig-cohen-s-d.svg - • estim_diff/create-fig-d-nozero.svg - • estim_diff/create-fig-nozero.svg - Error: Test failures - Execution halted + installed size is 22.5Mb + sub-directories of 1Mb or more: + data 2.0Mb + libs 19.9Mb ``` +# injurytools + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/lzumeta/injurytools +* Source code: https://github.com/cran/injurytools +* Date/Publication: 2023-11-14 17:20:05 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "injurytools")` for more info + +
+ +## Newly broken + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘neuroUp.Rmd’ + when running code in ‘model-injury-data-ii.Rmd’ ... - > set.seed(1234) - - > feedback_estim <- estim_diff(feedback_data, c("mfg_learning", - + "mfg_application"), 20:271, 20, "Feedback middle frontal gyrus") + seasonb=2018/2019 19 17 106 84 165 - > feedback_estim$fig_diff + > ggsurvplot(fit, data = injd_sub, palette = c("#E7B800", + + "#2E9FDF")) + xlab("Time [calendar days]") + ylab(expression("Survival probability ( ..." ... [TRUNCATED] + Warning in eval(ei, envir) : + Incompatible methods ("+.ggsurv", "+.gg") for "+" - When sourcing ‘neuroUp.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + When sourcing ‘model-injury-data-ii.R’: + Error: non-numeric argument to binary operator Execution halted - ‘neuroUp.Rmd’ using ‘UTF-8’... failed + ‘estimate-epi-measures.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-i.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-ii.Rmd’ using ‘UTF-8’... failed + ‘prepare-injury-data.Rmd’ using ‘UTF-8’... OK + ‘visualize-injury-data.Rmd’ using ‘UTF-8’... OK ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘neuroUp.Rmd’ using rmarkdown - - Quitting from lines 92-93 [unnamed-chunk-5] (neuroUp.Rmd) - Error: processing vignette 'neuroUp.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘neuroUp.Rmd’ - - SUMMARY: processing the following file failed: - ‘neuroUp.Rmd’ + --- re-building ‘estimate-epi-measures.Rmd’ using rmarkdown + --- finished re-building ‘estimate-epi-measures.Rmd’ - Error: Vignette re-building failed. - Execution halted + --- re-building ‘model-injury-data-i.Rmd’ using rmarkdown ``` -# NHSRplotthedots +# inTextSummaryTable
-* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/NHSRplotthedots -* Date/Publication: 2021-11-03 20:20:10 UTC -* Number of recursive dependencies: 88 +* Version: 3.3.3 +* GitHub: https://github.com/openanalytics/inTextSummaryTable +* Source code: https://github.com/cran/inTextSummaryTable +* Date/Publication: 2024-06-12 18:30:02 UTC +* Number of recursive dependencies: 112 -Run `revdepcheck::cloud_details(, "NHSRplotthedots")` for more info +Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info
@@ -18033,91 +11370,268 @@ Run `revdepcheck::cloud_details(, "NHSRplotthedots")` for more info * checking tests ... ERROR ``` - Running ‘spelling.R’ Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(NHSRplotthedots) + > library(inTextSummaryTable) > - > test_check("NHSRplotthedots") - [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + > test_check("inTextSummaryTable") + [ FAIL 59 | WARN 0 | SKIP 0 | PASS 881 ] + ══ Failed tests ════════════════════════════════════════════════════════════════ ... + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─inTextSummaryTable::subjectProfileSummaryPlot(...) + 7. ├─base::do.call(plyr::rbind.fill, ggplot_build(gg)$data) + 8. └─plyr (local) ``(``, ``) + 9. └─plyr:::output_template(dfs, nrows) + 10. └─plyr:::allocate_column(df[[var]], nrows, dfs, var) - `actual$type` is absent - `expected$type` is a character vector ('type') - - `actual$text` is absent - `expected$text` is a character vector ('text') - - [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + [ FAIL 59 | WARN 0 | SKIP 0 | PASS 881 ] Error: Test failures Execution halted ``` +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘inTextSummaryTable-aesthetics.Rmd’ + ... + > subjectProfileSummaryPlot(data = summaryTable, xVar = "visit", + + colorVar = "TRT") + + When sourcing ‘inTextSummaryTable-aesthetics.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 2nd layer. + Caused by error in `check_aesthetics()`: + ... + ✖ Fix the following mappings: `size`. + Execution halted + + ‘inTextSummaryTable-advanced.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-aesthetics.Rmd’ using ‘UTF-8’... failed + ‘inTextSummaryTable-createTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-exportTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-introduction.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-standardTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-visualization.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown + --- finished re-building ‘inTextSummaryTable-advanced.Rmd’ + + --- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown + + Quitting from lines 211-224 [aesthetics-defaultsVisualization] (inTextSummaryTable-aesthetics.Rmd) + Error: processing vignette 'inTextSummaryTable-aesthetics.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 2nd layer. + ... + ! Aesthetics must be either length 1 or the same as the data (28). + ✖ Fix the following mappings: `size`. + --- failed re-building ‘inTextSummaryTable-visualization.Rmd’ + + SUMMARY: processing the following files failed: + ‘inTextSummaryTable-aesthetics.Rmd’ + ‘inTextSummaryTable-visualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + ## In both -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Namespaces in Imports field not imported from: - ‘NHSRdatasets’ ‘grid’ ‘utils’ - All declared Imports should be used. + installed size is 10.3Mb + sub-directories of 1Mb or more: + doc 9.7Mb ``` -# nichetools +# inti
-* Version: 0.3.1 -* GitHub: https://github.com/benjaminhlina/nichetools -* Source code: https://github.com/cran/nichetools -* Date/Publication: 2024-09-06 17:00:02 UTC -* Number of recursive dependencies: 119 +* Version: 0.6.6 +* GitHub: https://github.com/flavjack/inti +* Source code: https://github.com/cran/inti +* Date/Publication: 2024-09-03 18:00:02 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "nichetools")` for more info +Run `revdepcheck::cloud_details(, "inti")` for more info
## Newly broken +* checking whether package ‘inti’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(variable, ': unused argument (colums_to_recode) + See ‘/tmp/workdir/inti/new/inti.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + metamorphosis : rename_levels: possible error in is.element(variable, + colums_to_recode): unused argument (colums_to_recode) + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘inti-Ex.R’ failed + The error most likely occurred in: + + > ### Name: H2cal + > ### Title: Broad-sense heritability in plant breeding + > ### Aliases: H2cal + > + > ### ** Examples + > + > + ... + + , fixed.model = "0 + (1|bloque) + geno" + + , random.model = "1 + (1|bloque) + (1|geno)" + + , emmeans = TRUE + + , plot_diag = FALSE + + , outliers.rm = TRUE + + ) + Error in initializePtr() : + function 'cholmod_factor_ldetA' not provided by package 'Matrix' + Calls: H2cal ... initialize -> -> initializePtr -> .Call + Execution halted + ``` + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘using-nichetools-with-the-package-SIBER.Rmd’ + when running code in ‘heritability.Rmd’ ... - + option = "A", alpha = 0.75) + > library(inti) - > ggplot() + stat_pointinterval(data = bays_95_overlap, - + aes(x = group_1, y = prop_overlap, point_fill = group_2), - + interval_colour = "gre ..." ... [TRUNCATED] + > dt <- potato - When sourcing ‘using-nichetools-with-the-package-SIBER.R’: - Error: unused argument (theme = list(list("black", 0.681818181818182, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.681818181818182, 1, TRUE), list("", "plain", "black", 15, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.681818181818182, 0.681818181818182, 1, 1, "", 5.27189705271897, 2.04545454545455, 19, TRUE), 7.5, c(7.5, 7.5, 7.5, 7.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, - NULL, c(3.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + > hr <- H2cal(data = dt, trait = "stemdw", gen.name = "geno", + + rep.n = 5, fixed.model = "0 + (1|bloque) + geno", random.model = "1 + (1|bloque) ..." ... [TRUNCATED] + + ... + When sourcing ‘heritability.R’: + Error: function 'cholmod_factor_ldetA' not provided by package 'Matrix' Execution halted - ‘using-nichetools-with-the-package-SIBER.Rmd’ using ‘UTF-8’... failed - ‘using-nichetools-with-the-package-nicheROVER.Rmd’ using ‘UTF-8’... OK + ‘apps.Rmd’ using ‘UTF-8’... OK + ‘heritability.Rmd’ using ‘UTF-8’... failed + ‘policy.Rmd’ using ‘UTF-8’... OK + ‘rticles.Rmd’ using ‘UTF-8’... OK + ‘tarpuy.Rmd’ using ‘UTF-8’... OK + ‘yupana.Rmd’ using ‘UTF-8’... OK ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘using-nichetools-with-the-package-SIBER.Rmd’ using rmarkdown + --- re-building ‘apps.Rmd’ using rmarkdown + --- finished re-building ‘apps.Rmd’ + + --- re-building ‘heritability.Rmd’ using rmarkdown + + Quitting from lines 105-116 [unnamed-chunk-2] (heritability.Rmd) + Error: processing vignette 'heritability.Rmd' failed with diagnostics: + function 'cholmod_factor_ldetA' not provided by package 'Matrix' + --- failed re-building ‘heritability.Rmd’ + ... + --- finished re-building ‘tarpuy.Rmd’ + + --- re-building ‘yupana.Rmd’ using rmarkdown + --- finished re-building ‘yupana.Rmd’ + + SUMMARY: processing the following file failed: + ‘heritability.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# inventorize + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "inventorize")` for more info + +
+ +## Newly broken + +* checking whether package ‘inventorize’ can be installed ... ERROR ``` + Installation failed. + See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in pm[[2]] : subscript out of bounds +Error: unable to load R code in package ‘inventorize’ +Execution halted +ERROR: lazy loading failed for package ‘inventorize’ +* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ + + +``` +### CRAN + +``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Warning in qgamma(service_level, alpha, beta) : NaNs produced +Warning in qgamma(service_level, alpha, beta) : NaNs produced +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (inventorize) -# NIMAA + +``` +# IPV
-* Version: 0.2.1 -* GitHub: https://github.com/jafarilab/NIMAA -* Source code: https://github.com/cran/NIMAA -* Date/Publication: 2022-04-11 14:12:45 UTC -* Number of recursive dependencies: 177 +* Version: 1.0.0 +* GitHub: https://github.com/NilsPetras/IPV +* Source code: https://github.com/cran/IPV +* Date/Publication: 2022-09-30 15:00:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "NIMAA")` for more info +Run `revdepcheck::cloud_details(, "IPV")` for more info
@@ -18125,117 +11639,74 @@ Run `revdepcheck::cloud_details(, "NIMAA")` for more info * checking examples ... ERROR ``` - Running examples in ‘NIMAA-Ex.R’ failed + Running examples in ‘IPV-Ex.R’ failed The error most likely occurred in: - > ### Name: extractSubMatrix - > ### Title: Extract the non-missing submatrices from a given matrix. - > ### Aliases: extractSubMatrix + > ### Name: nested_chart + > ### Title: Nested Chart + > ### Aliases: nested_chart > > ### ** Examples > - > # load part of the beatAML data + > # as simple as that ... - + row.vars = "inhibitor") - binmatnest.temperature - 13.21221 - Size of Square: 66 rows x 66 columns - Size of Rectangular_row: 6 rows x 105 columns - Size of Rectangular_col: 99 rows x 2 columns - Size of Rectangular_element_max: 59 rows x 79 columns - Error in pm[[2]] : subscript out of bounds - Calls: extractSubMatrix ... plotSubmatrix -> print -> -> ggplotly.ggplot -> gg2list + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 8. └─vctrs::vec_as_names(names, repair = "check_unique") + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_cannot_be_empty(names, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(NIMAA) - Warning message: - In check_dep_version() : ABI version mismatch: - lme4 was built with Matrix ABI version 1 - Current Matrix ABI version is 0 - Please re-install lme4 from source or restore original 'Matrix' package - ... - 1. └─NIMAA::extractSubMatrix(...) at test-extract-nonmissing-submatrix.R:5:3 - 2. └─NIMAA:::plotSubmatrix(...) - 3. ├─base::print(plotly::ggplotly(p)) - 4. ├─plotly::ggplotly(p) - 5. └─plotly:::ggplotly.ggplot(p) - 6. └─plotly::gg2list(...) - - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 7 ] - Error: Test failures - Execution halted - ``` - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘NIMAA-vignette.Rmd’ + when running code in ‘ipv-vignette.Rmd’ ... + Facet circle radius set to 0.211 based on the data. + cor_spacing set to 0.193 based on the data. + Relative scaling set to 3.78 based on the data. + Axis tick set to 0.1 based on the data. + dist_construct_label set to 0.5 based on the data. - > beatAML_incidence_matrix <- plotIncMatrix(x = beatAML_data, - + index_nominal = c(2, 1), index_numeric = 3, print_skim = FALSE, - + plot_weigh .... [TRUNCATED] - - Na/missing values Proportion: 0.2603 - - When sourcing ‘NIMAA-vignette.R’: - Error: subscript out of bounds + When sourcing ‘ipv-vignette.R’: + Error: Names can't be empty. + ✖ Empty name found at location 4. Execution halted - ‘NIMAA-vignette.Rmd’ using ‘UTF-8’... failed + ‘ipv-vignette.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown - - Quitting from lines 49-57 [plotIncMatrix function] (NIMAA-vignette.Rmd) - Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics: - subscript out of bounds - --- failed re-building ‘NIMAA-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘NIMAA-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘ipv-vignette.Rmd’ using rmarkdown ``` ## In both * checking installed package size ... NOTE ``` - installed size is 6.5Mb + installed size is 8.0Mb sub-directories of 1Mb or more: - data 2.0Mb - doc 4.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 24 marked UTF-8 strings + data 7.0Mb ``` -# nonmem2R +# IRon
-* Version: 0.2.5 -* GitHub: NA -* Source code: https://github.com/cran/nonmem2R -* Date/Publication: 2024-03-11 17:30:02 UTC -* Number of recursive dependencies: 64 +* Version: 0.1.4 +* GitHub: https://github.com/nunompmoniz/IRon +* Source code: https://github.com/cran/IRon +* Date/Publication: 2023-01-20 07:20:06 UTC +* Number of recursive dependencies: 84 -Run `revdepcheck::cloud_details(, "nonmem2R")` for more info +Run `revdepcheck::cloud_details(, "IRon")` for more info
@@ -18243,66 +11714,49 @@ Run `revdepcheck::cloud_details(, "nonmem2R")` for more info * checking examples ... ERROR ``` - Running examples in ‘nonmem2R-Ex.R’ failed + Running examples in ‘IRon-Ex.R’ failed The error most likely occurred in: - > ### Name: vpcfig2 - > ### Title: Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) - > ### generated VPC files (ggplot2-version). - > ### Aliases: vpcfig2 + > ### Name: sera + > ### Title: Squared Error-Relevance Area (SERA) + > ### Aliases: sera > > ### ** Examples > + > library(IRon) ... - VPC based on files: - /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat - and - /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv - Facetting was set using: - facet_wrap(~strata) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + 16. │ └─self$stat$setup_params(data, self$stat_params) + 17. │ └─ggplot2 (local) setup_params(...) + 18. │ └─base::match.fun(method) + 19. │ └─base::get(as.character(FUN), mode = "function", envir = envir) + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘VPCvignette.Rmd’ - ... - VPC based on files: - /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat - and - /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv - Facetting was set using: - facet_wrap(~strata) - - When sourcing ‘VPCvignette.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘GOFvignette.Rmd’ using ‘UTF-8’... OK - ‘VPCvignette.Rmd’ using ‘UTF-8’... failed - ``` +## In both -* checking re-building of vignette outputs ... NOTE +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘GOFvignette.Rmd’ using rmarkdown + installed size is 6.7Mb + sub-directories of 1Mb or more: + data 6.5Mb ``` -# nphRCT +# isoorbi
-* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/nphRCT -* Date/Publication: 2024-06-27 12:30:02 UTC -* Number of recursive dependencies: 120 +* Version: 1.3.1 +* GitHub: https://github.com/isoverse/isoorbi +* Source code: https://github.com/cran/isoorbi +* Date/Publication: 2024-08-27 05:10:03 UTC +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "nphRCT")` for more info +Run `revdepcheck::cloud_details(, "isoorbi")` for more info
@@ -18311,47 +11765,76 @@ Run `revdepcheck::cloud_details(, "nphRCT")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘explanation.Rmd’ + when running code in ‘dual_inlet.Rmd’ ... + |20230518_05_USGS32_vs_USGS34 | 16| 7|reference |changeover | NA| 10695| 11020| 65.019| 66.994| + |20230518_05_USGS32_vs_USGS34 | 17| 7|reference |data | NA| 11025| 12335| 67.025| 74.985| - > km <- survfit(Surv(time, event) ~ arm, data = dat) - - > p_km <- survminer::ggsurvplot(km, data = dat, risk.table = TRUE, - + break.x.by = 6, legend.title = "", xlab = "Time (months)", - + ylab = "Ov ..." ... [TRUNCATED] + > orbi_plot_raw_data(df_w_blocks, isotopocules = "15N", + + y = ions.incremental) - When sourcing ‘explanation.R’: - Error: argument is of length zero + When sourcing ‘dual_inlet.R’: + Error: Names can't be empty. + ✖ Empty name found at location 1. Execution halted - ‘explanation.Rmd’ using ‘UTF-8’... failed - ‘weighted_log_rank_tests.Rmd’ using ‘UTF-8’... OK + ‘dual_inlet.Rmd’ using ‘UTF-8’... failed + ‘flow_injection.Rmd’ using ‘UTF-8’... OK + ‘isoxl_demo.Rmd’ using ‘UTF-8’... OK + ‘quick_start.Rmd’ using ‘UTF-8’... OK + ‘shot_noise.Rmd’ using ‘UTF-8’... OK ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘explanation.Rmd’ using rmarkdown - - Quitting from lines 44-73 [unnamed-chunk-1] (explanation.Rmd) - Error: processing vignette 'explanation.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘explanation.Rmd’ - - --- re-building ‘weighted_log_rank_tests.Rmd’ using rmarkdown + --- re-building ‘dual_inlet.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + doc 2.0Mb + extdata 3.3Mb ``` -# nprobust +# jenga
-* Version: 0.4.0 +* Version: 1.3.0 * GitHub: NA -* Source code: https://github.com/cran/nprobust -* Date/Publication: 2020-08-26 10:40:02 UTC -* Number of recursive dependencies: 30 +* Source code: https://github.com/cran/jenga +* Date/Publication: 2022-08-18 08:10:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "jenga")` for more info + +
+ +## Newly broken + +* checking whether package ‘jenga’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::is.scale’ by ‘greybox::is.scale’ when loading ‘jenga’ + See ‘/tmp/workdir/jenga/new/jenga.Rcheck/00install.out’ for details. + ``` + +# karel + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/mpru/karel +* Source code: https://github.com/cran/karel +* Date/Publication: 2022-03-26 21:50:02 UTC +* Number of recursive dependencies: 89 -Run `revdepcheck::cloud_details(, "nprobust")` for more info +Run `revdepcheck::cloud_details(, "karel")` for more info
@@ -18359,43 +11842,73 @@ Run `revdepcheck::cloud_details(, "nprobust")` for more info * checking examples ... ERROR ``` - Running examples in ‘nprobust-Ex.R’ failed + Running examples in ‘karel-Ex.R’ failed The error most likely occurred in: - > ### Name: nprobust.plot - > ### Title: Graphical Presentation of Results from 'nprobust' Package. - > ### Aliases: nprobust.plot + > ### Name: acciones + > ### Title: Acciones que Karel puede realizar + > ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso + > ### girar_derecha darse_vuelta > > ### ** Examples > - > x <- runif(500) - > y <- sin(4*x) + rnorm(500) - > est <- lprobust(y,x) - > nprobust.plot(est) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + ... + 1. └─karel::ejecutar_acciones() + 2. ├─base::suppressWarnings(...) + 3. │ └─base::withCallingHandlers(...) + 4. ├─gganimate::animate(...) + 5. └─gganimate:::animate.gganim(...) + 6. └─args$renderer(frames_vars$frame_source, args$fps) + 7. └─gganimate:::png_dim(frames[1]) + 8. └─cli::cli_abort("Provided file ({file}) does not exist") + 9. └─rlang::abort(...) Execution halted ``` +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(karel) + > + > test_check("karel") + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 5. ├─gganimate::animate(...) + 6. └─gganimate:::animate.gganim(...) + 7. └─args$renderer(frames_vars$frame_source, args$fps) + 8. └─gganimate:::png_dim(frames[1]) + 9. └─cli::cli_abort("Provided file ({file}) does not exist") + 10. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + Error: Test failures + Execution halted + ``` + ## In both -* checking C++ specification ... NOTE +* checking dependencies in R code ... NOTE ``` - Specified C++11: please drop specification unless essential + Namespace in Imports field not imported from: ‘gifski’ + All declared Imports should be used. ``` -# nzelect +# kDGLM
-* Version: 0.4.0 -* GitHub: NA -* Source code: https://github.com/cran/nzelect -* Date/Publication: 2017-10-02 20:35:23 UTC -* Number of recursive dependencies: 95 +* Version: 1.2.0 +* GitHub: https://github.com/silvaneojunior/kDGLM +* Source code: https://github.com/cran/kDGLM +* Date/Publication: 2024-05-25 09:50:03 UTC +* Number of recursive dependencies: 136 -Run `revdepcheck::cloud_details(, "nzelect")` for more info +Run `revdepcheck::cloud_details(, "kDGLM")` for more info
@@ -18403,149 +11916,97 @@ Run `revdepcheck::cloud_details(, "nzelect")` for more info * checking examples ... ERROR ``` - Running examples in ‘nzelect-Ex.R’ failed + Running examples in ‘kDGLM-Ex.R’ failed The error most likely occurred in: - > ### Name: polls - > ### Title: New Zealand Opinion Polls - > ### Aliases: polls - > ### Keywords: datasets + > ### Name: forecast.fitted_dlm + > ### Title: Auxiliary function for forecasting + > ### Aliases: forecast.fitted_dlm > > ### ** Examples > + > ... - ℹ This can happen when ggplot fails to infer the correct grouping structure in - the data. - ℹ Did you forget to specify a `group` aesthetic or to convert a numerical - variable into a factor? - Warning: Removed 159 rows containing missing values or values outside the scale range - (`geom_line()`). - Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘README.Rmd’ - ... - > proportions <- nzge %>% filter(election_year == 2014) %>% - + group_by(voting_place, voting_type) %>% summarise(`proportion Labour` = sum(votes[p .... [TRUNCATED] - `summarise()` has grouped output by 'voting_place'. You can override using the - `.groups` argument. - - > ggpairs(proportions, aes(colour = voting_type), columns = 3:5) - - When sourcing ‘README.R’: - Error: argument is of length zero - Execution halted - - ‘README.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘README.Rmd’ using rmarkdown - - Quitting from lines 64-82 [unnamed-chunk-3] (README.Rmd) - Error: processing vignette 'README.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘README.Rmd’ - - SUMMARY: processing the following file failed: - ‘README.Rmd’ - - Error: Vignette re-building failed. + Warning: `aes_string()` was deprecated in ggplot2 3.0.0. + ℹ Please use tidy evaluation idioms with `aes()`. + ℹ See also `vignette("ggplot2-in-packages")` for more information. + ℹ The deprecated feature was likely used in the kDGLM package. + Please report the issue at . + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Error in pm[[2]] : subscript out of bounds + Calls: forecast ... lapply -> -> ggplotly.ggplot -> gg2list Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.3Mb - sub-directories of 1Mb or more: - data 5.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6409 marked UTF-8 strings - ``` - -# OBIC +# Keyboard
-* Version: 3.0.3 -* GitHub: https://github.com/AgroCares/Open-Bodem-Index-Calculator -* Source code: https://github.com/cran/OBIC -* Date/Publication: 2024-09-09 08:30:02 UTC -* Number of recursive dependencies: 75 +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/Keyboard +* Date/Publication: 2022-08-11 10:10:17 UTC +* Number of recursive dependencies: 30 -Run `revdepcheck::cloud_details(, "OBIC")` for more info +Run `revdepcheck::cloud_details(, "Keyboard")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking examples ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘obic_workability.Rmd’ - ... - > gg2 <- ggplot(data = dt, aes(x = field, fill = field)) + - + geom_col(aes(y = I_P_WO)) + theme_bw() + theme(axis.text = element_text(size = 10, - .... [TRUNCATED] + Running examples in ‘Keyboard-Ex.R’ failed + The error most likely occurred in: + + > ### Name: select.mtd.comb.kb + > ### Title: Maximum Tolerated Dose (MTD) Selection for Drug-combination + > ### Trials + > ### Aliases: select.mtd.comb.kb + > + > ### ** Examples + > + ... + 0.15 0.19 0.27 NA NA + NA NA 0.50 NA NA - > (gg | gg2) + plot_layout(guides = "collect") + plot_annotation(caption = "Baseline workability scores.", - + theme = theme(plot.caption = element .... [TRUNCATED] + NOTE: no estimate is provided for the doses at which no patient was treated. - When sourcing ‘obic_workability.R’: - Error: object is not a unit + > plot_kb(sel.comb) + Error in is.element(strpattern, c("none", names(objectPlot))) : + unused argument (c("none", names(objectPlot))) + Calls: plot_kb Execution halted - - ‘description-of-the-columns.Rmd’ using ‘UTF-8’... OK - ‘obic_introduction.Rmd’ using ‘UTF-8’... OK - ‘obic_score_aggregation.Rmd’ using ‘UTF-8’... OK - ‘obic_water_functions.Rmd’ using ‘UTF-8’... OK - ‘obic_workability.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE +* checking whether package ‘Keyboard’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘description-of-the-columns.Rmd’ using rmarkdown - --- finished re-building ‘description-of-the-columns.Rmd’ - - --- re-building ‘obic_introduction.Rmd’ using rmarkdown + Found the following significant warnings: + Note: possible error in 'is.element(strpattern, ': unused argument (c("none", names(objectPlot))) + See ‘/tmp/workdir/Keyboard/new/Keyboard.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -## In both - -* checking installed package size ... NOTE +* checking R code for possible problems ... NOTE ``` - installed size is 6.0Mb - sub-directories of 1Mb or more: - data 4.0Mb - doc 1.4Mb + plot_kb: possible error in is.element(strpattern, c("none", + names(objectPlot))): unused argument (c("none", names(objectPlot))) ``` -# oceanic +# latentcor
-* Version: 0.1.7 +* Version: 2.0.1 * GitHub: NA -* Source code: https://github.com/cran/oceanic -* Date/Publication: 2024-06-11 03:40:02 UTC -* Number of recursive dependencies: 52 +* Source code: https://github.com/cran/latentcor +* Date/Publication: 2022-09-05 20:50:02 UTC +* Number of recursive dependencies: 142 -Run `revdepcheck::cloud_details(, "oceanic")` for more info +Run `revdepcheck::cloud_details(, "latentcor")` for more info
@@ -18553,54 +12014,40 @@ Run `revdepcheck::cloud_details(, "oceanic")` for more info * checking examples ... ERROR ``` - Running examples in ‘oceanic-Ex.R’ failed + Running examples in ‘latentcor-Ex.R’ failed The error most likely occurred in: - > ### Name: dotplot - > ### Title: dotplot - > ### Aliases: dotplot + > ### Name: latentcor + > ### Title: Estimate latent correlation for mixed types. + > ### Aliases: latentcor > > ### ** Examples > - > dotplot(141,23) + > # Example 1 - truncated data type, same type for all variables ... - 4. └─ggplot2:::ggplot_build.ggplot(x) - 5. └─layout$setup(data, plot$data, plot$plot_env) - 6. └─ggplot2 (local) setup(..., self = self) - 7. └─self$coord$setup_params(data) - 8. └─ggplot2 (local) setup_params(..., self = self) - 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) - 10. └─ggplot2:::check_logical(expand) - 11. └─ggplot2:::stop_input_type(...) - 12. └─rlang::abort(message, ..., call = call, arg = arg) + > R_approx = latentcor(X = X, types = "tru", method = "approx")$R + > proc.time() - start_time + user system elapsed + 0.018 0.000 0.017 + > # Heatmap for latent correlation matrix. + > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx", + + showplot = TRUE)$plotR + Error in pm[[2]] : subscript out of bounds + Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.1Mb - sub-directories of 1Mb or more: - data 8.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1242 marked UTF-8 strings - ``` - -# oddsratio +# lcars
-* Version: 2.0.1 -* GitHub: https://github.com/pat-s/oddsratio -* Source code: https://github.com/cran/oddsratio -* Date/Publication: 2020-05-24 22:00:02 UTC -* Number of recursive dependencies: 63 +* Version: 0.4.0 +* GitHub: https://github.com/leonawicz/lcars +* Source code: https://github.com/cran/lcars +* Date/Publication: 2024-09-11 22:52:42 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "oddsratio")` for more info +Run `revdepcheck::cloud_details(, "lcars")` for more info
@@ -18608,72 +12055,59 @@ Run `revdepcheck::cloud_details(, "oddsratio")` for more info * checking examples ... ERROR ``` - Running examples in ‘oddsratio-Ex.R’ failed + Running examples in ‘lcars-Ex.R’ failed The error most likely occurred in: - > ### Name: insert_or - > ### Title: Insert odds ratios of GAM(M)s into smoothing function - > ### Aliases: insert_or + > ### Name: lcars_border + > ### Title: LCARS border plot + > ### Aliases: lcars_border > > ### ** Examples > - > library(oddsratio) + > lcars_border() ... - 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) - 7. └─vctrs::vec_as_names(names, repair = "check_unique") - 8. └─vctrs (local) ``() - 9. └─vctrs:::validate_unique(names = names, arg = arg, call = call) - 10. └─vctrs:::stop_names_cannot_be_empty(names, call = call) - 11. └─vctrs:::stop_names(...) - 12. └─vctrs:::stop_vctrs(...) - 13. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + invalid font type + Calls: lcars_border ... drawDetails -> drawDetails.text -> grid.Call.graphics Execution halted ``` * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘oddsratio.Rmd’ + when running code in ‘lcars.Rmd’ ... - + pred = "x2", values = c(0.4, 0.6)) - - > insert_or(plot, or_object2, or_yloc = 2.1, values_yloc = 2, - + line_col = "green4", text_col = "black", rect_col = "green4", - + rect_alpha = .... [TRUNCATED] + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database - When sourcing ‘oddsratio.R’: - Error: Names can't be empty. - ✖ Empty name found at location 1. + When sourcing ‘lcars.R’: + Error: invalid font type Execution halted - ‘oddsratio.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘oddsratio.Rmd’ using rmarkdown - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘gam’ + ‘lcars.Rmd’ using ‘UTF-8’... failed ``` -# ofpetrial +# lemon
-* Version: 0.1.1 -* GitHub: https://github.com/DIFM-Brain/ofpetrial -* Source code: https://github.com/cran/ofpetrial -* Date/Publication: 2024-05-15 08:50:03 UTC -* Number of recursive dependencies: 136 +* Version: 0.5.0 +* GitHub: https://github.com/stefanedwards/lemon +* Source code: https://github.com/cran/lemon +* Date/Publication: 2024-11-10 18:20:02 UTC +* Number of recursive dependencies: 75 -Run `revdepcheck::cloud_details(, "ofpetrial")` for more info +Run `revdepcheck::cloud_details(, "lemon")` for more info
@@ -18681,108 +12115,96 @@ Run `revdepcheck::cloud_details(, "ofpetrial")` for more info * checking examples ... ERROR ``` - Running examples in ‘ofpetrial-Ex.R’ failed + Running examples in ‘lemon-Ex.R’ failed The error most likely occurred in: - > ### Name: check_ortho_with_chars - > ### Title: Check the orthogonality with field/topographic characteristics - > ### Aliases: check_ortho_with_chars + > ### Name: annotate_y_axis + > ### Title: Annotations on the axis + > ### Aliases: annotate_y_axis annotate_x_axis > > ### ** Examples > - > data(td_single_input) + > library(ggplot2) ... - 33. │ └─ggplot2:::`+.gg`(init, x[[i]]) - 34. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 35. │ ├─ggplot2::ggplot_add(object, p, objectname) - 36. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 37. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 38. └─base::.handleSimpleError(...) - 39. └─purrr (local) h(simpleError(msg, call)) - 40. └─cli::cli_abort(...) - 41. └─rlang::abort(...) + is.element + + > + > p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point() + > + > l <- p + annotate_y_axis('mark at', y=200, tick=TRUE) + > l + Error in identicalUnits(x) : object is not a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> identicalUnits Execution halted ``` - -# OmicNavigator - -
- -* Version: 1.13.13 -* GitHub: https://github.com/abbvie-external/OmicNavigator -* Source code: https://github.com/cran/OmicNavigator -* Date/Publication: 2023-08-25 20:40:02 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "OmicNavigator")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. - Complete output: - > # Test files in inst/tinytest/ - > if (requireNamespace("tinytest", quietly = TRUE)) { - + suppressMessages(tinytest::test_package("OmicNavigator")) - + } - - testAdd.R..................... 0 tests - testAdd.R..................... 0 tests + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(lemon) + > + > + > if (TRUE) { + + test_check("lemon") + + } #else { ... - testPlot.R.................... 140 tests OK - testPlot.R.................... 140 tests OK - testPlot.R.................... 141 tests OK - testPlot.R.................... 141 tests OK - testPlot.R.................... 141 tests OK - testPlot.R.................... 142 tests OK - testPlot.R.................... 142 tests OK - testPlot.R.................... 143 tests OK Error in pm[[2]] : subscript out of bounds - Calls: suppressMessages ... plotStudy -> f -> -> ggplotly.ggplot -> gg2list + 13. └─gtable::gtable_add_row_space(panel_table, theme$panel.spacing.y %||% theme$panel.spacing) + 14. └─cli::cli_abort("{.arg height} must be of length 1 or nrow - 1") + 15. └─rlang::abort(...) + + [ FAIL 2 | WARN 13 | SKIP 3 | PASS 138 ] + Deleting unused snapshots: + • facet/facet-rep-wrap-spacing.svg + • facet_aux/facet-rep-wrap.svg + Error: Test failures Execution halted ``` -## In both - -* checking re-building of vignette outputs ... NOTE +* checking running R code from vignettes ... ERROR ``` - Error(s) in re-building vignettes: - --- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave - OmicNavigator R package version: 1.13.13 - The app is not installed. Install it with installApp() - Installing study "ABC" in /tmp/RtmpFyTBK9/file1d2273c45a46 - Exporting study "ABC" as an R package - Note: No maintainer email was specified. Using the placeholder: Unknown - Calculating pairwise overlaps. This may take a while... - Exported study to /tmp/RtmpFyTBK9/ONstudyABC - Success! - ... - l.14 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘OmicNavigatorUsersGuide.Rnw’ + Errors in running code in vignettes: + when running code in ‘capped-axes.Rmd’ + ... + > p + coord_capped_cart(bottom = "right") - SUMMARY: processing the following files failed: - ‘OmicNavigatorAPI.Rnw’ ‘OmicNavigatorUsersGuide.Rnw’ + > p + coord_capped_cart(bottom = "right", left = "none") - Error: Vignette re-building failed. + > ggplot(dat1, aes(gp, y)) + geom_point(position = position_jitter(width = 0.2, + + height = 0)) + coord_capped_cart(left = "none", bottom = bracke .... [TRUNCATED] + + ... + When sourcing ‘legends.R’: + Error: Could not find panel named `panel-1-5`. Execution halted + + ‘capped-axes.Rmd’ using ‘UTF-8’... failed + ‘facet-rep-labels.Rmd’ using ‘UTF-8’... failed + ‘geoms.Rmd’ using ‘UTF-8’... OK + ‘gtable_show_lemonade.Rmd’ using ‘UTF-8’... OK + ‘legends.Rmd’ using ‘UTF-8’... failed + ‘lemon_print.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘capped-axes.Rmd’ using rmarkdown ``` -# omu +# lfproQC
-* Version: 1.1.2 -* GitHub: https://github.com/connor-reid-tiffany/Omu -* Source code: https://github.com/cran/omu -* Date/Publication: 2024-03-06 23:40:02 UTC -* Number of recursive dependencies: 129 +* Version: 1.4.0 +* GitHub: https://github.com/kabilansbio/lfproQC +* Source code: https://github.com/cran/lfproQC +* Date/Publication: 2024-10-10 13:10:02 UTC +* Number of recursive dependencies: 145 -Run `revdepcheck::cloud_details(, "omu")` for more info +Run `revdepcheck::cloud_details(, "lfproQC")` for more info
@@ -18790,302 +12212,277 @@ Run `revdepcheck::cloud_details(, "omu")` for more info * checking examples ... ERROR ``` - Running examples in ‘omu-Ex.R’ failed + Running examples in ‘lfproQC-Ex.R’ failed The error most likely occurred in: - > ### Name: PCA_plot - > ### Title: Create a PCA plot - > ### Aliases: PCA_plot + > ### Name: Boxplot_data + > ### Title: Creating Boxplot for a dataset + > ### Aliases: Boxplot_data > > ### ** Examples > - > PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata, - + variable = "Treatment", color = "Treatment", response_variable = "Metabolite") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: PCA_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > Boxplot_data(yeast_data) + Using Majority protein IDs as id variables + Warning: Removed 269 rows containing non-finite outside the scale range + (`stat_boxplot()`). + Error in pm[[2]] : subscript out of bounds + Calls: Boxplot_data -> -> ggplotly.ggplot -> gg2list Execution halted ``` -* checking re-building of vignette outputs ... NOTE +* checking running R code from vignettes ... ERROR ``` - Error(s) in re-building vignettes: + Errors in running code in vignettes: + when running code in ‘user_guide.Rmd’ ... - --- re-building ‘Omu_vignette.Rmd’ using rmarkdown - - Quitting from lines 97-104 [unnamed-chunk-4] (Omu_vignette.Rmd) - Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘Omu_vignette.Rmd’ + > yeast$`Best combinations` + PCV_best_combination PEV_best_combination PMAD_best_combination + 1 rlr_knn, rlr_lls vsn_lls rlr_lls - SUMMARY: processing the following file failed: - ‘Omu_vignette.Rmd’ + > Boxplot_data(yeast$rlr_knn_data) + Using Majority protein IDs as id variables - Error: Vignette re-building failed. + When sourcing ‘user_guide.R’: + Error: subscript out of bounds Execution halted + + ‘user_guide.Rmd’ using ‘UTF-8’... failed ``` -## In both - -* checking running R code from vignettes ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Errors in running code in vignettes: - when running code in ‘Omu_vignette.Rmd’ + Error(s) in re-building vignettes: ... + --- re-building ‘user_guide.Rmd’ using rmarkdown - > library(knitr) + Quitting from lines 55-56 [unnamed-chunk-8] (user_guide.Rmd) + Error: processing vignette 'user_guide.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘user_guide.Rmd’ - > load("../data/c57_nos2KO_mouse_countDF.rda") - Warning in readChar(con, 5L, useBytes = TRUE) : - cannot open compressed file '../data/c57_nos2KO_mouse_countDF.rda', probable reason 'No such file or directory' + SUMMARY: processing the following file failed: + ‘user_guide.Rmd’ - When sourcing ‘Omu_vignette.R’: - Error: cannot open the connection + Error: Vignette re-building failed. Execution halted - - ‘Omu_vignette.Rmd’ using ‘UTF-8’... failed ``` -# OncoBayes2 +# lilikoi
-* Version: 0.8-9 +* Version: 2.1.1 * GitHub: NA -* Source code: https://github.com/cran/OncoBayes2 -* Date/Publication: 2023-07-20 18:40:05 UTC -* Number of recursive dependencies: 100 +* Source code: https://github.com/cran/lilikoi +* Date/Publication: 2022-10-05 19:00:02 UTC +* Number of recursive dependencies: 215 -Run `revdepcheck::cloud_details(, "OncoBayes2")` for more info +Run `revdepcheck::cloud_details(, "lilikoi")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘OncoBayes2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_blrm - > ### Title: Plot a fitted model - > ### Aliases: plot_blrm plot_toxicity_curve plot_toxicity_intervals - > ### plot_toxicity_intervals_stacked plot_toxicity_curve.blrmfit - > ### plot_toxicity_curve.blrm_trial plot_toxicity_intervals.blrmfit - > ### plot_toxicity_intervals.blrm_trial - > ### plot_toxicity_intervals_stacked.blrmfit - ... - > # Plot the dose-toxicity curve - > plot_toxicity_curve(blrmfit, - + x = "drug_A", - + group = ~ group_id * drug_B, - + newdata = subset(dose_info_combo2, group_id == "trial_AB"), - + facet_args = list(ncol = 4)) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE +* checking whether package ‘lilikoi’ can be installed ... WARNING ``` - installed size is 76.7Mb - sub-directories of 1Mb or more: - libs 74.7Mb + Found the following significant warnings: + Note: possible error in 'is.element(method, c("knn"))': unused argument (c("knn")) + Note: possible error in 'is.element(method, c("standard", ': unused argument (c("standard", "quantile", "median", "knn")) + See ‘/tmp/workdir/lilikoi/new/lilikoi.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -* checking for GNU extensions in Makefiles ... NOTE +* checking R code for possible problems ... NOTE ``` - GNU make is a SystemRequirements. + lilikoi.preproc_knn: possible error in is.element(method, c("knn")): + unused argument (c("knn")) + lilikoi.preproc_norm: possible error in is.element(method, + c("standard", "quantile", "median", "knn")): unused argument + (c("standard", "quantile", "median", "knn")) ``` -# oncomsm +# LMoFit
-* Version: 0.1.4 -* GitHub: https://github.com/Boehringer-Ingelheim/oncomsm -* Source code: https://github.com/cran/oncomsm -* Date/Publication: 2023-04-17 07:00:02 UTC -* Number of recursive dependencies: 126 +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/LMoFit +* Date/Publication: 2024-05-14 07:33:23 UTC +* Number of recursive dependencies: 62 -Run `revdepcheck::cloud_details(, "oncomsm")` for more info +Run `revdepcheck::cloud_details(, "LMoFit")` for more info
## Newly broken -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(dplyr) - - Attaching package: 'dplyr' - - The following objects are masked from 'package:stats': - - filter, lag - ... - 10. └─grid::unit.c(legend.box.margin[4], widths, legend.box.margin[2]) - 11. └─grid:::identicalUnits(x) - - [ FAIL 1 | WARN 0 | SKIP 2 | PASS 59 ] - Deleting unused snapshots: - • plots/plot-mstate-srp-model-2.svg - • plots/plot-mstate-srp-model-3.svg - • plots/plot-srp-model-2.svg - Error: Test failures - Execution halted - ``` - * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘avoiding-bias.Rmd’ + when running code in ‘LMoFit.Rmd’ ... - > mdl <- create_srpmodel(A = define_srp_prior(median_t_q05 = c(1, - + 4, 12), median_t_q95 = c(6, 8, 36), shape_q05 = c(0.99, 0.99, - + 0.99), s .... [TRUNCATED] - - > plot(mdl, confidence = 0.9) - - ... - - > plot(mdl, parameter_sample = smpl_prior, confidence = 0.75) + > lspace_BrIII - When sourcing ‘oncomsm.R’: - Error: object is not a unit + When sourcing ‘LMoFit.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, Execution halted - ‘avoiding-bias.Rmd’ using ‘UTF-8’... failed - ‘oncomsm.Rmd’ using ‘UTF-8’... failed - ‘prior-choice.Rmd’ using ‘UTF-8’... OK + ‘LMoFit.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘avoiding-bias.Rmd’ using rmarkdown - - Quitting from lines 35-46 [unnamed-chunk-2] (avoiding-bias.Rmd) - Error: processing vignette 'avoiding-bias.Rmd' failed with diagnostics: - object is not a unit - --- failed re-building ‘avoiding-bias.Rmd’ + ... + --- re-building ‘LMoFit.Rmd’ using rmarkdown - --- re-building ‘oncomsm.Rmd’ using rmarkdown + Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd) + Error: processing vignette 'LMoFit.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + ... + NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 11, list("white", NA, NULL, NULL, TRUE), list(), 5.5, NULL, NULL, list("grey92", NULL, NULL, NULL, FALSE, TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, + 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, c(5.5, 5.5, 5.5, 5.5), list("white", "black", 2, NULL, TRUE), NULL, NULL, "inherit", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, + NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75, list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5))) + --- failed re-building ‘LMoFit.Rmd’ - Quitting from lines 211-215 [plotting-the-prior] (oncomsm.Rmd) - Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: - object is not a unit - --- failed re-building ‘oncomsm.Rmd’ + SUMMARY: processing the following file failed: + ‘LMoFit.Rmd’ - --- re-building ‘prior-choice.Rmd’ using rmarkdown + Error: Vignette re-building failed. + Execution halted ``` ## In both * checking installed package size ... NOTE ``` - installed size is 59.2Mb + installed size is 7.0Mb sub-directories of 1Mb or more: - doc 1.1Mb - libs 57.0Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + data 6.5Mb ``` -# OneSampleLogRankTest +# LocalCop
-* Version: 0.9.2 -* GitHub: NA -* Source code: https://github.com/cran/OneSampleLogRankTest -* Date/Publication: 2024-02-03 12:30:15 UTC -* Number of recursive dependencies: 106 +* Version: 0.0.2 +* GitHub: https://github.com/mlysy/LocalCop +* Source code: https://github.com/cran/LocalCop +* Date/Publication: 2024-09-12 17:41:03 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "OneSampleLogRankTest")` for more info +Run `revdepcheck::cloud_details(, "LocalCop")` for more info
## Newly broken -* checking examples ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Running examples in ‘OneSampleLogRankTest-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotKM - > ### Title: Plot Kaplan-Meier Curve against Population - > ### Aliases: plotKM - > - > ### ** Examples - > - > # load data - > data(dataSurv_small) - > data(dataPop_2018_2021) - > - > plotKM(dataSurv_small, dataPop_2018_2021, type = "exact") - Error in if (new_name %in% existing) { : argument is of length zero - Calls: plotKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names - Execution halted + Error(s) in re-building vignettes: + --- re-building ‘LocalCop.Rmd’ using rmarkdown ``` +## In both + * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘oneSampleLogRankTest.Rmd’ + when running code in ‘LocalCop.Rmd’ ... - $estimate - std_mort_ratio_est lwr upr - 1 1.531173 0.8302562 2.823816 + > tibble(x = x0, True = BiCopEta2Tau(family, eta = eta_fun(x0)), + + Fitted = BiCopEta2Tau(fitseq$eta, family = family)) %>% pivot_longer(True:Fitt .... [TRUNCATED] + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_line()`). + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_point()`). + When sourcing ‘LocalCop.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted - > plotKM(dataSurv, dataPop_2018_2021_race_sex_eth, type = "approximate") + ‘LocalCop.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 56.2Mb + sub-directories of 1Mb or more: + libs 55.7Mb + ``` + +# lognorm + +
+ +* Version: 0.1.10 +* GitHub: https://github.com/bgctw/lognorm +* Source code: https://github.com/cran/lognorm +* Date/Publication: 2021-11-21 17:50:10 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "lognorm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘lognorm.Rmd’ + ... + > ans %>% ggplot(aes(x, density, linetype = sigmaStar, + + color = sigmaStar)) + geom_area(data = ansNormal, aes(linetype = NA, + + color = NA), .... [TRUNCATED] + Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2 + 3.5.0. + ℹ Please use the `legend.position.inside` argument of `theme()` instead. - When sourcing ‘oneSampleLogRankTest.R’: - Error: argument is of length zero + When sourcing ‘lognorm.R’: + Error: invalid hex digit in 'color' or 'lty' Execution halted - ‘oneSampleLogRankTest.Rmd’ using ‘UTF-8’... failed + ‘lognorm.Rmd’ using ‘UTF-8’... failed + ‘lognormalDiff.Rmd’ using ‘UTF-8’... OK + ‘lognormalSum.Rmd’ using ‘UTF-8’... OK ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - ... - --- re-building ‘oneSampleLogRankTest.Rmd’ using rmarkdown + --- re-building ‘lognorm.Rmd’ using rmarkdown - Quitting from lines 74-77 [unnamed-chunk-3] (oneSampleLogRankTest.Rmd) - Error: processing vignette 'oneSampleLogRankTest.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘oneSampleLogRankTest.Rmd’ + Quitting from lines 51-78 [lognormalDensities] (lognorm.Rmd) + Error: processing vignette 'lognorm.Rmd' failed with diagnostics: + invalid hex digit in 'color' or 'lty' + --- failed re-building ‘lognorm.Rmd’ - SUMMARY: processing the following file failed: - ‘oneSampleLogRankTest.Rmd’ - - Error: Vignette re-building failed. - Execution halted + --- re-building ‘lognormalDiff.Rmd’ using rmarkdown ``` -# onpoint +# lsl
-* Version: 1.0.5 -* GitHub: https://github.com/r-spatialecology/onpoint -* Source code: https://github.com/cran/onpoint -* Date/Publication: 2024-01-10 14:03:06 UTC -* Number of recursive dependencies: 72 +* Version: 0.5.6 +* GitHub: NA +* Source code: https://github.com/cran/lsl +* Date/Publication: 2017-11-08 05:30:21 UTC +* Number of recursive dependencies: 38 -Run `revdepcheck::cloud_details(, "onpoint")` for more info +Run `revdepcheck::cloud_details(, "lsl")` for more info
@@ -19093,40 +12490,47 @@ Run `revdepcheck::cloud_details(, "onpoint")` for more info * checking examples ... ERROR ``` - Running examples in ‘onpoint-Ex.R’ failed + Running examples in ‘lsl-Ex.R’ failed The error most likely occurred in: - > ### Name: plot.env_summarized - > ### Title: plot.env_summarized - > ### Aliases: plot.env_summarized + > ### Name: lslSEM-class + > ### Title: A Reference Class for Learning a SEM model via penalized + > ### likelihood. + > ### Aliases: lslSEM-class lslSEM > > ### ** Examples > - > set.seed(42) ... - 39. - - Done. > - > x <- summarize_envelope(cluster_env) - > plot(x) - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + > rc_sem <- lslSEM() + > rc_sem$input(raw = lavaan::HolzingerSwineford1939) + > rc_sem$specify(pattern = list(lambda = lambda)) + > rc_sem$learn(penalty = list(type = "l1", gamma = seq(.05, .10, .05)), variable = 7:15) + > rc_sem$draw(type = "individual", object = "lambda") + Error in is.element(path[, 1], theta_names_penalized) : + unused argument (theta_names_penalized) + Calls: Execution halted ``` -# ordbetareg +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# MAINT.Data
-* Version: 0.7.2 -* GitHub: https://github.com/saudiwin/ordbetareg_pack -* Source code: https://github.com/cran/ordbetareg -* Date/Publication: 2023-08-10 07:30:02 UTC -* Number of recursive dependencies: 174 +* Version: 2.7.1 +* GitHub: NA +* Source code: https://github.com/cran/MAINT.Data +* Date/Publication: 2023-04-04 08:10:02 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "ordbetareg")` for more info +Run `revdepcheck::cloud_details(, "MAINT.Data")` for more info
@@ -19134,148 +12538,220 @@ Run `revdepcheck::cloud_details(, "ordbetareg")` for more info * checking examples ... ERROR ``` - Running examples in ‘ordbetareg-Ex.R’ failed + Running examples in ‘MAINT.Data-Ex.R’ failed The error most likely occurred in: - > ### Name: pp_check_ordbeta - > ### Title: Accurate Posterior Predictive Plots for Ordbetareg Models - > ### Aliases: pp_check_ordbeta + > ### Name: ConfMat + > ### Title: Confussion Matrices for classification results + > ### Aliases: ConfMat + > ### Keywords: discriminant analysis error rates > > ### ** Examples > - > ... - 16. │ └─ggplot2 (local) setup_params(...) - 17. │ └─ggplot2:::make_summary_fun(...) - 18. │ └─rlang::as_function(fun.data) - 19. │ └─base::get(x, envir = env, mode = "function") - 20. └─base::.handleSimpleError(...) - 21. └─rlang (local) h(simpleError(msg, call)) - 22. └─handlers[[1L]](cnd) - 23. └─cli::cli_abort(...) - 24. └─rlang::abort(...) + > # on the temperatures by quarter in 60 Chinese meteorological stations. + > + > ChinaT <- IData(ChinaTemp[1:8],VarNames=c("T1","T2","T3","T4")) + > + > #Linear Discriminant Analysis + > + > ChinaT.lda <- lda(ChinaT,ChinaTemp$GeoReg) + Error in is.element(1, Config) : unused argument (Config) + Calls: lda -> lda -> .local -> IdtNmle Execution halted ``` -## In both +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("MAINT.Data") + Loading required package: MAINT.Data + Loading required package: Rcpp + + Attaching package: 'MAINT.Data' + + ... + ── Error ('test-mle.R:49:5'): mle computes correct standar errors for default Gaussian models ── + Error in `is.element(Conf, 1:4)`: unused argument (1:4) + Backtrace: + ▆ + 1. ├─MAINT.Data::mle(AbaloneIdt, CovCase = Cv) at test-mle.R:49:5 + 2. └─MAINT.Data::mle(AbaloneIdt, CovCase = Cv) + + [ FAIL 10 | WARN 24 | SKIP 0 | PASS 74 ] + Error: Test failures + Execution halted + ``` -* checking installed package size ... NOTE +* checking whether package ‘MAINT.Data’ can be installed ... WARNING ``` - installed size is 8.1Mb - sub-directories of 1Mb or more: - data 7.5Mb + Found the following significant warnings: + Note: possible error in 'is.element(4, CovCase)': unused argument (CovCase) + Note: possible error in 'is.element(model, names(x@allres$RepresHom))': unused argument (names(x@allres$RepresHom)) + Note: possible error in 'is.element(Conf, 1:4)': unused argument (1:4) + Note: possible error in 'is.element(ModE@ModelConfig[1], ': unused argument (RestMod) + Note: possible error in 'is.element(nCovCases + ': unused argument (RestMod) + Note: possible error in 'is.element(Config, 2:5)': unused argument (2:5) + Note: possible error in 'is.element(Config, 1:5)': unused argument (1:5) + Note: possible error in 'is.element(2, Config)': unused argument (Config) + Note: possible error in 'is.element(1, Config)': unused argument (Config) + ... + Note: possible error in 'is.element(5, Config)': unused argument (Config) + Note: possible error in 'is.element(4, Config)': unused argument (Config) + Note: possible error in 'is.element(3, Config)': unused argument (Config) + Note: possible error in 'is.element(x, Rewind)': unused argument (Rewind) + Note: possible error in 'is.element(Conf, 1:5)': unused argument (1:5) + Note: possible error in 'is.element(Config, c(1, ': unused argument (c(1, 4)) + See ‘/tmp/workdir/MAINT.Data/new/MAINT.Data.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + CovC1toRestCov: possible error in is.element(Config, 2:5): unused + argument (2:5) + GetCovPar: possible error in is.element(Config, 1:5): unused argument + (1:5) + GetSigmaPar: possible error in is.element(Config, 1:5): unused argument + (1:5) + IdtHetMxtNmle: possible error in is.element(2, Config): unused argument + (Config) + IdtNmle: possible error in is.element(1, Config): unused argument + (Config) + ... + summary,IdtMclust: possible error in is.element(model, + names(object@allres$RepresHom)): unused argument + (names(object@allres$RepresHom)) + summary,IdtMclust: possible error in is.element(model, + names(object@allres$RepresHet)): unused argument + (names(object@allres$RepresHet)) + testMod,IdtE: possible error in is.element(ModE@ModelConfig[1], + RestMod): unused argument (RestMod) + testMod,IdtE: possible error in is.element(nCovCases + 1, RestMod): + unused argument (RestMod) ``` -* checking data for non-ASCII characters ... NOTE +## In both + +* checking installed package size ... NOTE ``` - Note: found 36 marked UTF-8 strings + installed size is 19.3Mb + sub-directories of 1Mb or more: + R 3.5Mb + data 6.5Mb + libs 8.9Mb ``` -# packcircles +# MarketMatching
-* Version: 0.3.6 -* GitHub: https://github.com/mbedward/packcircles -* Source code: https://github.com/cran/packcircles -* Date/Publication: 2023-09-08 06:30:02 UTC -* Number of recursive dependencies: 57 +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/MarketMatching +* Date/Publication: 2024-01-31 09:40:02 UTC +* Number of recursive dependencies: 73 -Run `revdepcheck::cloud_details(, "packcircles")` for more info +Run `revdepcheck::cloud_details(, "MarketMatching")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking re-building of vignette outputs ... ERROR ``` - Errors in running code in vignettes: - when running code in ‘progressive_packing.Rmd’ + Error(s) in re-building vignettes: ... - + scale_fill_man .... [TRUNCATED] - - > if (requireNamespace("ggiraph")) { - + gg <- ggplot(data = dat.gg) + ggiraph::geom_polygon_interactive(aes(x, - + y, group = id, fill = fac .... [TRUNCATED] - Loading required namespace: ggiraph + --- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle - When sourcing ‘progressive_packing.R’: - Error: argument is of length zero - Execution halted + Quitting from lines 79-105 [unnamed-chunk-1] (MarketMatching-Vignette.Rmd) + Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics: + unused argument (c("B", "M", "K")) + --- failed re-building ‘MarketMatching-Vignette.Rmd’ - ‘graph_packing.Rmd’ using ‘UTF-8’... OK - ‘intro.Rmd’ using ‘UTF-8’... OK - ‘progressive_packing.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘graph_packing.Rmd’ using rmarkdown - --- finished re-building ‘graph_packing.Rmd’ + SUMMARY: processing the following file failed: + ‘MarketMatching-Vignette.Rmd’ - --- re-building ‘intro.Rmd’ using rmarkdown + Error: Vignette re-building failed. + Execution halted ``` -# pafr +# metacart
-* Version: 0.0.2 -* GitHub: https://github.com/dwinter/pafr -* Source code: https://github.com/cran/pafr -* Date/Publication: 2020-12-08 10:20:12 UTC -* Number of recursive dependencies: 110 +* Version: 2.0-3 +* GitHub: NA +* Source code: https://github.com/cran/metacart +* Date/Publication: 2020-07-10 11:30:05 UTC +* Number of recursive dependencies: 31 -Run `revdepcheck::cloud_details(, "pafr")` for more info +Run `revdepcheck::cloud_details(, "metacart")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(pafr) - Loading required package: ggplot2 - > - > test_check("pafr") - [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] - + Running examples in ‘metacart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: FEmrt + > ### Title: Fixed effect meta-tree + > ### Aliases: FEmrt + > + > ### ** Examples + > + > data(dat.BCT2009) ... - ── Failure ('test_plot.r:11:5'): dotplot works produces a plot ───────────────── - unname(labs["xintercept"]) not equal to "xintercept". - target is NULL, current is character - ── Failure ('test_plot.r:12:5'): dotplot works produces a plot ───────────────── - unname(labs["yintercept"]) not equal to "yintercept". - target is NULL, current is character - - [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] - Error: Test failures - Execution halted + 1) root 106 253.03570 0.2294837 + 2) T1=0 69 168.39650 0.2018800 * + 3) T1=1 37 67.44715 0.3222563 + 6) T4=0 15 20.19503 0.1906789 * + 7) T4=1 22 23.85478 0.4377661 * + > summary(FEtree) + Error in is.element("FEmrt", class(object)) : + unused argument (class(object)) + Calls: summary -> summary.FEmrt + Execution halted ``` -## In both +* checking whether package ‘metacart’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element("FEmrt", class(object))': unused argument (class(object)) + Note: possible error in 'is.element("REmrt", class(object))': unused argument (class(object)) + See ‘/tmp/workdir/metacart/new/metacart.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` -* checking LazyData ... NOTE +* checking R code for possible problems ... NOTE ``` - 'LazyData' is specified without a 'data' directory + summary.FEmrt: possible error in is.element("FEmrt", class(object)): + unused argument (class(object)) + summary.REmrt: possible error in is.element("REmrt", class(object)): + unused argument (class(object)) ``` -# patchwork +# MetAlyzer
-* Version: 1.2.0 -* GitHub: https://github.com/thomasp85/patchwork -* Source code: https://github.com/cran/patchwork -* Date/Publication: 2024-01-08 14:40:02 UTC -* Number of recursive dependencies: 80 +* Version: 1.1.0 +* GitHub: https://github.com/nilsmechtel/MetAlyzer +* Source code: https://github.com/cran/MetAlyzer +* Date/Publication: 2024-12-06 14:00:02 UTC +* Number of recursive dependencies: 98 -Run `revdepcheck::cloud_details(, "patchwork")` for more info +Run `revdepcheck::cloud_details(, "MetAlyzer")` for more info
@@ -19283,81 +12759,162 @@ Run `revdepcheck::cloud_details(, "patchwork")` for more info * checking examples ... ERROR ``` - Running examples in ‘patchwork-Ex.R’ failed + Running examples in ‘MetAlyzer-Ex.R’ failed The error most likely occurred in: - > ### Name: free - > ### Title: Free a plot from alignment - > ### Aliases: free + > ### Name: plotly_scatter + > ### Title: Plotly Log2FC Scatter Plot + > ### Aliases: plotly_scatter > > ### ** Examples > - > # Sometimes you have a plot that defies good composition alginment, e.g. due - ... - > p1 / p2 > - > # We can fix this be using free - > free(p1) / p2 + ... + Warning: Partial NA coefficients for 2 probe(s) > - > # We can still collect guides like before - > free(p1) / p2 + plot_layout(guides = "collect") - Error in identicalUnits(x) : object is not a unit - Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + > p_scatter <- plotly_scatter(metalyzer_se) + Warning in geom_rect(data = rects_df, inherit.aes = FALSE, aes(xmin = .data$Start, : + Ignoring unknown aesthetics: text + Warning in geom_point(size = 0.5, aes(text = paste0(.data$Metabolite, "\nClass: ", : + Ignoring unknown aesthetics: text + Error in pm[[2]] : subscript out of bounds + Calls: plotly_scatter -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` -# pathviewr +# metR
-* Version: 1.1.7 -* GitHub: https://github.com/ropensci/pathviewr -* Source code: https://github.com/cran/pathviewr -* Date/Publication: 2023-03-08 08:10:05 UTC -* Number of recursive dependencies: 182 +* Version: 0.17.0 +* GitHub: https://github.com/eliocamp/metR +* Source code: https://github.com/cran/metR +* Date/Publication: 2025-01-13 19:50:02 UTC +* Number of recursive dependencies: 120 -Run `revdepcheck::cloud_details(, "pathviewr")` for more info +Run `revdepcheck::cloud_details(, "metR")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘metR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_contour_tanaka + > ### Title: Illuminated contours + > ### Aliases: geom_contour_tanaka GeomContourTanaka + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 20. │ └─self$draw_panel(...) + 21. │ └─metR (local) draw_panel(...) + 22. │ └─metR:::stopf(...) + 23. │ └─base::stop(e) + 24. └─rlang (local) ``(``) + 25. └─handlers[[1L]](cnd) + 26. └─cli::cli_abort(...) + 27. └─rlang::abort(...) + Execution halted + ``` + * checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(pathviewr) - > #library(vdiffr) + > library(metR) + > # library(vdiffr) + > + > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false"))) + > if (on_cran) data.table::setDTthreads(2) > - > test_check("pathviewr") - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] - ... - ── Error ('test-plot_by_subject.R:168:3'): elev views wrangled correctly via tidyverse ── - Error in `expect_match(elev_all_plots[[3]][[4]][["labels"]][["x"]], "position_height")`: is.character(act$val) is not TRUE - Backtrace: - ▆ - 1. └─testthat::expect_match(...) at test-plot_by_subject.R:168:3 - 2. └─base::stopifnot(is.character(act$val)) + 26. │ └─metR:::stopf(...) + 27. │ └─base::stop(e) + 28. └─rlang (local) ``(``) + 29. └─handlers[[1L]](cnd) + 30. └─cli::cli_abort(...) + 31. └─rlang::abort(...) - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] + [ FAIL 1 | WARN 1 | SKIP 19 | PASS 184 ] Error: Test failures Execution halted ``` -# patientProfilesVis +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Visualization-tools.Rmd’ + ... + + > ggplot(temperature[lev == 300], aes(lon, lat, z = air.z)) + + + geom_contour_fill() + geom_contour_tanaka() + scale_fill_divergent() + + When sourcing ‘Visualization-tools.R’: + Error: Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + Execution halted + + ‘Visualization-tools.Rmd’ using ‘UTF-8’... failed + ‘Working-with-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Visualization-tools.Rmd’ using knitr + + Quitting from lines 241-245 [unnamed-chunk-16] (Visualization-tools.Rmd) + Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics: + Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + ... + --- failed re-building ‘Visualization-tools.Rmd’ + + --- re-building ‘Working-with-data.Rmd’ using knitr + --- finished re-building ‘Working-with-data.Rmd’ + + SUMMARY: processing the following file failed: + ‘Visualization-tools.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.0Mb + doc 1.8Mb + ``` + +# mgcViz
-* Version: 2.0.9 -* GitHub: https://github.com/openanalytics/patientProfilesVis -* Source code: https://github.com/cran/patientProfilesVis -* Date/Publication: 2024-06-18 09:00:02 UTC -* Number of recursive dependencies: 102 +* Version: 0.1.11 +* GitHub: https://github.com/mfasiolo/mgcViz +* Source code: https://github.com/cran/mgcViz +* Date/Publication: 2023-10-06 10:50:02 UTC +* Number of recursive dependencies: 112 -Run `revdepcheck::cloud_details(, "patientProfilesVis")` for more info +Run `revdepcheck::cloud_details(, "mgcViz")` for more info
@@ -19366,42 +12923,43 @@ Run `revdepcheck::cloud_details(, "patientProfilesVis")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘patientProfiles-template-SDTM.Rmd’ + when running code in ‘mgcviz.rmd’ ... - > patientProfilesPlots <- c(patientProfilesPlots, list(MH = mhPlots)) + > v <- getViz(b) - > cmPlots <- subjectProfileIntervalPlot(data = dataAll$CM, - + paramVar = c("CMTRT", "CMDOSE", "CMDOSU", "CMROUTE", "CMDOSFRQ"), - + timeStartVa .... [TRUNCATED] - 171 record(s) with missing Study Day of Start of Medication and 208 record(s) with missing Study Day of End of Medication are imputed with minimal imputation. - - ... - + paramVar = "AETERM", timeStartVar = "AESTDY", timeEndVar = "AEENDY", - + colorVar = " ..." ... [TRUNCATED] - 3 record(s) with missing Study Day of Start of Adverse Event and 19 record(s) with missing Study Day of End of Adverse Event are imputed with minimal imputation. + > pl <- plotSlice(x = sm(v, 1), fix = list(z = seq(-2, + + 2, length.out = 3), x = c(-1, 0, 1))) - When sourcing ‘patientProfilesVis-introduction.R’: - Error: argument is of length zero + When sourcing ‘mgcviz.R’: + Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `rows` argument instead. Execution halted - ‘patientProfiles-template-SDTM.Rmd’ using ‘UTF-8’... failed - ‘patientProfilesVis-introduction.Rmd’ using ‘UTF-8’... failed + ‘mgcviz.rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘patientProfiles-template-SDTM.Rmd’ using rmarkdown - - Quitting from lines 129-153 [patientProfiles-concomitantMedications] (patientProfiles-template-SDTM.Rmd) - Error: processing vignette 'patientProfiles-template-SDTM.Rmd' failed with diagnostics: - argument is of length zero - --- failed re-building ‘patientProfiles-template-SDTM.Rmd’ - - --- re-building ‘patientProfilesVis-introduction.Rmd’ using rmarkdown + Error(s) in re-building vignettes: + --- re-building ‘mgcviz.rmd’ using rmarkdown ``` -## In both +# migraph + +
+ +* Version: 1.4.5 +* GitHub: https://github.com/stocnet/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2024-12-02 10:00:10 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "migraph")` for more info + +
+ +## Newly broken * checking tests ... ERROR ``` @@ -19409,103 +12967,77 @@ Run `revdepcheck::cloud_details(, "patientProfilesVis")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(patientProfilesVis) + > library(manynet) + > library(migraph) > - > test_check("patientProfilesVis") - [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] - - ══ Skipped tests (20) ══════════════════════════════════════════════════════════ + > test_check("migraph") + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] ... - 11. └─patientProfilesVis (local) .fun(piece, ...) - 12. └─ggplot2:::`+.gg`(...) - 13. └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. ├─ggplot2::ggplot_add(object, p, objectname) - 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + `expected` is a character vector ('Statistic') + ── Failure ('test-model_tests.R:73:3'): qap plot works ───────────────────────── + qapplot$labels$x (`actual`) not identical to "Statistic" (`expected`). + + `actual` is NULL + `expected` is a character vector ('Statistic') - [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] Error: Test failures Execution halted ``` -* checking installed package size ... NOTE - ``` - installed size is 5.7Mb - sub-directories of 1Mb or more: - doc 5.2Mb - ``` - -# PCADSC +# mikropml
-* Version: 0.8.0 -* GitHub: https://github.com/annepetersen1/PCADSC -* Source code: https://github.com/cran/PCADSC -* Date/Publication: 2017-04-19 10:07:43 UTC -* Number of recursive dependencies: 35 +* Version: 1.6.1 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2023-08-21 15:10:05 UTC +* Number of recursive dependencies: 129 -Run `revdepcheck::cloud_details(, "PCADSC")` for more info +Run `revdepcheck::cloud_details(, "mikropml")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘PCADSC-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CEPlot - > ### Title: Cumulative eigenvalue plot - > ### Aliases: CEPlot - > - > ### ** Examples - > - > #load iris data + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mikropml) + > test_check("mikropml") + Fraction of data in the training set: 0.778 + Groups in the training set: A C D + Groups in the testing set: B + Fraction of data in the training set: 0.778 ... - > CEPlot(irisPCADSC_fast) - Warning: The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in - ggplot2 3.3.4. - ℹ Please use "none" instead. - ℹ The deprecated feature was likely used in the PCADSC package. - Please report the issue at . - Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Matrix’ ‘pander’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘data.table’ - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory + `names(expected)` is absent + ── Failure ('test-plot.R:140:3'): plot_mean_prc uses geom ribbon, line, and hline ── + ... %>% unlist() (`actual`) not equal to c(...) (`expected`). + + `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...) + `names(expected)` is absent + + [ FAIL 2 | WARN 19 | SKIP 12 | PASS 314 ] + Error: Test failures + Execution halted ``` -# pcutils +# MiMIR
-* Version: 0.2.6 -* GitHub: https://github.com/Asa12138/pcutils -* Source code: https://github.com/cran/pcutils -* Date/Publication: 2024-06-25 21:20:05 UTC -* Number of recursive dependencies: 281 +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/MiMIR +* Date/Publication: 2024-02-01 08:50:02 UTC +* Number of recursive dependencies: 192 -Run `revdepcheck::cloud_details(, "pcutils")` for more info +Run `revdepcheck::cloud_details(, "MiMIR")` for more info
@@ -19513,88 +13045,40 @@ Run `revdepcheck::cloud_details(, "pcutils")` for more info * checking examples ... ERROR ``` - Running examples in ‘pcutils-Ex.R’ failed + Running examples in ‘MiMIR-Ex.R’ failed The error most likely occurred in: - > ### Name: gghist - > ### Title: gg histogram - > ### Aliases: gghist + > ### Name: LOBOV_accuracies + > ### Title: LOBOV_accuracies + > ### Aliases: LOBOV_accuracies > > ### ** Examples > - > if (requireNamespace("ggpubr")) { + > require(pROC) ... - 12. │ └─ggplot2:::`+.gg`(...) - 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) - 14. │ ├─ggplot2::ggplot_add(object, p, objectname) - 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) - 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) - 17. └─base::.handleSimpleError(...) - 18. └─purrr (local) h(simpleError(msg, call)) - 19. └─cli::cli_abort(...) - 20. └─rlang::abort(...) - Execution halted - ``` - -# pdxTrees - -
- -* Version: 0.4.0 -* GitHub: https://github.com/mcconvil/pdxTrees -* Source code: https://github.com/cran/pdxTrees -* Date/Publication: 2020-08-17 14:00:02 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "pdxTrees")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘pdxTrees-vignette.Rmd’ - ... - + y = Pollution_Removal_value, color = Mature_Size)) + geom_point(size = 2, - + .... [TRUNCATED] - - > berkeley_graph + transition_states(states = Mature_Size, - + transition_length = 10, state_length = 8) + enter_grow() + - + exit_shrink() - - When sourcing ‘pdxTrees-vignette.R’: - Error: argument "theme" is missing, with no default + 56 metabolites x 500 samples + | Pruning samples on5SD: + 56 metabolites x 500 samples + | Performing scaling ... DONE! + | Imputation ... DONE! + > p_avail<-colnames(b_p)[c(1:5)] + > LOBOV_accuracies(sur$surrogates, b_p, p_avail, MiMIR::acc_LOBOV) + Error in pm[[2]] : subscript out of bounds + Calls: LOBOV_accuracies -> -> ggplotly.ggplot -> gg2list Execution halted - - ‘pdxTrees-vignette.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# personalized +# miRetrieve
-* Version: 0.2.7 -* GitHub: https://github.com/jaredhuling/personalized -* Source code: https://github.com/cran/personalized -* Date/Publication: 2022-06-27 20:20:03 UTC -* Number of recursive dependencies: 94 +* Version: 1.3.4 +* GitHub: NA +* Source code: https://github.com/cran/miRetrieve +* Date/Publication: 2021-09-18 17:30:02 UTC +* Number of recursive dependencies: 125 -Run `revdepcheck::cloud_details(, "personalized")` for more info +Run `revdepcheck::cloud_details(, "miRetrieve")` for more info
@@ -19605,37 +13089,37 @@ Run `revdepcheck::cloud_details(, "personalized")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: - > Sys.setenv("R_TESTS" = "") > library(testthat) - > library(personalized) - Loading required package: glmnet - Loading required package: Matrix - Loaded glmnet 4.1-8 - Loading required package: mgcv + > library(miRetrieve) + > + > test_check("miRetrieve") + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ ... - 4. └─personalized:::plot.subgroup_validated(subgrp.val, type = "stability") - 5. ├─plotly::subplot(...) - 6. │ └─plotly:::dots2plots(...) - 7. ├─plotly::ggplotly(p.primary, tooltip = paste0("tooltip", 1:4)) - 8. └─plotly:::ggplotly.ggplot(...) - 9. └─plotly::gg2list(...) + Backtrace: + ▆ + 1. └─miRetrieve::compare_mir_terms_scatter(df_merged, "miR-21", title = "Test_title") at test-comparemirterms.R:56:1 + 2. ├─plotly::ggplotly(plot) + 3. └─plotly:::ggplotly.ggplot(plot) + 4. └─plotly::gg2list(...) - [ FAIL 1 | WARN 2 | SKIP 0 | PASS 215 ] + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] Error: Test failures Execution halted ``` -# phyloseqGraphTest +# MiscMetabar
-* Version: 0.1.1 -* GitHub: https://github.com/jfukuyama/phyloseqGraphTest -* Source code: https://github.com/cran/phyloseqGraphTest -* Date/Publication: 2024-02-05 19:00:02 UTC -* Number of recursive dependencies: 97 +* Version: 0.10.1 +* GitHub: https://github.com/adrientaudiere/MiscMetabar +* Source code: https://github.com/cran/MiscMetabar +* Date/Publication: 2024-10-07 21:40:01 UTC +* Number of recursive dependencies: 411 -Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info +Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info
@@ -19643,77 +13127,65 @@ Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info * checking examples ... ERROR ``` - Running examples in ‘phyloseqGraphTest-Ex.R’ failed + Running examples in ‘MiscMetabar-Ex.R’ failed The error most likely occurred in: - > ### Name: plot_test_network - > ### Title: Plots the graph used for testing - > ### Aliases: plot_test_network + > ### Name: ggscatt_pq + > ### Title: Scatterplot with marginal distributions and statistical results + > ### against Hill diversity of phyloseq object + > ### Aliases: ggscatt_pq > > ### ** Examples > - > library(phyloseq) ... - > plot_test_network(gt) - Warning in fortify(data, ...) : - Arguments in `...` must be used. - ✖ Problematic argument: - • layout = layout - ℹ Did you misspell an argument name? - Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘gt_vignette.Rmd’ - ... - > plot_test_network(gt) - Warning in fortify(data, ...) : - Arguments in `...` must be used. - ✖ Problematic argument: - • layout = layout - ℹ Did you misspell an argument name? - - When sourcing ‘gt_vignette.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 + Cleaning suppress 0 taxa and 0 samples. + Taxa are now in rows. + Joining with `by = join_by(Sample)` + [[1]] + `stat_xsidebin()` using `bins = 30`. Pick better value with `binwidth`. + `stat_ysidebin()` using `bins = 30`. Pick better value with `binwidth`. + Error in is.element(panel_type, c("x", "y")) : + unused argument (c("x", "y")) + Calls: ... -> draw_panel -> -> render_fg Execution halted - - ‘gt_vignette.Rmd’ using ‘UTF-8’... failed ``` -* checking re-building of vignette outputs ... NOTE +* checking tests ... ERROR ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘gt_vignette.Rmd’ using rmarkdown - - Quitting from lines 175-176 [unnamed-chunk-5] (gt_vignette.Rmd) - Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics: - invalid line type: must be length 2, 4, 6 or 8 - --- failed re-building ‘gt_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘gt_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(MiscMetabar) + Loading required package: phyloseq + Loading required package: ggplot2 + + Attaching package: 'ggplot2' + + ... + 'test_tuckey.R:26:3', 'test_targets.R:5:3', 'test_targets.R:56:3', + 'test_targets.R:84:3', 'test_targets.R:101:3', 'test_targets.R:111:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ─────────────── + `graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings. + + [ FAIL 1 | WARN 1 | SKIP 75 | PASS 83 ] + Error: Test failures + Execution halted ``` -# PieGlyph +# misspi
-* Version: 1.0.0 -* GitHub: https://github.com/rishvish/PieGlyph -* Source code: https://github.com/cran/PieGlyph -* Date/Publication: 2024-06-28 12:00:02 UTC -* Number of recursive dependencies: 91 +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/misspi +* Date/Publication: 2023-10-17 09:50:02 UTC +* Number of recursive dependencies: 88 -Run `revdepcheck::cloud_details(, "PieGlyph")` for more info +Run `revdepcheck::cloud_details(, "misspi")` for more info
@@ -19721,29 +13193,45 @@ Run `revdepcheck::cloud_details(, "PieGlyph")` for more info * checking examples ... ERROR ``` - Running examples in ‘PieGlyph-Ex.R’ failed + Running examples in ‘misspi-Ex.R’ failed The error most likely occurred in: - > ### Name: geom_pie_interactive - > ### Title: Scatter plots with interactive pie-chart glyphs - > ### Aliases: geom_pie_interactive + > ### Name: evaliq + > ### Title: Evaluate the Imputation Quality + > ### Aliases: evaliq > > ### ** Examples > - > #' ## Load libraries + > # A very quick example ... - > # One of the interactive aesthetics is tooltip. It is set that by default - > # it shows the value and percentage of each slice in the pie-chart. - > # Hover over any pie-chart in the plot to see this - > plot_obj1 <- ggplot(data = plot_data, aes(x = system, y = response)) + - + geom_pie_interactive(slices = c("A", "B", "C", "D"), - + data = plot_data)+ - + theme_classic() - Error in if (new_name %in% existing) { : argument is of length zero - Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + > # Default plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx]) + `geom_smooth()` using formula = 'y ~ x' + > + > # Interactive plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx], interactive = TRUE) + `geom_smooth()` using formula = 'y ~ x' + Error in pm[[2]] : subscript out of bounds + Calls: evaliq -> print -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted ``` +# mizer + +
+ +* Version: 2.5.3 +* GitHub: https://github.com/sizespectrum/mizer +* Source code: https://github.com/cran/mizer +* Date/Publication: 2024-10-17 07:10:09 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "mizer")` for more info + +
+ +## Newly broken + * checking tests ... ERROR ``` Running ‘spelling.R’ @@ -19757,62 +13245,38 @@ Run `revdepcheck::cloud_details(, "PieGlyph")` for more info > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview ... - • geom_pie_interactive/custom-tooltip.svg - • geom_pie_interactive/data-id.svg - • geom_pie_interactive/long-form-data-works.svg - • geom_pie_interactive/multiple-interactive-parameters.svg - • geom_pie_interactive/only-one-attribute.svg - • pie-grob/pie-grob-with-multiple-values-no-fill-works.svg - • pie-grob/pie-grob-with-single-non-zero-value-no-fill-works.svg - • pie-grob/pie-grob-with-single-non-zero-value-works.svg + • plots/plot-feeding-level.svg + • plots/plot-single-growth-curve.svg + • plots/plot-spectra.svg + • plots/plot-yield-by-gear.svg + • plots/plot-yield.svg + • plots/plotfishing-mortality.svg + • plots/plotfmort-truncated.svg + • plots/plotpredation-mortality.svg Error: Test failures Execution halted ``` -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘PieGlyph.Rmd’ using rmarkdown - ``` - ## In both -* checking running R code from vignettes ... ERROR +* checking installed package size ... NOTE ``` - Errors in running code in vignettes: - when running code in ‘PieGlyph.Rmd’ - ... - + geom_pie_glyph(slices = "Attributes", values = "values") + - + theme_cla .... [TRUNCATED] - - > plot_obj <- ggplot(data = plot_data) + geom_pie_interactive(aes(x = system, - + y = response, data_id = system), slices = c("A", "B", "C", - + .... [TRUNCATED] - - ... - before plotting. - Execution halted - - ‘PieGlyph.Rmd’ using ‘UTF-8’... failed - ‘interactive-pie-glyphs.Rmd’ using ‘UTF-8’... failed - ‘multinomial-classification-example.Rmd’ using ‘UTF-8’... OK - ‘pie-lollipop-example.Rmd’ using ‘UTF-8’... OK - ‘spatial-example.Rmd’ using ‘UTF-8’... OK - ‘time-series-example.Rmd’ using ‘UTF-8’... failed - ‘unusual-situations.Rmd’ using ‘UTF-8’... failed + installed size is 5.5Mb + sub-directories of 1Mb or more: + help 1.8Mb ``` -# Plasmidprofiler +# MLEce
-* Version: 0.1.6 +* Version: 2.1.0 * GitHub: NA -* Source code: https://github.com/cran/Plasmidprofiler -* Date/Publication: 2017-01-06 01:10:47 -* Number of recursive dependencies: 90 +* Source code: https://github.com/cran/MLEce +* Date/Publication: 2023-09-27 14:50:06 UTC +* Number of recursive dependencies: 42 -Run `revdepcheck::cloud_details(, "Plasmidprofiler")` for more info +Run `revdepcheck::cloud_details(, "MLEce")` for more info
@@ -19820,40 +13284,52 @@ Run `revdepcheck::cloud_details(, "Plasmidprofiler")` for more info * checking examples ... ERROR ``` - Running examples in ‘Plasmidprofiler-Ex.R’ failed + Running examples in ‘MLEce-Ex.R’ failed The error most likely occurred in: - > ### Name: main - > ### Title: Main: Run everything - > ### Aliases: main + > ### Name: MLEce + > ### Title: Calculating MLEces for three different distributions + > ### Aliases: MLEce > > ### ** Examples > - > main(blastdata, - ... - Saving 12 x 7 in image - Warning: Vectorized input to `element_text()` is not officially supported. - ℹ Results may be unexpected or may change in future versions of ggplot2. - Warning in geom_tile(aes(x = Plasmid, y = Sample, label = AMR_gene, fill = Inc_group, : - Ignoring unknown aesthetics: label and text - Warning: Use of `report$Sureness` is discouraged. - ℹ Use `Sureness` instead. - Error in pm[[2]] : subscript out of bounds - Calls: main ... -> ggplotly -> ggplotly.ggplot -> gg2list + > #bivariate gamma distribution + > data_BiGam <- rBiGam(100, c(1,4,5)) + > res_BiGam <- MLEce(data_BiGam, "BiGam") + Error in is.element(distname, distlist) : unused argument (distlist) + Calls: MLEce Execution halted ``` -# platetools +* checking whether package ‘MLEce’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(distname, ': unused argument (distlist) + See ‘/tmp/workdir/MLEce/new/MLEce.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` + +* checking R code for possible problems ... NOTE + ``` + MLEce: possible error in is.element(distname, distlist): unused + argument (distlist) + benchMLEce: possible error in is.element(distname, distlist): unused + argument (distlist) + ``` + +# modeltime.resample
-* Version: 0.1.7 -* GitHub: https://github.com/swarchal/platetools -* Source code: https://github.com/cran/platetools -* Date/Publication: 2024-03-07 16:50:02 UTC -* Number of recursive dependencies: 48 +* Version: 0.2.3 +* GitHub: https://github.com/business-science/modeltime.resample +* Source code: https://github.com/cran/modeltime.resample +* Date/Publication: 2023-04-12 15:50:02 UTC +* Number of recursive dependencies: 234 -Run `revdepcheck::cloud_details(, "platetools")` for more info +Run `revdepcheck::cloud_details(, "modeltime.resample")` for more info
@@ -19865,36 +13341,45 @@ Run `revdepcheck::cloud_details(, "platetools")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(platetools) > - > test_check("platetools") - [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] - - ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ + > # Machine Learning + > library(tidymodels) + ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ── + ✔ broom 1.0.7 ✔ recipes 1.1.0 + ✔ dials 1.3.0 ✔ rsample 1.2.1 ... - length(out96) not equal to length(ggplot()). - 1/1 mismatches - [1] 11 - 10 == 1 - ── Failure ('test-plot_wrapper.R:34:5'): returns expected ggplot object ──────── - names(out96) not equal to names(ggplot()). - Lengths differ: 11 is not 10 + ▆ + 1. ├─m750_models_resample %>% ... at test-modeltime_fit_resamples.R:116:5 + 2. └─modeltime.resample::plot_modeltime_resamples(., .interactive = TRUE) + 3. ├─plotly::ggplotly(g) + 4. └─plotly:::ggplotly.ggplot(g) + 5. └─plotly::gg2list(...) - [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 16 ] Error: Test failures Execution halted ``` -# PLNmodels +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’ + All declared Imports should be used. + ``` + +# moreparty
-* Version: 1.2.0 -* GitHub: https://github.com/pln-team/PLNmodels -* Source code: https://github.com/cran/PLNmodels -* Date/Publication: 2024-03-05 15:50:03 UTC -* Number of recursive dependencies: 155 +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/moreparty +* Date/Publication: 2023-11-22 14:30:02 UTC +* Number of recursive dependencies: 163 -Run `revdepcheck::cloud_details(, "PLNmodels")` for more info +Run `revdepcheck::cloud_details(, "moreparty")` for more info
@@ -19903,101 +13388,170 @@ Run `revdepcheck::cloud_details(, "PLNmodels")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘PLNPCA.Rmd’ + when running code in ‘Titanic_example.Rmd’ ... - 3 "$contrib" "contributions of the individuals" + 24 Age 57 0.3187270 + 25 Embarked Cherbourg 0.4603041 + [ reached 'max' / getOption("max.print") -- omitted 2 rows ] - > factoextra::fviz_pca_biplot(myPCA_ICL) + > ggForestEffects(pdep, vline = mean(pred_foret), xlab = "Probability of survival") + + + xlim(c(0, 1)) - When sourcing ‘PLNPCA.R’: - Error: ℹ In index: 1. - ℹ With name: y. - ... - ! argument is of length zero + When sourcing ‘Titanic_example.R’: + Error: `x` must be a vector, not a object. Execution halted - ‘Import_data.Rmd’ using ‘UTF-8’... OK - ‘PLN.Rmd’ using ‘UTF-8’... OK - ‘PLNLDA.Rmd’ using ‘UTF-8’... OK - ‘PLNPCA.Rmd’ using ‘UTF-8’... failed - ‘PLNmixture.Rmd’ using ‘UTF-8’... failed - ‘PLNnetwork.Rmd’ using ‘UTF-8’... OK - ‘Trichoptera.Rmd’ using ‘UTF-8’... OK + ‘Titanic_example.Rmd’ using ‘UTF-8’... failed ``` * checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: - --- re-building ‘Import_data.Rmd’ using rmarkdown - --- finished re-building ‘Import_data.Rmd’ + --- re-building ‘Titanic_example.Rmd’ using rmarkdown + ``` + +# mppR + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/vincentgarin/mppR +* Source code: https://github.com/cran/mppR +* Date/Publication: 2024-02-22 17:20:02 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "mppR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘mppR_gen_vignette.Rmd’ + ... + + > set.seed(89341) - --- re-building ‘PLN.Rmd’ using rmarkdown + > CV <- mpp_CV(pop.name = "USNAM", trait.name = "ULA", + + mppData = mppData, Q.eff = "cr", her = 0.4, Rep = 2, k = 5, + + verbose = FALSE, outp .... [TRUNCATED] + + When sourcing ‘mppR_gen_vignette.R’: + Error: unused argument (QTL.names) + Execution halted + + ‘MPP_ME_QTL_detect.Rmd’ using ‘UTF-8’... OK + ‘mppR_gen_vignette.Rmd’ using ‘UTF-8’... failed ``` -## In both +* checking whether package ‘mppR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Note: possible error in 'is.element(mk.list, QTL.names)': unused argument (QTL.names) + See ‘/tmp/workdir/mppR/new/mppR.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. + ``` -* checking installed package size ... NOTE +* checking R code for possible problems ... NOTE ``` - installed size is 26.0Mb - sub-directories of 1Mb or more: - R 1.0Mb - data 3.5Mb - doc 2.1Mb - libs 18.6Mb + mpp_CV: possible error in is.element(mk.list, QTL.names): unused + argument (QTL.names) + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown ``` -# plotBart +# MPTmultiverse
-* Version: 0.1.7 -* GitHub: https://github.com/priism-center/plotBart -* Source code: https://github.com/cran/plotBart -* Date/Publication: 2022-05-27 07:50:06 UTC -* Number of recursive dependencies: 94 +* Version: 0.4-2 +* GitHub: https://github.com/mpt-network/MPTmultiverse +* Source code: https://github.com/cran/MPTmultiverse +* Date/Publication: 2020-06-24 09:40:11 UTC +* Number of recursive dependencies: 99 -Run `revdepcheck::cloud_details(, "plotBart")` for more info +Run `revdepcheck::cloud_details(, "MPTmultiverse")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(vdiffr) - > library(plotBart) - Loading required package: bartCause - Loading required package: ggplot2 - > - > test_check("plotBart") # run tests - ... - • plots/mod-search.svg - • plots/overlappscoresdensity.svg - • plots/overlapvarsdensity.svg - • plots/pate.svg - • plots/sate.svg - • plots/supportchi.svg - • plots/supportsd.svg - • plots/waterfall2.svg - Error: Test failures - Execution halted + Running examples in ‘MPTmultiverse-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fit_mpt + > ### Title: Multiverse Analysis for MPT Models + > ### Aliases: fit_mpt + > + > ### ** Examples + > + > + ... + Backtrace: + ▆ + 1. ├─base::plot(fit_all, which = "est") + 2. └─MPTmultiverse:::plot.multiverseMPT(fit_all, which = "est") + 3. └─MPTmultiverse:::plot_est(x, shapes = shapes) + 4. └─ggplot2::facet_grid(facets = ". ~ condition") + 5. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") + 6. └─lifecycle:::deprecate_stop0(msg) + 7. └─rlang::cnd_signal(...) + Execution halted ``` -# plotDK +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction-bayen_kuhlmann_2011.rmd’ + ... + ℹ Please use tidy evaluation idioms with `aes()` + ℹ The deprecated feature was likely used in the MPTmultiverse package. + Please report the issue at + . + + When sourcing ‘introduction-bayen_kuhlmann_2011.R’: + Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 + and is now defunct. + ℹ Please use the `rows` argument instead. + Execution halted + + ‘introduction-bayen_kuhlmann_2011.rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction-bayen_kuhlmann_2011.rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# mtb
-* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/plotDK -* Date/Publication: 2021-10-01 08:00:02 UTC -* Number of recursive dependencies: 86 +* Version: 0.1.8 +* GitHub: https://github.com/yh202109/mtb +* Source code: https://github.com/cran/mtb +* Date/Publication: 2022-10-20 17:22:35 UTC +* Number of recursive dependencies: 63 -Run `revdepcheck::cloud_details(, "plotDK")` for more info +Run `revdepcheck::cloud_details(, "mtb")` for more info
@@ -20009,49 +13563,68 @@ Run `revdepcheck::cloud_details(, "plotDK")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(plotDK) + > library(mtb) > - > test_check("plotDK") - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + > test_check("mtb") + + Attaching package: 'ggplot2' - ══ Failed tests ════════════════════════════════════════════════════════════════ ... - Error in `expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), - names(labels))`: `object` and `expected` must both be vectors - Backtrace: - ▆ - 1. └─testthat::expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), names(labels)) at test-plotDK.R:67:5 - 2. └─rlang::abort("`object` and `expected` must both be vectors") + - "yend" [6] + - "xmin" [7] + - "xmax" [8] + - "ymin" [9] + - "ymax" [10] + ... ... ... and 3 more ... - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] Error: Test failures Execution halted ``` -## In both +# mudfold + +
+ +* Version: 1.1.21 +* GitHub: https://github.com/cran/mudfold +* Source code: https://github.com/cran/mudfold +* Date/Publication: 2022-11-24 09:30:02 UTC +* Number of recursive dependencies: 50 -* checking dependencies in R code ... NOTE +Run `revdepcheck::cloud_details(, "mudfold")` for more info + +
+ +## Newly broken + +* checking whether package ‘mudfold’ can be installed ... WARNING ``` - Namespace in Imports field not imported from: ‘mapproj’ - All declared Imports should be used. + Found the following significant warnings: + Note: possible error in 'is.element(visitSequence, ': unused argument (names(blocks)) + See ‘/tmp/workdir/mudfold/new/mudfold.Rcheck/00install.out’ for details. + Information on the location(s) of code generating the ‘Note’s can be + obtained by re-running with environment variable R_KEEP_PKG_SOURCE set + to ‘yes’. ``` -* checking data for non-ASCII characters ... NOTE +* checking R code for possible problems ... NOTE ``` - Note: found 12992 marked UTF-8 strings + check.visitSequence: possible error in is.element(visitSequence, + names(blocks)): unused argument (names(blocks)) ``` -# plotly +# mulgar
-* Version: 4.10.4 -* GitHub: https://github.com/plotly/plotly.R -* Source code: https://github.com/cran/plotly -* Date/Publication: 2024-01-13 22:40:02 UTC -* Number of recursive dependencies: 148 +* Version: 1.0.2 +* GitHub: https://github.com/dicook/mulgar +* Source code: https://github.com/cran/mulgar +* Date/Publication: 2023-08-25 22:00:02 UTC +* Number of recursive dependencies: 43 -Run `revdepcheck::cloud_details(, "plotly")` for more info +Run `revdepcheck::cloud_details(, "mulgar")` for more info
@@ -20059,372 +13632,348 @@ Run `revdepcheck::cloud_details(, "plotly")` for more info * checking examples ... ERROR ``` - Running examples in ‘plotly-Ex.R’ failed + Running examples in ‘mulgar-Ex.R’ failed The error most likely occurred in: - > ### Name: style - > ### Title: Modify trace(s) - > ### Aliases: style + > ### Name: ggmcbic + > ### Title: Produces an mclust summary plot with ggplot + > ### Aliases: ggmcbic > > ### ** Examples > - > ## Don't show: + > require(mclust) ... - + # this clobbers the previously supplied marker.line.color - + style(p, marker.line = list(width = 2.5), marker.size = 10) - + ## Don't show: - + }) # examplesIf - > (p <- ggplotly(qplot(data = mtcars, wt, mpg, geom = c("point", "smooth")))) - Warning: `qplot()` was deprecated in ggplot2 3.4.0. - `geom_smooth()` using method = 'loess' and formula = 'y ~ x' - Error in pm[[2]] : subscript out of bounds - Calls: ... eval -> eval -> ggplotly -> ggplotly.ggplot -> gg2list + Type 'citation("mclust")' for citing this R package in publications. + > data(clusters) + > clusters_BIC <- mclustBIC(clusters[,1:5], G=2:6) + > ggmcbic(clusters_BIC) + Warning: Removed 5 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library("testthat") - > library("plotly") - Loading required package: ggplot2 - - Attaching package: 'plotly' - - The following object is masked from 'package:ggplot2': - ... - • plotly-subplot/subplot-bump-axis-annotation.svg - • plotly-subplot/subplot-bump-axis-image.svg - • plotly-subplot/subplot-bump-axis-shape-shared.svg - • plotly-subplot/subplot-bump-axis-shape.svg - • plotly-subplot/subplot-reposition-annotation.svg - • plotly-subplot/subplot-reposition-image.svg - • plotly-subplot/subplot-reposition-shape-fixed.svg - • plotly-subplot/subplot-reposition-shape.svg - Error: Test failures - Execution halted - ``` - ## In both * checking installed package size ... NOTE ``` - installed size is 7.1Mb + installed size is 8.8Mb sub-directories of 1Mb or more: - R 1.0Mb - htmlwidgets 4.0Mb + data 8.5Mb ``` -# pmartR +# MultiTraits
-* Version: 2.4.5 -* GitHub: https://github.com/pmartR/pmartR -* Source code: https://github.com/cran/pmartR -* Date/Publication: 2024-05-21 15:50:02 UTC -* Number of recursive dependencies: 148 +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/MultiTraits +* Date/Publication: 2024-12-21 14:10:02 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "pmartR")` for more info +Run `revdepcheck::cloud_details(, "MultiTraits")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(pmartR) - > - > test_check("pmartR") - [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] - - ══ Skipped tests (11) ══════════════════════════════════════════════════════════ + Running examples in ‘MultiTraits-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CSR_plot + > ### Title: Create a ternary plot of CSR strategies + > ### Aliases: CSR_plot + > + > ### ** Examples + > + > data(PFF) ... - • plots/plot-spansres-color-high-color-low.svg - • plots/plot-spansres.svg - • plots/plot-statres-anova-volcano.svg - • plots/plot-statres-anova.svg - • plots/plot-statres-combined-volcano.svg - • plots/plot-statres-combined.svg - • plots/plot-statres-gtest.svg - • plots/plot-totalcountfilt.svg - Error: Test failures - Execution halted + 3. ├─ggtern::ggplot_build(x) + 4. └─ggtern:::ggplot_build.ggplot(x) + 5. └─ggtern:::layers_add_or_remove_mask(plot) + 6. └─ggint$plot_theme(plot) + 7. └─ggplot2:::validate_theme(theme) + 8. └─base::mapply(...) + 9. └─ggplot2 (local) ``(...) + 10. └─cli::cli_abort(...) + 11. └─rlang::abort(...) + Execution halted ``` -## In both +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MultiTraits_tutorial.Rmd’ + ... + 4 490 20 16 30.293240 30.891427 38.81533 CSR + 5 51 14 31 4.068212 0.000000 95.93179 R + 6 66 27 13 5.131786 73.958953 20.90926 S/SR + + > CSR_plot(data = result, expand_margin = 1) + + When sourcing ‘MultiTraits_tutorial.R’: + Error: The `tern.axis.ticks.length.major` theme element must be a + object. + Execution halted + + ‘MultiTraits_tutorial.Rmd’ using ‘UTF-8’... failed + ``` -* checking installed package size ... NOTE +* checking re-building of vignette outputs ... NOTE ``` - installed size is 10.8Mb - sub-directories of 1Mb or more: - R 1.5Mb - help 1.5Mb - libs 6.7Mb + Error(s) in re-building vignettes: + ... + --- re-building ‘MultiTraits_tutorial.Rmd’ using rmarkdown + + Quitting from lines 106-120 [unnamed-chunk-4] (MultiTraits_tutorial.Rmd) + Error: processing vignette 'MultiTraits_tutorial.Rmd' failed with diagnostics: + The `tern.axis.ticks.length.major` theme element must be a + object. + --- failed re-building ‘MultiTraits_tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘MultiTraits_tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# pmxTools +# mvSLOUCH
-* Version: 1.3 -* GitHub: https://github.com/kestrel99/pmxTools -* Source code: https://github.com/cran/pmxTools -* Date/Publication: 2023-02-21 16:00:08 UTC -* Number of recursive dependencies: 85 +* Version: 2.7.6 +* GitHub: NA +* Source code: https://github.com/cran/mvSLOUCH +* Date/Publication: 2023-11-20 18:20:06 UTC +* Number of recursive dependencies: 101 -Run `revdepcheck::cloud_details(, "pmxTools")` for more info +Run `revdepcheck::cloud_details(, "mvSLOUCH")` for more info
## Newly broken -* checking tests ... ERROR +* checking re-building of vignette outputs ... NOTE ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(pmxTools) - Loading required package: patchwork - > - > test_check("pmxTools") - [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ] - + Error(s) in re-building vignettes: + --- re-building ‘mvSLOUCH_Carnivorans.Rmd’ using rmarkdown + trying URL 'datadryad.org/api/v2/datasets/doi%253A10.5061%252Fdryad.77tm4/download' + downloaded 51 KB + +